Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae

Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var 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Mengyao Zeng , Linying Wang , Ruiyue Zheng , Zhuang Zhao , Xuyong Gao , Jr-Han Lai , Kai-Lun Yeh , Li-Sheng Zhang , Jinliao Chen , Xiaokai Ma , Yuanyuan Li , Deqiang Chen , Jun Li , Meng-Meng Zhang , Xin He , Ye Huang , Cuili Zhang , Xiaopei Wu , Chen Chen , Liang Ma , Junwen Zhai , Ye Ai , Ming-He Li , Yuzhen Zhou , Zhuang Zhou , Shasha Wu , Kai Zhao , Yunxiao Guan , Xiong-De Tu , Danqi Zeng , Xiaotong Ji , Ning Liu , Shuangquan Zou , You-Yi Chen , Shao-Ting Lin , Wen-Yu Su , Zhi-Wen Wang , Yi-Bo Luo , Wufang Zhang , Yan-Yan Guo , Ying-Qiu Tian , Long-Hai Zou , Xiaohui Lv , Xiaokang Zhuo , Jin Zhu , Dong-Hui Peng , Chuan-Ming Yeh , View ORCID Profile Haibao Tang , Wen-Chieh Tsai , Yves Van de Peer , View ORCID Profile Zhong-Jian Liu doi: https://doi.org/10.1101/2025.06.13.659439 Siren Lan 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ke-Wei Liu 3 Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University , Shenzhen 518055, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Zhen Li 4 Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium 5 VIB Center for Plant Systems Biology , VIB, 9052 Ghent, Belgium Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Zhen Li Yu-Yun Hsiao 6 Crown-Orchid Co., Ltd. , Tainan 701, Taiwan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Yuanyuan Liu 7 Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University , 350002 Fuzhou, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Yuanyuan Liu Diyang Zhang 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xuewei Zhao 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Wei-Hong Sun 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ding-Kun Liu 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ming-Zhong Huang 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Cheng-Yuan Zhou 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Mengyao Zeng 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Linying Wang 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ruiyue Zheng 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Zhuang Zhao 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xuyong Gao 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jr-Han Lai 8 Institute of Molecular Biology, National Chung Hsing University , Taichung 40227, Taiwan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Kai-Lun Yeh 8 Institute of Molecular Biology, National Chung Hsing University , Taichung 40227, Taiwan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Li-Sheng Zhang 8 Institute of Molecular Biology, National Chung Hsing University , Taichung 40227, Taiwan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jinliao Chen 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xiaokai Ma 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 7 Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University , 350002 Fuzhou, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Yuanyuan Li 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Deqiang Chen 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jun Li 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Meng-Meng Zhang 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xin He 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ye Huang 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Cuili Zhang 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xiaopei Wu 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Chen Chen 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Liang Ma 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Junwen Zhai 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ye Ai 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ming-He Li 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Yuzhen Zhou 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Zhuang Zhou 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 9 Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences , Wenzhou 325005, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Shasha Wu 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Kai Zhao 