Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives

Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives | 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 j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives View ORCID Profile Cassandra L. Ettinger , Jennifer Arroyo , View ORCID Profile Jason E. Stajich doi: https://doi.org/10.1101/2025.01.23.634575 Cassandra L. Ettinger 1 Department of Microbiology and Plant Pathology, University of California , Riverside, CA, United States Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Cassandra L. Ettinger For correspondence: clettinger{at}ucdavis.edu Jennifer Arroyo 2 Department of Biology, California State University Channel Islands , Camarillo, CA, United States 3 The University of Arizona , Tucson, AZ, United States Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jason E. Stajich 1 Department of Microbiology and Plant Pathology, University of California , Riverside, CA, United States 4 Institute for Integrative Genome Biology, University of California , Riverside, Riverside, CA, United States Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jason E. Stajich Abstract Full Text Info/History Metrics Supplementary material Preview PDF Summary Arbuscular mycorrhizal fungi (AMF) form beneficial associations with plants, and are thought to have been critical to the adaptation of the ancestor of terrestrial plants during the transition onto land. However, the ability of AMF to associate with aquatic plants is unclear. To address this, we used 65 publicly available genomes and transcriptomes (25 freshwater, 23 terrestrial and 17 marine plants) to interrogate the genomic potential to form AMF associations in aquatic plant lineages in the order Alismatales. We explored the presence or absence of homologs of 45 genes, with a a special focus on six critical genes including three that co-evolved with AMF associations ( RAD1, STR1, STR2 ) and three necessary for intracellular symbiosis ( SymRK, CCaMK/DMI3, CYCLOPS/IDP3 ). Our results indicate a pattern likely consistent with independent gene losses (or extreme divergence) of symbiosis genes across aquatic lineages suggesting a possible inability to form AMF associations. However, some of these conserved genes (i.e., CCaMK/DMI3 ) are purported to function in other types of fungal symbioses, such as ectomycorrhizal symbiosis, and were observed here in a subset of aquatic lineages, including seagrasses. Overall, our findings highlight the complex evolutionary trajectories of symbiosis-related genes in aquatic plants, suggesting that while AMF associations may have been lost in certain lineages, others have genes that may allow them to form alternative fungal symbioses which may still play an underappreciated role in their ecology. Introduction Arbuscular mycorrhizal fungi (AMF) are obligate mutualistic root symbionts that assist host plants in nutrient uptake in exchange for carbon compounds ( Parniske, 2008 ; Bonfante & Anca, 2009 ). These fungi are thought to have been essential in facilitating the transition of ancestral plants from an aquatic to terrestrial environment ( Redecker et al ., 2000 ; Heckman et al ., 2001 ; Wang et al ., 2010 ; Humphreys et al ., 2010 ). These partnerships are widespread, with the majority of flowering plants (82-85%) maintaining AMF associations, underscoring their ecological importance ( Wang & Qiu, 2006 ; Brundrett, 2009 ). AMF were historically thought not to colonize aquatic environments, but have since been observed in wetlands, estuaries, mangrove forests and freshwater ecosystems ( Beck-Nielsen & Madsen, 2001 ; Bohrer et al ., 2004 ; Šraj-Kržič et al ., 2006 ; Kohout et al ., 2012 ). AMF have been reported to form associations with freshwater Alismatales, an order of flowering plants that includes many aquatic lineages, although these associations appear sporadic ( Clayton & Bagyaraj, 1984 ; Wigand & Stevenson, 1994 ; Khan & Belik, 1995 ; Beck-Nielsen & Madsen, 2001 ; Wang & Qiu, 2006 ; Šraj-Kržič et al ., 2006 ; Radhika & Rodrigues, 2007 ; Brundrett, 2009 ). Notably, marine Alismatales (i.e., seagrasses) have not been observed to form AMF associations, which may be due to the additional selective pressures of the marine environment ( Nielsen et al ., 1999 ). Instead there have been reports of ectomycorrhizal-like fungal root symbioses in Mediterranean seagrasses, Posidonia oceanica and Thalassodendron ciliatum ( Vohník et al., 2015 , 2019; Borovec & Vohník, 2018 ; Vohník & Josefiová, 2024 ). Further, a recent study surveying 34 conserved plant genes involved in AMF profiled two Alismatales species, the freshwater duckweed Spirodela polyrhiza and the seagrass Zostera marina , and concluded both were likely non-mycorrhizal (NM) based on gene loss ( Radhakrishnan et al ., 2020 ). However, seagrasses and freshwater lineages in the Alismatales have interesting evolutionary histories which involve multiple independent transitions into aquatic ecosystems ( Les et al ., 1997 ; Chen et al ., 2022 ). Therefore, we set out to more robustly profile the Alismatales overall to better understand how aquatic transitions might inform the evolutionary trajectory of genes involved in fungal symbiosis. To interrogate the genomic potential to form AMF associations in aquatic plant lineages in the order Alismatales, including seagrasses and freshwater relatives, we searched for the presence or absence of key genes implicated in AMF symbiosis in a set of plant genomes and transcriptomes. We used 65 publicly available genomes and transcriptomes downloaded from NCBI GenBank (Table S1). This included 25 freshwater, 23 terrestrial and 17 marine representatives, with 49 representing members of the order Alismatales. We performed reciprocal blast searches of protein sequences to explore the presence or absence of homologs of 45 genes reported to be related to AMF symbiosis (Table S2) ( Delaux et al ., 2013 , 2014; Radhakrishnan et al ., 2020 ), with a special focus on six critical genes highlighted by Radhakrishnan et al . (2020) including three that co-evolved with AMF associations ( RAD1, STR1, STR2 ) and three necessary for intracellular symbiosis ( SymRK, CCaMK/DMI3, CYCLOPS/IDP3 ). Materials and Methods Publicly available genomes and transcriptomes from 65 plants were downloaded from NCBI (Table S1). This included 25 freshwater, 23 terrestrial and 17 marine representatives, with 49 representing members of the order Alismatales (‘Darwin Tree of Life’; Ouyang et al ., 2006 ; The International Brachypodium Initiative, 2010 ; Massa et al ., 2011 ; Lamesch et al ., 2011 ; Bennetzen et al ., 2012 ; Ming et al ., 2013 , 2015; Droc et al ., 2013 ; Regier et al ., 2013 ; Motamayor et al ., 2013 ; Wang et al ., 2014 , 2023, 2024; Schmutz et al ., 2014 ; Yang et al ., 2015 ; Hirsch et al ., 2016 ; D’Esposito et al ., 2016 ; Michael et al ., 2017 , 2021; Suzuki et al ., 2017 ; Ruocco et al ., 2017 ; Malandrakis et al ., 2017 ; Zhang et al ., 2017 ; Entrambasaguas et al ., 2017 ; McCormick et al ., 2018 ; Hoang et al ., 2018 , 2020; Pecrix et al ., 2018 ; An et al ., 2019 ; Bellinger et al ., 2020 ; Yin et al ., 2021 ; Ma et al ., 2021 , 2024; Park et al ., 2021 ; Rowarth et al ., 2021 ; Abramson et al ., 2021 ; Gao et al ., 2022 ; Frisse et al ., 2022 ; Tang et al ., 2022 ; Bayer et al ., 2022 ; Ndhlovu & von der Heyden, 2022 ; Li et al ., 2023 ; Pasaribu et al ., 2023 ; Qian et al ., 2024 ). We obtained the predicted AMF status for each plant family from FungalRoot v. 2 ( Soudzilovskaia et al ., 2022 ). FungalRoot classifies plant families as obligate arbuscular mycorrhizal (AM), non-mycorrhizal (NM), or AM-NM which refers to facultative AMs - plants that are occasionally colonized by AMF, but are often observed without AMF in other conditions. Of the 65 plants included in this work: 22 were AM, 23 were NM and 20 were AM-NM. Using a set of 45 genes reported previously to be involved in AMF symbiosis (Table S2), including six genes, SymR/DMI2, CCaMK/DMI3, CYCLOPS/IPD3 , GRAS transcription factor RAD1 , and two half-ATP-binding cassette (ABC) transporters, STR and STR2 , thought to be critically important for forming intracellular symbioses and AMF ( Delaux et al ., 2013 , 2014; Radhakrishnan et al ., 2020 ), we surveyed the genetic landscape of several plants across the order Alismatales to assess whether they have maintained the potential to form AMF associations as many species in this order have ancestors that evolutionarily transitioned from terrestrial to aquatic habitats. We used command-line NCBI BLAST v. 2.16.0+ ( Camacho et al ., 2009 ) to perform reciprocal blast searches for the set of 45 genes using protein sequences from Medicago truncatula (v.4) as a reference, similar to searches performed in other studies of AMF ( Delaux et al ., 2014 ; Radhakrishnan et al ., 2020 ). For annotated genomes (n=53) we searched with blastp using the protein sequences from M. truncatula . Top matches were then reciprocally searched back against the annotation for M. truncatula using blastp. While, for unannotated genomes (n=2) and transcriptomes (n=14), we instead searched with tblastn using the protein sequences from M. truncatula . Top matches were then reciprocally searched against the M. truncatula annotation using blastx. Subsequent analysis and visualization of reciprocal matches was performed in R v. 4.3.1 ( R Core Team, 2021 ) using the tidyverse v. 2.0.0 R package ( Wickham et al ., 2019 ). For the purposes of this study, we consider cases where a positive reciprocal