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Shazib SUA, Ahsan R, Leleu M, McManus GB, Katz LA, Santoferrara LF. Phylogenomic workflow for uncultivable microbial eukaryotes using single-cell RNA sequencing - A case study with planktonic ciliates (Ciliophora, Oligotrichea). Mol Phylogenet Evol 2025; 204:108239. [PMID: 39551225 DOI: 10.1016/j.ympev.2024.108239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 10/25/2024] [Accepted: 11/10/2024] [Indexed: 11/19/2024]
Abstract
Phylogenetic analyses increasingly rely on genomic and transcriptomic data to produce better supported inferences on the evolutionary relationships among microbial eukaryotes. Such phylogenomic analyses, however, require robust workflows, bioinformatic expertise and computational power. Microbial eukaryotes pose additional challenges given the complexity of their genomes and the presence of non-target sequences (e.g., symbionts, prey) in data obtained from single cells of uncultivable lineages. To address these challenges, we developed a phylogenomic workflow based on single-cell RNA sequencing, integrating all essential steps from cell isolation to data curation and species tree inference. We assessed our workflow by using publicly available and newly generated transcriptomes (11 and 28, respectively) from the Oligotrichea, a diverse group of marine planktonic ciliates. This group's phylogenetic relationships have been relatively well-studied based on ribosomal RNA gene markers, which we reconstructed by read mapping of transcriptome sequences and compared to our phylogenomic inferences. We also compared phylogenomic analyses based on single-copy protein-coding genes (well-curated orthologs) and multi-copy genes (including paralogs) by sequence concatenation and a coalescence approach (Asteroid), respectively. Finally, using subsets of up to 1,014 gene families (GFs), we assessed the influence of missing data in our phylogenomic inferences. All our analyses yielded similar results, and most inferred relationships were consistent and well-supported. Overall, we found that Asteroid provides robust support for species tree inferences, while simplifying curation steps, minimizing the effects of missing data and maximizing the number of GFs represented in the analyses. Our workflow can be adapted for phylogenomic analyses based on single-cell RNA sequencing of other uncultivable microbial eukaryotes.
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Affiliation(s)
- Shahed U A Shazib
- Department of Biological Sciences, Smith College, Northampton, MA, USA
| | - Ragib Ahsan
- Department of Biological Sciences, Smith College, Northampton, MA, USA; University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, USA
| | - Marie Leleu
- Department of Biological Sciences, Smith College, Northampton, MA, USA
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, MA, USA; University of Massachusetts Amherst, Program in Organismic and Evolutionary Biology, Amherst, MA, USA.
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Cull A, Joly DL. Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars. BMC Genomics 2025; 26:83. [PMID: 39875833 PMCID: PMC11773717 DOI: 10.1186/s12864-025-11263-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 01/20/2025] [Indexed: 01/30/2025] Open
Abstract
BACKGROUND Due to its previously illicit nature, Cannabis sativa had not fully reaped the benefits of recent innovations in genomics and plant sciences. However, Canada's legalization of C. sativa and products derived from its flower in 2018 triggered significant new demand for robust genotyping tools to assist breeders in meeting consumer demands. Early molecular marker-based research on C. sativa focused on screening for plant sex and chemotype, and more recent research has sought to use molecular markers to target traits of agronomic interest, to study populations and to differentiate between C. sativa cultivars. RESULTS In this study, we have conducted whole genome sequencing of 32 cultivars, mined the sequencing data for SNPs, developed a reduced SNP genotyping panel to discriminate between sequenced cultivars, then validated the 20-SNP panel using DNA from the sequenced cultivars and tested the assays on commercially available dried flower. The assay conversion rate was higher in DNA extracted from fresh plant material than in DNA extracted from dried flower samples. However, called genotypes were internally consistent, highlighting discrepancies between genotypes detected using sequencing data and observed using genotyping assays. The primary contributions of this work are to clearly document the process used to develop minimal SNP genotyping panels, the feasibility of using such panels to differentiate between C. sativa cultivars, and outline improvements and goals for future iterations of PCR-based, minimal SNP panels to enable efficient development genotyping tools to identify and screen C. sativa cultivars. CONCLUSIONS Our key recommendations are to increase sampling density to account for intra-cultivar variability; leverage higher read length paired-end short-read technology; conduct in-depth pre- and post-processing of reads, mapping, and variant calling data; integrate trait-associated loci to develop multi-purpose panels; and use iterative approaches for in vitro validation to ensure that only the most discriminant and performant SNPs are retained.
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Affiliation(s)
- Alex Cull
- Cannabis Innovation and Research Center, Université de Moncton, Moncton, New-Brunswick, Canada
| | - David L Joly
- Cannabis Innovation and Research Center, Université de Moncton, Moncton, New-Brunswick, Canada.