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Yunxiao Guan 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xiong-De Tu 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Danqi Zeng 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xiaotong Ji 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ning Liu 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Shuangquan Zou 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site You-Yi Chen 10 Department of Agronomy, National Chiayi University , Chiayi, Taiwan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Shao-Ting Lin 11 Graduate Program in Translational Agriculture Sciences, National Cheng Kung University and Academic Sinica , Tainan, Taiwan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Wen-Yu Su 11 Graduate Program in Translational Agriculture Sciences, National Cheng Kung University and Academic Sinica , Tainan, Taiwan Find this author on Google Scholar Find this author on PubMed Search for this author on this site Zhi-Wen Wang 12 PubBio-Tech , Wuhan 430070, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Yi-Bo Luo 13 State Key Laboratory of Plant Diversity and Prominent Crops, Institute of Botany, Chinese Academy of Sciences , Beijing 10093, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Wufang Zhang 14 State Key Laboratory of Resource Insects, Chinese Academy of Agricultural Sciences , Beijing 10093, China 15 Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences , Beijing 10093, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Yan-Yan Guo 16 College of Plant Protection, Henan Agricultural University , Zhengzhou 450046, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ying-Qiu Tian 17 College of Notoginseng Medicine and Pharmacy, Wenshan University , Wenshan 663000, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Long-Hai Zou 18 State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang Agriculture and Forestry University , Hangzhou 311300, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xiaohui Lv 19 Institute of Leisure Agriculture, Shandong Academy of Agricultural Sciences , Jinan 250100, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xiaokang Zhuo 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 20 College of Horticulture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jin Zhu 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 20 College of Horticulture, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site Dong-Hui Peng 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site For correspondence: fjpdh{at}fafu.edu.cn chuanmingy{at}nchu.edu.tw tanghaibao{at}gmail.com tsaiwc{at}mail.ncku.edu.tw yves.vandepeer{at}psb.vib-ugent.be zjliu{at}fafu.edu.cn Chuan-Ming Yeh 8 Institute of Molecular Biology, National Chung Hsing University , Taichung 40227, Taiwan 21 Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University , Taichung, Taiwan 22 . Biomanufacturing Process Research Center, National Institute of Advanced Industrial Science and Technology (AIST) , Tsukuba, Japan Find this author on Google Scholar Find this author on PubMed Search for this author on this site For correspondence: fjpdh{at}fafu.edu.cn chuanmingy{at}nchu.edu.tw tanghaibao{at}gmail.com tsaiwc{at}mail.ncku.edu.tw yves.vandepeer{at}psb.vib-ugent.be zjliu{at}fafu.edu.cn Haibao Tang 7 Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University , 350002 Fuzhou, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Haibao Tang For correspondence: fjpdh{at}fafu.edu.cn chuanmingy{at}nchu.edu.tw tanghaibao{at}gmail.com tsaiwc{at}mail.ncku.edu.tw yves.vandepeer{at}psb.vib-ugent.be zjliu{at}fafu.edu.cn Wen-Chieh Tsai 11 Graduate Program in Translational Agriculture Sciences, National Cheng Kung University and Academic Sinica , Tainan, Taiwan 23 Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University , Tainan 701, Taiwan 24 Orchid Research and Development Center, National Cheng Kung University , Tainan City 701, Taiwan 25 Department of Life Sciences, National Cheng Kung University , Tainan 701, Taiwan 26 University Center for Bioscience and Biotechnology, National Cheng Kung University , Tainan 701, Taiwan Find this author on Google Scholar Find this author on PubMed Search for this author on this site For correspondence: fjpdh{at}fafu.edu.cn chuanmingy{at}nchu.edu.tw tanghaibao{at}gmail.com tsaiwc{at}mail.ncku.edu.tw yves.vandepeer{at}psb.vib-ugent.be zjliu{at}fafu.edu.cn Yves Van de Peer 4 Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium 5 VIB Center for Plant Systems Biology , VIB, 9052 Ghent, Belgium 27 College of Horticulture, Nanjing Agricultural University, Academy for Advanced Interdisciplinary Studies , Nanjing 210095, China 28 Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria , Pretoria, South Africa Find this author on Google Scholar Find this author on PubMed Search for this author on this site For correspondence: fjpdh{at}fafu.edu.cn chuanmingy{at}nchu.edu.tw tanghaibao{at}gmail.com tsaiwc{at}mail.ncku.edu.tw yves.vandepeer{at}psb.vib-ugent.be zjliu{at}fafu.edu.cn Zhong-Jian Liu 1 Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University , Fuzhou 350002, China 2 Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University , Fuzhou 350002, China 9 Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences , Wenzhou 325005, China 29 Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences , Jinan 250100, China 30 Guangzhou Institute of Forestry and Landscape Architecture , Guangzhou 510405, China Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Zhong-Jian Liu For correspondence: fjpdh{at}fafu.edu.cn chuanmingy{at}nchu.edu.tw tanghaibao{at}gmail.com tsaiwc{at}mail.ncku.edu.tw yves.vandepeer{at}psb.vib-ugent.be zjliu{at}fafu.edu.cn Abstract Full Text Info/History Metrics Preview PDF Abstract Orchidaceae (orchids) is commonly known as one of the largest families of seed plants, and grow in an extensive range of habitats worldwide. In the present study, we generated chromosome-level reference genomes for two orchids using a combination of PacBio, Illumina, and Hi-C sequencing, Cypripedium singchii has the largest genome and chromosomes among the sequenced species so far, with a genome size of 43.19 Gb (1C) with ten chromosomes, and Apostasia fujianica has the smallest known genome and chromosomes in Orchidaceae, with a genome size of 340.90 Mb (1C) with 35 chromosomes. We predicted a total of 32,412 and 21,724 protein-coding genes for C. singchii and A. fujianica , respectively. The overall BUSCO score was 85.01% for C. singchii and 91.80% in A. fujianica . Based on protein-coding sequences from 55 conserved single-copy families across 21 plant species, we constructed a high-confidence phylogenetic tree and estimated the divergence times. The high-quality genomes of super-giga and tiny orchids offer key insight for future evolutionary researches. One prominent example is the orchid family (Orchidaceae), which comprises approximately 31,000 recognized species ( Freudenstein, 2025 ), spanning five subfamilies: Apostasioideae, Vanilloideae, Cypripedioideae, Orchidoideae, and Epidendroideae. Orchids exhibit genome sizes ranging from 0.29 Gb to 54.18 Gb ( Leitch et al ., 2009 ), highlighting a remarkable range of genomic diversity that can occur within a single plant family. More interestingly, these species ecologically occupy habitats across the globe, from tropical rainforests to alpine regions, and display a vast array of growth forms, including terrestrial, epiphytic, and mycoheterotrophic lifestyles, suggesting that analysis of its genome should allow novel insights into the key innovations that contributed to the explosive diversification within the flowering plants. Here, we focus on Cypripedioideae and Apostasioideae orchids, two subfamilies that showcase distinct evolutionary histories and ecological adaptations. Cypripedium singchii Z. J. Liu et L. J. Chen ( Figures 1a, b ), C. wardii Rolfe ( Figures 1e, f ), and C. subtropicum S. C. Chen et K. Y. Lang ( Figures 1g, h ) thrive in cold alpine habitats ( Chen et al ., 2013 ). In contrast, Apostasia fujianica Y. Li et S. Lan ( Li et al ., 2023 ) ( Figures 1c, d ) grows at lower altitude habitats. By generating chromosomal-scale genome assemblies for C. singchii and A. fujianica , and lower coverage sequence for C. wardii and C. subtropicum , using Illumina, PacBio, and Hi-C technologies, we aim to dissect the different genomic architectures. Download figure Open in new tab Figure 1. The morphology of C. singchii (a, b), A. fujianica (c, d), C. wardii (e, f) and C. subtropicum (g, h). The sequenced C. singchii has a karyotype of 2 N = 2X = 20 ( Leitch et al ., 2009 ), while the sequenced A. fujianica has 2 N = 2X = 70 ( Li et al ., 2023 ). To obtain complete sequences for both genomes, we generated 3957.88 Gb and 39.01 Gb PacBio Sequel reads for C. singchii and A. fujianica , respectively. K- mer analyses estimated genome sizes of C. singchii at 43.19 Gb and that of A. fujianica at 349.46 Mb, C. subropicum at 34.95 Gb and C. wardii at 19.17 Gb ( Figures 2 ). The final assembly was 40.77 Gb for C. singchii , with a contig N50 value of 1.17 Mb. The final assembly was 340.90 Mb for A. fujianica with a contig N50 value of 2.37 Mb ( Figures 3a, b ). Download figure Open in new tab Figure 2. K-mer distribution of sequencing reads. a. C. singchii ; b. A. fujianica ; c. C. subtropicum ; d. C. wardii . Download figure Open in new tab Figure 3. High-quality assembly and genome features of C. singchii and A. fujianica . a, b. The statistics for the initial contig assembly of C. singchii ( a ) and A. fujianica ( b ). c. Ten pseudomoleules scaffolding with Hi-C data of C. singchii . d. 35 pseudomoleules scaffolding with Hi-C data of A. fujianica . e . Intrachromosomal contact matrix. The intensity of pixels represents the normalized count of Hi-C links between 1 Mb windows on C. singchii chromosome 01 on a logarithmic scale. f . Intrachromosomal contact matrix. The intensity of pixels represents the normalized count of Hi-C links between 1 Mb windows on A. fujianica chromosome 01 on a logarithmic scale. g, h. The correlation between assembly lengths and observed physical lengths of all chromosomes in C. singchii ( g ) and A. fujianica ( h ). Data are represented as mean ± SD. i, j . Genome features depicted by using 20-Mb-wide bine across ten chromosomes of C. singchii ( i ) and 35 chromosomes of A. fujianica ( j ). To generate chromosome-scale assemblies, we further produced 3,292.09 Gb of Hi-C reads for C. singchii and 71.68 Gb for A. fujianica and clustered the assembled scaffolds into pseudomolecules ( Figures 3c, d ). In C. singchii , ten pseudochromosomes ranged from 3,011.81 Mb to 5,061.45 Mb, with a N50 of 3,726.49 Mb (total length 40.929 Gb) ( Figure 3e ; Table 1 ). In A. fujianica , 35 pseudomolecules ranged from 5.66 Mb to 13.69 Mb, with a N50 value of 9.88 Mb (total length 333.35 Mb) ( Figure 3f ; Table 2 ). The assemblies achieved high completeness, with 93.42 % of C. singchii and 97.79 % of A. fujianica scaffolds assigned to assembled chromosomes. View this table: View inline View popup Download powerpoint Table 1. Hi-C auxiliary assembly result of C. singchii . View this table: View inline View popup Download powerpoint Table 2. Hi-C auxiliary assembly result of A. fujianica . Benchmarking Universal Single-Copy Orthologs (BUSCO) ( Simão et al ., 2015 ) analysis showed 85.01% of the complete BUSCOs in the assembled C. singchii and 91.80% of the complete BUSCOs in the assembled A. fujianica , suggesting that both genome assemblies are largely complete and of high quality ( Tables 3 , 4 ). In total, we annotated 32,412 and 21,724 protein-coding genes for C. singchii ( Table 3 ) and A. fujianica ( Table 4 ), respectively. The proportion of complete BUSCO genes was 85.01% in C. singchii and 91.80% in A. fujianica ( Table 5 ), suggesting that both genomes annotating of high quality. View this table: View inline View popup Download powerpoint Table 3. Prediction of gene structures of the C. singchii . View this table: View inline View popup Download powerpoint Table 4. Prediction of gene structures of the A. fujianica . View this table: View inline View popup Download powerpoint Table 5. BUSCO assessment of C. singchii and A. fujianica genome assemblies. In addition, we detected more non-coding RNAs in C. singchii than in A. fujianica ( Table 6 ). Specifically, C. singchii has a higher number of microRNAs (234 vs. 78 A. fujianica ). The abundance of tRNAs (5,981 vs. 246 in A. fujianica ) and rRNAs (2,989 vs. 771 in A. fujianica ) in C. singchii may indicate a higher capacity for protein synthesis ( Palos et al ., 2023 ). Additionally, the increased number of snRNAs in C. singchii (746 vs. 368 in A. fujianica ) could reflect