match was made (i.e. where the initially searched M. truncatula gene was subsequently the top hit in the reciprocal search) to be homologous genes. Note, we did not further assess whether positive reciprocal matches represented genes that were complete or functional. Further we consider cases where an initial match was made, but the reciprocal match was negative, to potentially indicate distant homology, such as paralogs, or genes that have undergone significant evolution or divergence. Finally, we consider cases where no matches were made to most likely indicate gene loss as the ancestral state of these genes is present. Note that for unannotated genomes and transcriptomes, there are several additional reasons genes might be missed using this approach including assembly issues, transcriptional variability, abundance or long introns. However, including both unannotated genomes and transcriptomes allows us to have a more robust understanding of the Alismatales gene space using currently available public data. Results and Discussion Across the 45 surveyed genes, positive reciprocal matches using protein sequences were found in 57.27 ± 3.08% of predicted AM plants, 11.78 ± 2.83% of NM-AM plants, and 18.36 ± 4.25% of NM plants ( Figure 1 ). A similar trend emerged across habitat types: 61.26 ± 3.30% in terrestrial plants, 10.22 ± 2.97% in freshwater plants, and 14.90 ± 4.32% in marine plants. Recovery of positive reciprocal matches was highest in annotated genomes, followed by transcriptomes, and lowest in unannotated genomes (e.g., for AM plants: 82.04 ± 4.04%, 45.56 ± 4.44%, and 23.05 ± 3.23%, respectively). This suggests that efforts to expand available Alismatales assembled and annotated genomes, particularly for aquatic Alismatales, would improve detection accuracy, and likely yield additional insights into the presence and absence of these genes in aquatic lineages. Download figure Open in new tab Figure 1. Loss of conserved symbiotic genes in aquatic plants. Heatmap showing initial blast and reciprocal blast results across marine, freshwater and terrestrial plants. Data type (genome [annotated], genome [unannotated], transcriptome) and FungalRoot v. 2 predicted AMF status (arbuscular mycorrhizal [AM], facultative arbuscular mycorrhizal [AM-NM], non-arbuscular mycorrhizal [NM]) are shown to aid interpretation. Regardless, the lower detection of positive reciprocal matches in freshwater and marine plants suggests that these plants have lost or have experienced divergence in many of the genes involved in AMF symbiosis. These findings support the idea that plants transitioning back into aquatic environments have repeatedly lost the ability to form AMF associations, largely aligning with the NM and NM-AM predictions for these lineages from the FungalRoot database based on observational reports. Overall, our results show a pattern of likely independent loss of conserved AMF associated genes across aquatic and marine Alismatales lineages and are consistent with previous research showing convergent loss of AMF genes in other NM plants ( Delaux et al ., 2014 ; Radhakrishnan et al ., 2020 ). Focusing on the six key genes previously identified as vital to AMF symbiosis ( Radhakrishnan et al ., 2020 ), we observed similar patterns to the full gene set (Figure S1). Specifically for the three genes that co-evolved with AMF associations ( RAD1, STR1, STR2 ), reciprocal matches using protein sequences were primarily found in terrestrial AM plants (83.33 ± 3.21%), with occasional matches in NM-AM freshwater plants, but none in marine plants. Radhakrishnan et al. (2020) suggested that the observed consistent loss of RAD1, STR1 and STR2 following the abandonment of AMF associations indicates there may be selection against these genes once AMF symbiosis is no longer needed. The absence of these genes in marine lineages reinforces previous observational reports that seagrasses lack AMF associations ( Nielsen et al ., 1999 ). For the three genes required for intracellular symbiosis ( SymRK, CCaMK / DMI3, CYCLOPS/IDP3 ) most reciprocal matches using protein sequences were from terrestrial plants (73.91 ± 4.35%), with only CCaMK / DMI3 detected in both freshwater and marine plants. Radhakrishnan et al . (2020) found that these three genes were not absent from all species that have lost AMF associations and instead observed that they were maintained in species that formed other types of fungal and bacterial symbiosis. They also highlighted several additional genes ( KinF, EPP1, VAPYRIN, LIN, CASTOR , and SYN ) which were maintained in species capable of other types of intracellular symbioses. Of these additional genes, we only recovered positive matches to VAPYRIN in aquatic plants. Our results suggest that