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Musker SD, Nürk NM, Pirie MD. Maximising informativeness for target capture-based phylogenomics in Erica (Ericaceae). PHYTOKEYS 2025; 251:87-118. [PMID: 39867481 PMCID: PMC11758362 DOI: 10.3897/phytokeys.251.136373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 12/03/2024] [Indexed: 01/28/2025]
Abstract
Plant phylogenetics has been revolutionised in the genomic era, with target capture acting as the primary workhorse of most recent research in the new field of phylogenomics. Target capture (aka Hyb-Seq) allows researchers to sequence hundreds of genomic regions (loci) of their choosing, at relatively low cost per sample, from which to derive phylogenetically informative data. Although this highly flexible and widely applicable method has rightly earned its place as the field's de facto standard, it does not come without its challenges. In particular, users have to specify which loci to sequence-a surprisingly difficult task, especially when working with non-model groups, as it requires pre-existing genomic resources in the form of assembled genomes and/or transcriptomes. In the absence of taxon-specific genomic resources, target sets exist that are designed to work across broad taxonomic scales. However, the highly conserved loci that they target may lack informativeness for difficult phylogenetic problems, such as that presented by the rapid radiation of Erica in southern Africa. We designed a target set for Erica phylogenomics intended to maximise informativeness and minimise paralogy while maintaining universality by including genes from the widely used Angiosperms353 set. Comprising just over 300 genes, the targets had excellent recovery rates in roughly 90 Erica species as well as outgroups from Calluna, Daboecia, and Rhododendron, and had high information content as measured by parsimony informative sites and Quartet Internode Resolution Probability (QIRP) at shallow nodes. Notably, QIRP was positively correlated with intron content, while including introns in targets-rather than recovering them via exon-flanking "bycatch"-substantially improved intron recovery. Overall, our results show the value of building a custom target set, and we provide a suite of open-source tools that can be used to replicate our approach in other groups (https://github.com/SethMusker/TargetVet).
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Affiliation(s)
- Seth D. Musker
- Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, South AfricaUniversity of BayreuthBayreuthGermany
- Department of Plant Systematics, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, GermanyUniversity of Cape TownCape TownSouth Africa
| | - Nicolai M. Nürk
- Department of Plant Systematics, Bayreuth Centre of Ecology and Environmental Research (BayCEER), University of Bayreuth, Universitätsstraße 30, 95447, Bayreuth, GermanyUniversity of Cape TownCape TownSouth Africa
| | - Michael D. Pirie
- University Museum, The University of Bergen, Postboks 7800, N-5020, Bergen, NorwayThe University of BergenBergenNorway
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Ousmael KM, Hansen OK. From phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis? APPLICATIONS IN PLANT SCIENCES 2025; 13:e11624. [PMID: 39906492 PMCID: PMC11788909 DOI: 10.1002/aps3.11624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 02/06/2025]
Abstract
Premise Leveraging DNA markers, particularly single-nucleotide polymorphisms (SNPs), in parentage analysis, sib-ship reconstruction, and genomic relatedness analysis can enhance plant breeding efficiency. However, the limited availability of genomic information, confined to the most commonly used species, hinders the broader application of SNPs in species of lower economic interest (e.g., most tree species). We explored the possibility of using universal target capture probes, namely Angiosperms353, to identify SNPs and assess their effectiveness in genomic relatedness analysis. Methods We tested the approach in 11 tree species, six of which had a half-sib family structure. Variants were called within species, and genomic relatedness analysis was conducted in species with two or more families. Scalability via amplicon sequencing was tested by designing primers and testing them in silico. Results Adequate SNPs for relatedness analysis were identified in all species. Relatedness values from Angiosperms353-based SNPs highly correlated with those from thousands of genome-wide DArTseq SNPs in Cordia africana, one of the species with a family structure. The in silico performance of designed primers demonstrated the potential for scaling up via amplicon sequencing. Discussion Utilizing universal target capture probes for SNP identification can help overcome the limitations of genomic information availability, thereby enhancing the application of genomic markers in breeding plant species with lower economic interest.
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Affiliation(s)
- Kedra M. Ousmael
- Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenRolighedsvej 23, 1958 Frederiksberg CDenmark
| | - Ole K. Hansen
- Department of Geosciences and Natural Resource ManagementUniversity of CopenhagenRolighedsvej 23, 1958 Frederiksberg CDenmark
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Shin S, Baker AJ, Enk J, McKenna DD, Foquet B, Vandergast AG, Weissman DB, Song H. Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales. Sci Rep 2024; 14:21377. [PMID: 39271747 PMCID: PMC11399444 DOI: 10.1038/s41598-024-72622-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 09/09/2024] [Indexed: 09/15/2024] Open
Abstract
Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.