more complex splicing processes. These features suggest that C. singchii may have evolved robust transcriptional and translational mechanisms to cope with highly variable alpine limestone environments. View this table: View inline View popup Download powerpoint Table 6. Statistics of non-coding RNA annotation results. We constructed a high-confidence phylogenetic tree and estimated the divergence times of 21 different plant species using coding (CDS) and protein sequences from 55 conserved single-copy families (see Methods ). The analysis confirmed that the orchid clade consists of five independent subclades, consistent with previous expectations ( Figure 4 ). Since the emergence of common Orchidaceae ancestor, large contraction and small expansion through genes (much more than the expanded, 2,457 vs 486, 1,998 vs 526 and 194 vs 56 differentiated into Apostasioideae, Orchidoideae and Epidendroideae, while massive expansion and massive contraction (3,365 vs 2,072 and 2,762 vs 2,048) differentiated into Vanilloideae and Cypripedioideae. By utilizing these new genomic resources alongside previously published orchid genome data in the other three subfamilies (Vanilloideae, Orchidoideae, and Epidendroideae), we provide a broader perspective on the evolution of orchids and aim to illustrate key genomic innovations that have contributed to their diversification among flowering plant. Download figure Open in new tab Figure 4. Phylogenetic tree showing divergence times and the evolution of gene family size in 21 species. The green and red numbers are the numbers of expanded and contracted gene families, respectively. The blue portions of the pie charts represent the gene families whose copy numbers are constant. The orange portions of the pie charts represent the proportion of the 11,457 gene families found in the most recent common ancestor (MRCA) that expanded or contracted during recent differentiation. Methods Sample preparation and sequencing The plant materials used in this study were collected from wild. C. singchii in Xichou (alt. 700m), Yunnan, China, C. subtropicum in Motuo (alt. 1,400 m), Xizang, C. wardii in Huanglong (alt. 3,000 m), Sichuan, and A. fujianica in Zhaoan (alt. 50 m), Fujian, China during 2018. The plant materials were cleaned with 75% alcohol and then pure water for DNA extraction. Genomic DNA was extracted based on cetyltrimethylammonium bromide (CTAB) methods. DNA sequencing of C. singchii and A. fujianica was performed using PacBio to sequence a 20 kb single-molecule real-time (SMRT) DNA library on the PacBio Sequel platform. SMRTbell template preparation involved DNA concentration, damage repair, end repair, ligation of hairpin adapters, and template purification, and was undertaken using AMPure PB Magnetic Beads (Pacific Biosciences). Finally, we obtained 3957.88 Gb and 39.01 Gb PacBio data for C. singchii and A. fujianica genome assembly, respectively. C. subtropicum and C. wardii underwent shallow sequencing to estimate their genome size and the composition of repetitive sequences. Genome size estimation According to the Lander-Waterman theory ( Lander and Waterman, 1988 ), the genome size and heterozygosity can be calculated by the total number of K -mers divided by the peak value of the K -mer distribution. K -mer analysis iteratively selected K bp sequences from a continuous sequence; if the length of reads was L and the length of the K -mer was K, then we obtained an L-K+1 K -mer. Here, we took K as 17 bp, and the 17 mer frequency table was generated by Jellyfish v2.1.4 ( Marçais et al ., 2011 ). Finally, we used the GenomeScope ( Vurture et al., 2017 ) software to estimate the genome size, heterozygosity, and repeat sequence. Genome assembly and Hi-C scaffolding We used wtdbg software to perform an initial assembly of the Cypripedium genome using PacBio CLR data. Next, we aligned the second-generation data to the initial assembly using Bwa, and then corrected the assembly errors with Pilon software based on the alignment results. This error correction step was repeated twice to obtain a high-quality contig-level assembly. We mounted the contig-level assembly results of Cypripedium using Hi-C data to achieve chromosome-level assembly. We employed the strategies of Juicer