some genes involved in AMF associations (i.e., CCaMK/DMI3 ) are retained in aquatic lineages, including seagrasses. Many of the 45 surveyed conserved genes are involved in other microbial symbioses beyond AMF (e.g., orchid mycorrhizas, ericoid mycorrhizas and legume-rhizobia symbioses) and their retention, loss or divergence may be important for understanding their interactions with other microorganisms. For example, CCaMK/DMI3 is thought to play a role in ectomycorrhizal (ECM) symbioses ( Li et al ., 2024 ). In our study, we found positive reciprocal matches for CCaMK/DMI3 in the seagrass Posidonia oceanica , which may relate to its reported ECM-like symbiotic relationship with the fungal root endophyte Posidoniomyces atricolor ( Vohník et al., 2015 , 2019; Borovec & Vohník, 2018 ). However, the function of CCaMK/DMI3 in aquatic plants remains unclear. For example, in the aquatic Nelumbo nucifera , which has also been reported to have CCaMK/DMI3 , recent work has documented a deletion in the kinase domain that likely renders it non-functional ( Bravo et al ., 2016 ; Radhakrishnan et al ., 2020 ). These findings highlight the need for further research to confirm whether CCaMK/DMI3 and other symbiosis-related genes detected in aquatic Alismatales remain functional and whether they have been co-opted for use in alternative symbiotic relationships. The loss of AMF associations in plants has been speculated to be due to adaptation to nutrient-rich ecological niches, which are known to inhibit the formation of AMF ( Read & Perez-Moreno, 2003 ). While aquatic environments are not wholly nutrient-rich, it is possible that the selective pressures of freshwater and marine life, such as low oxygen or high salinity, make it harder to maintain AMF ( Nielsen et al ., 1999 ; Fusconi & Mucciarelli, 2018 ). Additionally, many aquatic plants utilize their leaves, in addition to their roots, for uptake of nutrients which may make AMF associations, which are traditionally thought to occur in roots, less necessary ( Short & McRoy, 1984 ; Terrados & Williams, 1997 ). Overall, the Alismatales are a notable group for investigating the evolution of plant-fungal symbiosis and the impact of aquatic transitions on host-microbe interactions. This work serves to highlight the need for additional genome assembly and annotation efforts for plants in this group in order to understand the molecular basis of these interactions and the functional significance of retained symbiosis-related genes. Competing interests The authors declare no competing interests. Author contributions CLE conceived and designed the analysis, analyzed the data, prepared figures and/or tables, wrote and reviewed drafts of the paper. JA prepared figures and/or tables, and wrote and reviewed drafts of the paper. JES reviewed drafts of the paper. Data availability All code used in this work has been deposited on Github (casett/Seagrass_AMF) and archived in Zenodo (DOI: 10.5281/zenodo.14218123). The genomic and transcriptomic data used in this work are publicly available and were obtained from NCBI GenBank (Table S1). Funding sources CLE was supported by the National Science Foundation (NSF) under a NSF Ocean Sciences Postdoctoral Fellowship (Award No. 2205744). JA was supported by the NSF REU The National Summer Undergraduate Research Project, Award No. 2149582. JES is a CIFAR Fellow in the program Fungal Kingdom: Threats and Opportunities and was partially supported by NSF awards EF-2125066 and IOS-2134912. Computations were performed using the computer clusters and data storage resources of the UC Riverside HPCC, which were funded by grants from NSF (MRI-2215705, MRI-1429826) and NIH (1S10OD016290-01A1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Acknowledgements We would like to thank Jonathan A. Eisen for engaging in initial conversations around this work and for feedback on this manuscript. We would like to thank the Darwin Tree of Life project ( https://www.darwintreeoflife.org ) for making their genome assemblies publicly available without restriction. Footnotes Corresponding author email updated; no manuscript changes References ↵ Abramson BW , Novotny M , Hartwick NT , Colt K , Aevermann BD , Scheuermann RH , Michael TP . 2021 . The genome and preliminary single-nuclei transcriptome of Lemna minuta reveals mechanisms of invasiveness . Plant physiology 188 : 879 – 897 . OpenUrl ↵ An D , Zhou Y , Li C , Xiao Q , Wang T , Zhang Y , Wu Y , Li Y , Chao D-Y , Messing J , et al. 2019 . Plant evolution and environmental adaptation unveiled by long-read whole-genome sequencing of Spirodela . Proceedings of the National Academy of Sciences 116 : 18893 – 18899 . OpenUrl Abstract / FREE Full Text ↵ Bayer PE , Fraser MW , Martin BC , Petereit J , Severn-Ellis AA , Sinclair EA , Batley J , Kendrick GA , Edwards D. 2022 . Not all pathways are the same – unique adaptations to submerged environments emerge from comparative seagrass genomics . bioRxiv : 2022.11.22.517588. ↵ Beck-Nielsen D , Madsen TV . 