Species discrimination in Pedicularis (Orobanchaceae) based on the chloroplast genome

Species discrimination in Pedicularis (Orobanchaceae) based on the chloroplast genome | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL This is a preprint and has not been peer reviewed. Data may be preliminary. 21 July 2024 V1 Latest version Share on Species discrimination in Pedicularis (Orobanchaceae) based on the chloroplast genome Authors : You Wu , Rong Liu , Wei-Jia Wang , De-Zhu Li 0000-0002-4990-724X , Kevin Burgess , Wen-Bin Yu , and Hong Wang 0000-0003-2618-0196 [email protected] Authors Info & Affiliations https://doi.org/10.22541/au.172153162.28917098/v1 365 views 313 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Complete plastid genomes have recently been proposed as ”super-barcodes” for genetic identification and delineation in plants, for which standard DNA barcodes may fail. However, relatively few studies have fully considered the genetic mechanisms inherent to the taxonomic complexity of specious genera and how this may affect species resolution via complete plastome barcodes. Pedicularis is a highly diversified group of plants whose floral traits have undergone rapid radiation in the Himalaya-Hengduan Mountains, which can complicate identification and classification within the group based on morphological traits alone. In this study, we analyzed 292 plastomes representing 96 species of Pedicularis to compare species discrimination rates with those based on standard DNA barcodes. The results show that the traditional standard barcode (nrITS+matK+rbcL+trnH-psbA) and the large single copy (LSC) region of the plastid genome share the highest discrimination rates (80.21%), followed by the plastid genome, the supermatrixes of protein-coding genes and high variable regions (79.17%), and the matK gene and ycf1 gene alone could discriminate 78.13% of species. Further, we found that the sequence length and percentage of parsimony-informative sites significantly influence species discrimination rates, and genes with higher species discrimination rates are more likely to be conservative in selection. Given the extra costs and time required for generating such “super-barcodes” to try to discern species in taxonomically complex genera, this study questions their use and calls for more efforts to explore nuclear markers that may improve discrimination rates in future studies with relatively low-cost and effort. Supplementary Material File (manuscript.pdf) Download 1.39 MB Information & Authors Information Version history V1 Version 1 21 July 2024 Copyright This work is licensed under a Non Exclusive No Reuse License. Keywords genome skimming himalaya-hengduan mountains pedicularis plastome-scale barcodes species identification standard barcodes Authors Affiliations You Wu View all articles by this author Rong Liu View all articles by this author Wei-Jia Wang View all articles by this author De-Zhu Li 0000-0002-4990-724X View all articles by this author Kevin Burgess View all articles by this author Wen-Bin Yu View all articles by this author Hong Wang 0000-0003-2618-0196 [email protected] Kunming Institute of Botany Chinese Academy of Sciences View all articles by this author Metrics & Citations Metrics Article Usage 365 views 313 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation You Wu, Rong Liu, Wei-Jia Wang, et al. Species discrimination in Pedicularis (Orobanchaceae) based on the chloroplast genome. Authorea . 21 July 2024. DOI: https://doi.org/10.22541/au.172153162.28917098/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . Format Please select one from the list RIS (ProCite, Reference Manager) EndNote BibTex Medlars RefWorks Direct import Tips for downloading citations document.getElementById('citMgrHelpLink').addEventListener('click', function() { popupHelp(this.href); return false; }); $(".js__slcInclude").on("change", function(e){ if ($(this).val() == 'refworks') $('#direct').prop("checked", false); $('#direct').prop("disabled", ($(this).val() == 'refworks')); }); View Options View options PDF View PDF Figures Tables Media Share Share Share article link Copy Link Copied! Copying failed. 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