and 3ddna. First, we used Juicer software to align the Hi-C data and filter out reliable and effective Hi-C data. Then, we used 3ddna software to cluster the contigs based on Hi-C contact intensity. Finally, we manually corrected the clustering results using Juicebox software. Genome annotation Gene prediction and functional annotation were conducted by a combination of homology-based prediction, de novo prediction and transcriptome-based prediction methods. In the homology-based prediction method, we mapped the protein sequences of three published plant genomes ( Ar. thaliana , Zea mays and Orazy sativa ) onto the C. singchii and A. fujianica genomes by TBLASTN (E-value 1×10 −5 ) and then used GeneWise v.2.4.1 ( Birney et al ., 2004 ) to predict the gene structures. In the de novo prediction method, the homology-based results, Augustus v.2.7 ( Stanke and Waack, 2003 ), GlimmerHMM v.3.02 ( Majoros et al ., 2004 ) and SNAP (version 2006-07-28) ( Korf, 2004 ) were combined to predict the genes. The transcriptome data from multiple tissues were mapped onto the genome assembly using TopHat v2.1.1 ( Trapnell et al ., 2012 ), and then Cufflinks v2.1.1 ( Trapnell et al ., 2012 ) was used to assemble the transcripts into gene models. MAKER v.1.0 ( Holt and Yandell, 2011 ) was used to generate a consensus gene set based on the homology-based, de novo , and transcriptome-based predictions. Functional annotation of the predicted protein sequences was achieved by aligning protein sequences against public databases, including SwissProt, TrEMBLE and KEGG, with BLASTP (E-value < 1×10 −5 ). Additionally, protein motifs and domains were annotated using the InterPro and Gene Ontology (GO) databases by InterProScan v.4.8 ( Finn et al ., 2017 ). The tRNA genes were searched by tRNAscan-SE ( Lowe and Eddy, 1997 ). For rRNA identification, we downloaded the Arabidopsis rRNA sequences from NCBI and aligned them with the Acorus genomes to identify possible rRNAs. Additionally, other types of noncoding RNAs, including miRNAs and snRNAs, were identified by using INFERNAL ( Nawrocki et al ., 2009 ) to search the Rfam database. Single copy gene family identification Single-copy gene families and multicopy gene families were obtained by identifying homologous genes and clusters of gene families. First, protein sequence data sets were constructed, including those for C. singchii and A. fujianica and 19 other plant species: Amborella trichopoda , Ar. thaliana , Spirodela polyrhiza , O. sativa , Elaeis guineensis , As. officinalis , A. shenzhenica , V. planifolia , P. zijinensis , P. guangdongensis , Gastrodia elata , Bletilla striata , D. catenatum , D. chrysotoxum , Phalaenopsis equestris , Ph. aphrodite , Cymbidium goeringii , Cymbidium ensifolium and Cymbidium sinense . Then, the protein sequence dataset was used for BLASTP alignment, the results were filtered by an E-value threshold of 1×10 −5 , a similarity threshold of 30%, and a coverage (alignment length divided by sequence length) threshold of 50%. The filtered results were used to construct orthologous groups through ORTHOMCL v2.0.9 ( Li et al ., 2003 ; Chen et al ., 2006 ). Phylogenetic tree construction and phylogenomic dating To obtain a reliable phylogenetic tree, it is necessary to obtain a reliable single-copy gene dataset. Orthogroups were constructed with C. singchii , A. fujianica , and 19 sequenced plant genomes. Single-copy gene families containing proteins less than 200 bp in length were filtered out. The filtered protein sequences were aligned by MUSCLE v3.8.31 ( Edgar, 2010 ), and the CDS (coding sequence) alignment results were obtained according to the relationship between the protein and CDS. The conserved sequences were obtained from the CD alignment results using Gblocks software ( Talavera and Castresana, 2007 ), and the supergene was concatenated by all the conserved sequences. A phylogenetic analysis of the data set was performed using MrBayes ( Huelsenbeck and Ronquist, 2001 ) with the GTR + gamma model. The divergence time was estimated by MCMCtree of the PAML v.4.7 ( Yang, 2007 ) package. The nucleotide replacement model was the GTR model. The Markov chain Monte Carlo (MCMC) process consists of a burn-in of 500,000 iterations and 150,000,000 iterations with a sample frequency of 150. The calibration times were as follows: 1. Divergence time of Gnetum montanum and Ginkgo biloba was 230– 282 Mya. 2. The upper limit of angiosperm formation time was 200 Mya ( Magallón et al ., 2013 ). 