2001 . Occurrence of vesicular–arbuscular mycorrhiza in aquatic macrophytes from lakes and streams . Aquatic botany 71 : 141 – 148 . OpenUrl CrossRef Web of Science ↵ Bellinger MR , Paudel R , Starnes S , Kambic L , Kantar MB , Wolfgruber T , Lamour K , Geib S , Sim S , Miyasaka SC , et al. 2020 . Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight . G3 Genes|Genomes|Genetics 10 : 2763 – 2775 . OpenUrl ↵ Bennetzen JL , Schmutz J , Wang H , Percifield R , Hawkins J , Pontaroli AC , Estep M , Feng L , Vaughn JN , Grimwood J , et al. 2012 . Reference genome sequence of the model plant Setaria . Nature biotechnology 30 : 555 – 561 . OpenUrl CrossRef PubMed ↵ Bohrer KE , Friese CF , Amon JP . 2004 . Seasonal dynamics of arbuscular mycorrhizal fungi in differing wetland habitats . Mycorrhiza 14 : 329 – 337 . OpenUrl CrossRef PubMed Web of Science ↵ Bonfante P , Anca IA . 2009 . Plants, mycorrhizal fungi, and bacteria: a network of interactions . Annual review of microbiology 63 . ↵ Borovec O , Vohník M. 2018 . Ontogenetic transition from specialized root hairs to specific rootfungus symbiosis in the dominant Mediterranean seagrass Posidonia oceanica . Scientific reports 8 : 10773 . OpenUrl PubMed ↵ Bravo A , York T , Pumplin N , Mueller LA , Harrison MJ . 2016 . Genes conserved for arbuscular mycorrhizal symbiosis identified through phylogenomics . Nature plants 2 : 15208 . OpenUrl PubMed ↵ Brundrett MC . 2009 . Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis . Plant and soil 320 : 37 – 77 . OpenUrl CrossRef Web of Science ↵ Camacho C , Coulouris G , Avagyan V , Ma N , Papadopoulos J , Bealer K , Madden TL . 2009 . BLAST+: architecture and applications . BMC bioinformatics 10 . ↵ Chen L-Y , Lu B , Morales-Briones DF , Moody ML , Liu F , Hu G-W , Huang C-H , Chen J-M , Wang Q-F. 2022 . Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments . Molecular biology and evolution 39 . ↵ Clayton JS , Bagyaraj DJ . 1984 . Vesicular-arbuscular mycorrhizas in submerged aquatic plants of New Zealand . Aquatic botany 19 : 251 – 262 . OpenUrl CrossRef Web of Science Darwin Tree of Life . ↵ Delaux P-M , Séjalon-Delmas N , Bécard G , Ané J-M. 2013 . Evolution of the plant-microbe symbiotic ‘toolkit’ . Trends in plant science 18 : 298 – 304 . OpenUrl CrossRef PubMed Web of Science ↵ Delaux P-M , Varala K , Edger PP , Coruzzi GM , Pires JC , Ané J-M. 2014 . Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution . PLoS genetics 10 : e1004487 . OpenUrl ↵ D’Esposito D , Orrù L , Dattolo E , Bernardo L , Lamontanara A , Orsini L , Serra IA , Mazzuca S , Procaccini G. 2016 . Transcriptome characterisation and simple sequence repeat marker discovery in the seagrass Posidonia oceanica . Scientific Data 3 : 1 – 9 . OpenUrl ↵ Droc G , Larivière D , Guignon V , Yahiaoui N , This D , Garsmeur O , Dereeper A , Hamelin C , Argout X , Dufayard J-F , et al. 2013 . The Banana Genome Hub . Database: the journal of biological databases and curation 2013 : bat035 . ↵ Entrambasaguas L , Jahnke M , Biffali E , Borra M. , Sanges R , Marín-Guirao L , Procaccini G. 2017 . Tissue-specific transcriptomic profiling provides new insights into the reproductive ecology and biology of the iconic seagrass species Posidonia oceanica . Marine genomics 35 : 51 – 61 . OpenUrl CrossRef PubMed ↵ Frisse L , Martinez MA , Pirro S. 2022 . The Complete Genome Sequence of Amorphophallus titanum, the Corpse Flower . Biodiversity Genomes . ↵ Fusconi A , Mucciarelli M. 2018 . How important is arbuscular mycorrhizal colonization in wetland and aquatic habitats? Environmental and Experimental Botany 155 : 128 – 141 . OpenUrl CrossRef ↵ Gao Y , Zhang Y , Feng C , Chu H , Feng C , Wang H , Wu L , Yin S , Liu C , Chen H , et al. 2022 . A chromosome-level genome assembly of Amorphophallus konjac provides insights into konjac glucomannan biosynthesis . Computational and structural biotechnology journal 20 . ↵ Heckman DS , Geiser DM , Eidell BR , Stauffer RL , Kardos NL , Hedges SB . 2001 . Molecular evidence for the early colonization of land by fungi and plants . Science (New York, N.Y .) 293 . ↵ Hirsch CN , Hirsch CD , Brohammer AB , Bowman MJ , Soifer I , Barad O , Shem-Tov D , Baruch K , Lu F , Hernandez AG , et al. 2016 . Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize . The Plant cell 28 : 2700 – 2714 . OpenUrl Abstract / FREE Full Text Hoang PTN , Fiebig A , Novák P , Macas J , Cao HX , Stepanenko A , Chen G , Borisjuk N , Scholz U , Schubert I. 2020 . Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries . Scientific reports 10 : 1 – 14 . OpenUrl PubMed ↵ Hoang PNT , Michael TP , Gilbert S , Chu P , Motley ST , Appenroth KJ , Schubert I , Lam E. 2018 . Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies . The Plant journal: for cell and molecular biology 96 . ↵ Humphreys CP , Franks PJ , Rees M , Bidartondo MI , Leake JR , Beerling DJ . 2010 . Mutualistic mycorrhiza-like symbiosis in the most ancient group of land plants . Nature communications 1 : 103 . OpenUrl PubMed ↵ Khan AG , Belik M. 1995 . Occurence and Ecological Significance of Mycorrhizal Symbiosis in Aquatic Plants . Mycorrhiza : 627 – 666 . ↵ Kohout P , Sýkorová Z , Ctvrtlíková M , Rydlová J , Suda J , Vohník M , Sudová R. 2012 . Surprising spectra of root-associated fungi in submerged aquatic plants . FEMS microbiology ecology 80 : 216 – 235 . OpenUrl CrossRef PubMed ↵ Lamesch P , Berardini TZ , Li D , Swarbreck D , Wilks C , Sasidharan R , Muller R , Dreher K , Alexander DL , Garcia-Hernandez M , et al. 2011 . The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools . Nucleic acids research 40 : D1202 – D1210 . OpenUrl PubMed Web of Science ↵ Les DH , Cleland MA , Waycott M. 1997 . Phylogenetic Studies in Alismatidae, II: Evolution of Marine Angiosperms (Seagrasses) and Hydrophily . Systematic Botany 22 : 443 – 463 . OpenUrl CrossRef Web of Science ↵ Li H , Ge Y , Zhang Z , Zhang H , Wang Y , Wang M , Zhao X , Yan J , Li Q , Qin L , et al. 2024 . Arbuscular mycorrhizal conserved genes are recruited for ectomycorrhizal symbiosis . The New phytologist 242 : 1860 – 1864 . OpenUrl PubMed ↵ Li F , Yang J-J , Sun Z-Y , Wang L , Qi L-Y , Sina A , Liu Y-Q , Zhang H-M , Dang L-F , Wang S-J , et al. 2023 . Plant-on-chip: Core morphogenesis processes in the tiny plant Wolffia australiana . PNAS Nexus 2 : gad141 . OpenUrl ↵ Malandrakis E , Dadali O , Kavouras M , Danis T , Panagiotaki P , Miliou H , Tsioli S , Orfanidis S , Küpper FC , Exadactylos A. 2017 . Identification of the abiotic stress-related transcription in little Neptune grass Cymodocea nodosa with RNA-seq . Marine genomics 34 : 47 – 56 . OpenUrl CrossRef PubMed ↵ Ma X , Olsen JL , Reusch TBH , Procaccini G , Kudrna D , Williams M , Grimwood J , Rajasekar S , Jenkins J , Schmutz J , et al. 2021 . Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass) . F1000Research 10 : 289 . OpenUrl ↵ Massa SI , Pearson GA , Aires T , Kube M , Olsen JL , Reinhardt R , Serrao EA , Arnaud-Haond S. 2011 . Expressed sequence tags from heat-shocked seagrass Zostera noltii (Hornemann) from its southern distribution range . Marine genomics 4 : 181 – 188 . OpenUrl CrossRef PubMed Ma X , Vanneste S , Chang J , Ambrosino L , Barry K , Bayer T , Bobrov AA , Boston L , Campbell JE , Chen H , et al. 2024 . Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment . Nature Plants 10 : 240 – 255 . OpenUrl PubMed ↵ McCormick RF , Truong SK , Sreedasyam A , Jenkins J , Shu S , Sims D , Kennedy M , Amirebrahimi M , Weers BD , McKinley B , et al. 2018 . The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization . The Plant journal: for cell and molecular biology 93 : 338 – 354 . OpenUrl CrossRef ↵ Michael TP , Bryant D , Gutierrez R , Borisjuk N , Chu P , Zhang H , Xia J , Zhou J , Peng H , El Baidouri M , et al. 2017 . Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies . The Plant journal: for cell and molecular biology 89 . Michael TP , Ernst E , Hartwick N , Chu P , Bryant D , Gilbert S , Ortleb S , Baggs EL , Sowjanya Sree K , Appenroth KJ , et al. 2021 . Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control . Genome research 31 : 225 – 238 . OpenUrl Abstract / FREE Full Text ↵ Ming R , VanBuren R , Liu Y , Yang M , Han Y , Li L-T , Zhang Q , Kim M-J , Schatz MC , Campbell M , et al. 2013 . Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn .). Genome biology 14 : 1 – 11 . OpenUrl CrossRef Ming R , VanBuren R , Wai CM , Tang H , Schatz MC , Bowers JE , Lyons E , Wang M-L , Chen J , Biggers E , et al. 2015 . The pineapple genome and the evolution of CAM photosynthesis . Nature genetics 47 : 1435 – 1442 . OpenUrl CrossRef PubMed ↵ Motamayor JC , Mockaitis K , Schmutz J , Haiminen N , Iii DL , Cornejo O , Findley SD , Zheng P , Utro F , Royaert S , et al. 2013 . The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color . Genome biology 14 : 1 – 25 . OpenUrl CrossRef ↵ Ndhlovu A , von der Heyden S. 2022 . De novo assembly and annotation of the transcriptome of the endangered seagrass Zostera capensis: Insights from differential gene expression under thermal stress . Marine genomics 66 : 100984 . OpenUrl CrossRef PubMed ↵ Nielsen SL , Thingstrup I , Wigand C. 1999 . Apparent lack of vesicular–arbuscular mycorrhiza (VAM) in the seagrasses Zostera marina L. and