3. Divergence time of Ar. thaliana and Gnetum montanum was 289 – 330 Mya. 4. Divergence time of Azolla and Ar. thaliana was 392–422 Mya. 5. The lower limit of the divergence time of monocotyledons and dicotyledons was 140 Mya ( Chaw et al ., 2004 ). 6. Divergence time of Physcomitrium patens and Ar. thaliana was 465–533 Mya. Funder Information Declared Fujian Agriculture and Forestry University, https://ror.org/04kx2sy84 , 115-KJG19005A References ↵ Birney , E. et al. GeneWise and Genomewise . Genome Res . 14 , 988 – 995 ( 2004 ). OpenUrl Abstract / FREE Full Text Cai , J. , et al. The genome sequence of the orchid Phalaenopsis equestris . Nat. Genet . 47 , 65 – 72 ( 2015 ). OpenUrl CrossRef PubMed ↵ Chaw , S. M. , et al. Dating the monocot–dicot divergence and the origin of core eudicots using whole chloroplast genomes . J. Mol. Evol . 58 , 424 – 441 ( 2004 ). OpenUrl CrossRef PubMed Web of Science ↵ Chen , F. et al. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups . Nucleic Acids Res . 34 ( Database issue ): D363 – D368 ( 2006 ). OpenUrl CrossRef PubMed Web of Science ↵ Chen , S. , et al. The genus Cypripedium in China . Science Press , Beijing , Pp 1 – 317 ( 2013 ). ↵ Edgar , R.C . Quality measures for protein alignment benchmarks . Nucleic Acids Res . 2010 , 1 – 9 ( 2010 ). OpenUrl ↵ Freudenstein J V . Orchid phylogenetics and evolution: History, current status and prospects . Ann Bot . 135 , 805 – 822 ( 2025 ). OpenUrl CrossRef PubMed ↵ Finn , R. D. et al. InterPro in 2017—beyond protein family and domain annotations . Nucleic Acids Res . 45 , D190 – D199 ( 2017 ). OpenUrl CrossRef PubMed ↵ Holt , C. and Yandell , M . MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects . BMC Bioinform . 12 , 491 ( 2011 ). OpenUrl CrossRef PubMed ↵ Huelsenbeck J. P. and Ronquist F . MRBAYES: Bayesian inference of phylogenetic trees . Bioinformatics 17 , 754 – 755 ( 2001 ). OpenUrl CrossRef PubMed Web of Science ↵ Korf , I . Gene finding in novel genomes . BMC Bioinformation 5 , 59 ( 2004 ). ↵ Lander , E. S. and Waterman , M. S . Genomic mapping by fingerprinting random clones: a mathematical analysis . Genomics 2 , 231 – 239 ( 1988 ). OpenUrl CrossRef PubMed ↵ Leitch , I. J. , et al. Genome size diversity in orchids: consequences and evolution . Ann Bot . 104 , 469 – 81 ( 2009 ). OpenUrl CrossRef PubMed ↵ Li , L. , et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes . Genome Res . 13 , 2178 – 2189 ( 2003 ). OpenUrl Abstract / FREE Full Text Li , M. H. , et al. 2022. Genomes of leafy and leafless Platanthera orchids provide insights into the evolution of mycoheterotrophy . Nature Plants 8 , 373 – 388 ( 2022 ). OpenUrl CrossRef PubMed ↵ Li , Y. , et al. Apostasia fujianica (Apositasioideae, Orchidaceae), a new Chinese species: evidence from morphological, genome size and molecular analyses . Phytotaxa 583 , 277 – 284 ( 2023 ). OpenUrl ↵ Lowe , T. M. and Eddy , S. R . tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence . Nucleic Acids Res . 25 , 955 – 964 ( 1997 ). OpenUrl CrossRef PubMed ↵ Magallón , S. , et al. Land plant evolutionary timeline: gene effects are secondary to fossil constraints in relaxed clock estimation of age and substitution rates . Am. J. Bot . 100 , 556 – 573 ( 2013 ). OpenUrl Abstract / FREE Full Text ↵ Majoros , W. H. , et al. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders . Bioinformatics 20 , 2878 – 2879 ( 2004 ). OpenUrl CrossRef PubMed Web of Science ↵ Marçais , G. and Carl K . A fast, lock-free approach for efficient parallel counting of occurrences of k -mers . Bioinformatics 27 , 764 – 770 ( 2011 ). OpenUrl CrossRef PubMed Web of Science ↵ Nawrocki , E. P. , et al. Infernal 1.0: inference of RNA alignments . Bioinformatics 25 , 1335 – 1337 ( 2009 ). OpenUrl CrossRef PubMed Web of Science ↵ Palos , K. , et al. Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs . The Plant Cell 35 , 1762 – 1786 ( 2023 ). OpenUrl CrossRef PubMed ↵ Simão , F. A. , et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs . Bioinformatics 31 , 3210 – 3212 ( 2015 ). OpenUrl CrossRef PubMed ↵ Stanke , M. and Waack , S . Gene prediction with a hidden Markov model and a new intron submodel . Bioinformatics 19 , ii215 – ii225 ( 2003 ). OpenUrl CrossRef PubMed Web of Science ↵ Talavera , G. and Castresana , J . Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments . Syst. Biol . 56 , 564 – 577 ( 2007 ). OpenUrl CrossRef PubMed Web of Science ↵ Trapnell , C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks . Nat. Protoc . 7 , 562 – 578 ( 2012 ). OpenUrl CrossRef PubMed ↵ Vurture , G. W. et al. GenomeScope: fast reference-free genome profiling from short reads . Bioinformatics 33 , 2202 – 2204 ( 2017 ). OpenUrl CrossRef PubMed ↵ Yang , Z . PAML 4: phylogenetic analysis by maximum likelihood . Mol. Biol. Evol . 24 , 1586 – 1591 ( 2007 ). OpenUrl CrossRef PubMed Web of Science Yang , F. X. , et al. The genome of Cymbidium sinense revealed the evolution of orchid traits . Plant Biotechnol J . 19 , 2501 – 2516 ( 2021 ). OpenUrl CrossRef PubMed Zhang , G. Q. , et al. The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, flower development and adaptive evolution . Scientific Reports 6 , 19029 . ( 2016 ). Zhang , G.Q. , et al. The Apostasia genome and the evolution of orchids . Nature 549 , 379 – 383 . ( 2017 ). OpenUrl CrossRef PubMed View the discussion thread. Back to top Previous Next Posted June 17, 2025. Download PDF Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. 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Share Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae Siren Lan , Ke-Wei Liu , Zhen Li , Yu-Yun Hsiao , Yuanyuan Liu , Diyang Zhang , Xuewei Zhao , Wei-Hong Sun , Ding-Kun Liu , Ming-Zhong Huang , Cheng-Yuan Zhou , Mengyao Zeng , Linying Wang , Ruiyue Zheng , Zhuang Zhao , Xuyong Gao , Jr-Han Lai , Kai-Lun Yeh , Li-Sheng Zhang , Jinliao Chen , Xiaokai Ma , Yuanyuan Li , Deqiang Chen , Jun Li , Meng-Meng Zhang , Xin He , Ye Huang , Cuili Zhang , Xiaopei Wu , Chen Chen , Liang Ma , Junwen Zhai , Ye Ai , Ming-He Li , Yuzhen Zhou , Zhuang Zhou , Shasha Wu , Kai Zhao , Yunxiao Guan , Xiong-De Tu , Danqi Zeng , Xiaotong Ji , Ning Liu , Shuangquan Zou , You-Yi Chen , Shao-Ting Lin , Wen-Yu Su , Zhi-Wen Wang , Yi-Bo Luo , Wufang Zhang , Yan-Yan Guo , Ying-Qiu Tian , Long-Hai Zou , Xiaohui Lv , Xiaokang Zhuo , Jin Zhu , Dong-Hui Peng , Chuan-Ming Yeh , Haibao Tang , Wen-Chieh Tsai , Yves Van de Peer , Zhong-Jian Liu bioRxiv 2025.06.13.659439; doi: https://doi.org/10.1101/2025.06.13.659439 Share This Article: Copy Citation Tools Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae Siren Lan , Ke-Wei Liu , Zhen Li , Yu-Yun Hsiao , Yuanyuan Liu , Diyang Zhang , Xuewei Zhao , Wei-Hong Sun , Ding-Kun Liu , Ming-Zhong Huang , Cheng-Yuan Zhou , Mengyao Zeng , Linying Wang , Ruiyue Zheng , Zhuang Zhao , Xuyong Gao , Jr-Han Lai , Kai-Lun Yeh , Li-Sheng Zhang , Jinliao Chen , Xiaokai Ma , Yuanyuan Li , Deqiang Chen , Jun Li , Meng-Meng Zhang , Xin He , Ye Huang , Cuili Zhang , Xiaopei Wu , Chen Chen , Liang Ma , Junwen Zhai , Ye Ai , Ming-He Li , Yuzhen Zhou , Zhuang Zhou , Shasha Wu , Kai Zhao , Yunxiao Guan , Xiong-De Tu , Danqi Zeng , Xiaotong Ji , Ning Liu , Shuangquan Zou , You-Yi Chen , Shao-Ting Lin , Wen-Yu Su , Zhi-Wen Wang , Yi-Bo Luo , Wufang Zhang , Yan-Yan Guo , Ying-Qiu Tian , Long-Hai Zou , Xiaohui Lv , Xiaokang Zhuo , Jin Zhu , Dong-Hui Peng , Chuan-Ming Yeh , Haibao Tang , Wen-Chieh Tsai , Yves Van de Peer , Zhong-Jian Liu bioRxiv 2025.06.13.659439; doi: https://doi.org/10.1101/2025.06.13.659439 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Genomics Subject Areas All Articles Animal Behavior and Cognition (7617) Biochemistry (17633) Bioengineering (13856) Bioinformatics (41841) Biophysics (21399) Cancer Biology (18529) Cell Biology (25422) Clinical Trials (138) Developmental Biology (13352) Ecology (19860) Epidemiology (2067) Evolutionary Biology (24281) Genetics (15582) Genomics (22461) Immunology (17700) Microbiology (40295) Molecular Biology (17140) Neuroscience (88413) Paleontology (666) Pathology (2823) Pharmacology and Toxicology (4813) Physiology (7632) Plant Biology (15107) Scientific Communication and Education (2042) Synthetic Biology (4284) Systems Biology (9808) Zoology (2267)