Thalassia testudinum Banks ex König . Aquatic botany 63 : 261 – 266 . OpenUrl ↵ Ouyang S , Zhu W , Hamilton J , Lin H , Campbell M , Childs K , Thibaud-Nissen F , Malek RL , Lee Y , Zheng L , et al. 2006 . The TIGR Rice Genome Annotation Resource: improvements and new features . Nucleic acids research 35 : D883 – D887 . OpenUrl PubMed Web of Science ↵ Park H , Park JH , Lee Y , Woo DU , Jeon HH , Sung YW , Shim S , Kim SH , Lee KO , Kim J-Y , et al. 2021 . Genome of the world’s smallest flowering plant, Wolffia australiana, helps explain its specialized physiology and unique morphology . Communications Biology 4 : 1 – 12 . OpenUrl PubMed ↵ Parniske M. 2008 . Arbuscular mycorrhiza: the mother of plant root endosymbioses . Nature reviews. Microbiology 6 : 763 – 775 . OpenUrl CrossRef PubMed Web of Science ↵ Pasaribu B , Acosta K , Aylward A , Liang Y , Abramson BW , Colt K , Hartwick NT , Shanklin J , Michael TP , Lam E. 2023 . Genomics of turions from the Greater Duckweed reveal its pathways for dormancy and re-emergence strategy . The New phytologist 239 : 116 – 131 . OpenUrl PubMed ↵ Pecrix Y , Staton SE , Sallet E , Lelandais-Brière C , Moreau S , Carrère S , Blein T , Jardinaud M-F , Latrasse D , Zouine M , et al. 2018 . Whole-genome landscape of Medicago truncatula symbiotic genes . Nature Plants 4 : 1017 – 1025 . OpenUrl PubMed ↵ Qian Z-H , Li W , Wang Q-F , Liang S-C , Wu S , Li Z-Z , Chen J-M. 2024 . The chromosome-level genome of the submerged plant Cryptocoryne crispatula provides insights into the terrestrial– freshwater transition in Araceae . DNA research: an international journal for rapid publication of reports on genes and genomes 31 : dsae003 . OpenUrl ↵ Radhakrishnan GV , Keller J , Rich MK , Vernié T , Mbadinga Mbadinga DL , Vigneron N , Cottret L , Clemente HS , Libourel C , Cheema J , et al. 2020 . An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages . Nature plants 6 : 280 – 289 . OpenUrl PubMed ↵ Radhika KP , Rodrigues BF . 2007 . Arbuscular Mycorrhizae in association with aquatic and marshy plant species in Goa, India . Aquatic botany 86 : 291 – 294 . OpenUrl CrossRef Web of Science ↵ R Core Team . 2021 . R: A Language and Environment for Statistical Computing . ↵ Read DJ , Perez-Moreno J. 2003 . Mycorrhizas and nutrient cycling in ecosystems - a journey towards relevance? The New phytologist 157 : 475 – 492 . OpenUrl PubMed ↵ Redecker D , Kodner R , Graham LE . 2000 . Glomalean fungi from the Ordovician . Science (New York, N.Y .) 289 : 1920 – 1921 . OpenUrl ↵ Regier N , Baerlocher L , Münsterkötter M , Farinelli L , Cosio C. 2013 . Analysis of the Elodea nuttallii Transcriptome in Response to Mercury and Cadmium Pollution: Development of Sensitive Tools for Rapid Ecotoxicological Testing . ↵ Rowarth NM , Curtis BA , Einfeldt AL , Archibald JM , Lacroix CR , Gunawardena AHLAN . 2021 . RNA-Seq analysis reveals potential regulators of programmed cell death and leaf remodelling in lace plant (Aponogeton madagascariensis) . BMC plant biology 21 : 1 – 20 . OpenUrl PubMed ↵ Ruocco M , Musacchia F , Olivé I , Costa MM , Barrote I , Santos R , Sanges R , Procaccini G , Silva J. 2017 . Genomewide transcriptional reprogramming in the seagrass Cymodocea nodosa under experimental ocean acidification . Molecular ecology 26 . ↵ Schmutz J , McClean PE , Mamidi S , Wu GA , Cannon SB , Grimwood J , Jenkins J , Shu S , Song Q , Chavarro C , et al. 2014 . A reference genome for common bean and genome-wide analysis of dual domestications . Nature genetics 46 : 707 – 713 . OpenUrl CrossRef PubMed ↵ Short FT , McRoy CP . 1984 . Nitrogen Uptake by Leaves and Roots of the Seagrass Zostera marina L . Botanica marina 27 : 547 – 556 . OpenUrl ↵ Soudzilovskaia NA , He J , Rahimlou S , Abarenkov K , Brundrett MC , Tedersoo L. 2022 . FungalRoot v.2.0 - an empirical database of plant mycorrhizal traits: A response to Bueno et al. (2021) ‘Towards a consistent benchmark for plant mycorrhizal association databases’ . The New phytologist 235 : 1689 – 1691 . OpenUrl PubMed ↵ Šraj-Kržič N , Pongrac P , Klemenc M , Kladnik A , Regvar M , Gaberščik A. 2006 . Mycorrhizal colonisation in plants from intermittent aquatic habitats . Aquatic botany 85 : 331 – 336 . OpenUrl CrossRef ↵ Suzuki JY , Amore TD , Calla B , Palmer NA , Scully ED , Sattler SE , Sarath G , Lichty JS , Myers RY , Keith LM , et al. 2017 . Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler . Scientific reports 7 : 1 – 15 . OpenUrl CrossRef PubMed ↵ Tang H , Saina JK , Long Z-C , Chen J , Dai C. 2022 . De novo transcriptome assembly using Illumina sequencing and development of EST-SSR markers in a monoecious herb Sagittaria trifolia Linn . PeerJ 10 : e14268 . OpenUrl CrossRef PubMed ↵ Terrados J , Williams SL . 1997 . Leaf versus root nitrogen uptake by the surfgrass Phyllospadix torreyi . Marine Ecology Progress Series 149 : 267 – 277 . OpenUrl ↵ The International Brachypodium Initiative . 2010 . Genome sequencing and analysis of the model grass Brachypodium distachyon . Nature 463 : 763 – 768 . OpenUrl CrossRef PubMed Web of Science Vohník M , Borovec O , Kolaříková Z , Sudová R , Réblová M. 2019 . Extensive sampling and high-throughput sequencing reveal Posidoniomyces atricolor gen. et sp. nov. (Aigialaceae, Pleosporales) as the dominant root mycobiont of the dominant Mediterranean seagrass Posidonia oceanica . MycoKeys 55 : 59 – 86 . OpenUrl PubMed ↵ Vohník M , Borovec O , Župan I , Vondrášek D , Petrtýl M , Sudová R. 2015 . Anatomically and morphologically unique dark septate endophytic association in the roots of the Mediterranean endemic seagrass Posidonia oceanica . Mycorrhiza 25 : 663 – 672 . OpenUrl CrossRef PubMed ↵ Vohník M , Josefiová J. 2024 . Novel epiphytic root-fungus symbiosis in the Indo-Pacific seagrass Thalassodendron ciliatum from the Red Sea . Mycorrhiza . ↵ Wang W , Haberer G , Gundlach H , Gläßer C , Nussbaumer T , Luo MC , Lomsadze A , Borodovsky M , Kerstetter RA , Shanklin J , et al. 2014 . The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle . Nature communications 5 : 1 – 13 . OpenUrl ↵ Wang B , Qiu YL . 2006 . Phylogenetic distribution and evolution of mycorrhizas in land plants . Mycorrhiza 16 . Wang Z-F , Wu L-F , Chen L , Zhu W-G , Yu E-P , Xu F-X , Cao H-L. 2024 . Genome assembly of Ottelia alismoides, a multiple-carbon utilisation aquatic plant . BMC Genomic Data 25 : 1 – 4 . OpenUrl PubMed Wang Y , Yang T , Wang D , Gou R , Jiang Y , Zhang G , Zheng Y , Gao D , Chen L , Zhang X , et al. 2023 . Chromosome level genome assembly of colored calla lily (Zantedeschia elliottiana) . Scientific Data 10 : 1 – 7 . OpenUrl PubMed ↵ Wang B , Yeun LH , Xue J-Y , Liu Y , Ané J-M , Qiu Y-L. 2010 . Presence of three mycorrhizal genes in the common ancestor of land plants suggests a key role of mycorrhizas in the colonization of land by plants . The New phytologist 186 : 514 – 525 . OpenUrl PubMed ↵ Wickham H , Averick M , Bryan J , Chang W , McGowan L , François R , Grolemund G , Hayes A , Henry L , Hester J , et al. 2019 . Welcome to the Tidyverse . Journal of Open Source Software 4 : 1686 . OpenUrl ↵ Wigand C , Stevenson JC . 1994 . The presence and possible ecological significance of mycorrhizae of the submersed macrophyte, Vallisneria americana . Estuaries 17 : 206 – 215 . OpenUrl CrossRef ↵ Yang Y , Chen X , Xu B , Li Y , Ma Y , Wang G. 2015 . Phenotype and transcriptome analysis reveals chloroplast development and pigment biosynthesis together influenced the leaf color formation in mutants of Anthurium andraeanum ‘Sonate’ . Frontiers in plant science 6 : 131822 . OpenUrl ↵ Yin J , Jiang L , Wang L , Han X , Guo W , Li C , Zhou Y , Denton M , Zhang P. 2021 . A high-quality genome of taro (Colocasia esculenta (L.) Schott), one of the world’s oldest crops . Molecular ecology resources 21 : 68 – 77 . OpenUrl PubMed ↵ Zhang G-Q , Liu K-W , Li Z , Lohaus R , Hsiao Y-Y , Niu S-C , Wang J-Y , Lin Y-C , Xu Q , Chen L-J , et al. 2017 . The Apostasia genome and the evolution of orchids . Nature 549 : 379 – 383 . OpenUrl CrossRef PubMed View the discussion thread. Back to top Previous Next Posted March 12, 2026. Download PDF Supplementary Material 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 Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives 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. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives Cassandra L. Ettinger , Jennifer Arroyo , Jason E. Stajich bioRxiv 2025.01.23.634575; doi: https://doi.org/10.1101/2025.01.23.634575 Share This Article: Copy Citation Tools Assessing the Evolutionary Trajectory of Arbuscular Mycorrhizal Conserved Genes in Seagrasses and Aquatic Close Relatives Cassandra L. Ettinger , Jennifer Arroyo , Jason E. Stajich bioRxiv 2025.01.23.634575; doi: https://doi.org/10.1101/2025.01.23.634575 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 Evolutionary Biology Subject Areas All Articles Animal Behavior and Cognition (7637) Biochemistry (17705) Bioengineering (13899) Bioinformatics (41968) Biophysics (21460) Cancer Biology (18603) Cell Biology (25526) Clinical Trials (138) Developmental Biology (13385) Ecology (19910) Epidemiology (2067) Evolutionary Biology (24328) Genetics (15614) Genomics (22513) Immunology (17741) Microbiology (40423) Molecular Biology (17193) Neuroscience (88646) Paleontology (667) Pathology (2835) Pharmacology and Toxicology (4827) Physiology (7647) Plant Biology (15160) Scientific Communication and Education (2046) Synthetic Biology (4302) Systems Biology (9825) Zoology (2271)