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Affiliation(s)
- Seunggwan Shin
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Austin J Baker
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
- Entomology Department, Natural History Museum of Los Angeles County, Los Angeles, CA, USA
| | - Jacob Enk
- Daicel Arbor Biosciences, Ann Arbor, MI, USA
| | - Duane D McKenna
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN, USA
| | - Bert Foquet
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Amy G Vandergast
- San Diego Field Station, Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, USA
| | - David B Weissman
- Department of Entomology, California Academy of Sciences, Golden Gate Park, San Francisco, CA, USA
| | - Hojun Song
- Department of Entomology, Texas A&M University, College Station, TX, USA.
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Ning W, Meudt HM, Tate JA. A roadmap of phylogenomic methods for studying polyploid plant genera. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11580. [PMID: 39184196 PMCID: PMC11342234 DOI: 10.1002/aps3.11580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/10/2023] [Accepted: 01/13/2024] [Indexed: 08/27/2024]
Abstract
Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole-genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid-rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long-read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids.
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Affiliation(s)
- Weixuan Ning
- School of Natural SciencesMassey UniversityPalmerston North4442New Zealand
| | - Heidi M. Meudt
- Museum of New Zealand Te Papa TongarewaWellington6011New Zealand
| | - Jennifer A. Tate
- School of Natural SciencesMassey UniversityPalmerston North4442New Zealand
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Xie P, Guo Y, Teng Y, Zhou W, Yu Y. GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data. Mol Ecol Resour 2024; 24:e13924. [PMID: 38197287 DOI: 10.1111/1755-0998.13924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 12/14/2023] [Accepted: 12/21/2023] [Indexed: 01/11/2024]
Abstract
The advancement of next-generation sequencing (NGS) technologies has been revolutionary for the field of evolutionary biology. This technology has led to an abundance of available genomes and transcriptomes for researchers to mine. Specifically, researchers can mine for various types of molecular markers that are vital for phylogenetic, evolutionary and ecological studies. Numerous tools have been developed to extract these molecular markers from NGS data. However, due to an insufficient number of well-annotated reference genomes for non-model organisms, it remains challenging to obtain these markers accurately and efficiently. Here, we present GeneMiner, an improved and expanded version of our previous tool, Easy353. GeneMiner combines the reference-guided de Bruijn graph assembly with seed self-discovery and greedy extension. Additionally, it includes a verification step using a parameter-bootstrap method to reduce the pitfalls associated with using a relatively distant reference. Our results, using both experimental and simulation data, showed GeneMiner can accurately acquire phylogenetic molecular markers for plants using transcriptomic, genomic and other NGS data. GeneMiner is designed to be user-friendly, fast and memory-efficient. Further, it is compatible with Linux, Windows and macOS. All source codes are publicly available on GitHub (https://github.com/sculab/GeneMiner) and Gitee (https://gitee.com/sculab/GeneMiner) for easy accessibility and transparency.
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Affiliation(s)
- Pulin Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongling Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yue Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Wenbin Zhou
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yan Yu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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Kuo LY, Su HJ, Koubínová D, Xie PJ, Whitehouse C, Ebihara A, Grant JR. Organellar phylogenomics of Ophioglossaceae fern genera. FRONTIERS IN PLANT SCIENCE 2024; 14:1294716. [PMID: 38288414 PMCID: PMC10823028 DOI: 10.3389/fpls.2023.1294716] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024]
Abstract
Previous phylogenies showed conflicting relationships among the subfamilies and genera within the fern family Ophioglossaceae. However, their classification remains unsettled where contrasting classifications recognize four to 15 genera. Since these treatments are mostly based on phylogenetic evidence using limited, plastid-only loci, a phylogenomic understanding is actually necessary to provide conclusive insight into the systematics of the genera. In this study, we have therefore compiled datasets with the broadest sampling of Ophioglossaceae genera to date, including all fifteen currently recognized genera, especially for the first time the South African endemic genus Rhizoglossum. Notably, our comprehensive phylogenomic matrix is based on both plastome and mitogenome genes. Inferred from the coding sequences of 83 plastid and 37 mitochondrial genes, a strongly supported topology for these subfamilies is presented, and is established by analyses using different partitioning approaches and substitution models. At the generic level, most relationships are well resolved except for few within the subfamily Ophioglossoideae. With this new phylogenomic scheme, key morphological and genomic changes were further identified along this backbone. In addition, we confirmed numerous horizontally transferred (HGT) genes in the genera Botrypus, Helminthostachys, Mankyua, Sahashia, and Sceptridium. These HGT genes are most likely located in mitogenomes and are predominately donated from angiosperm Santalales or non-Ophioglossaceae ferns. By our in-depth searches of the organellar genomes, we also provided phylogenetic overviews for the plastid and mitochondrial MORFFO genes found in these Ophioglossaceae ferns.
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Affiliation(s)
- Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Huei-Jiun Su
- Department of Earth and Life Sciences, University of Taipei, Taipei, Taiwan
| | - Darina Koubínová
- University of Neuchâtel, Laboratory of Evolutionary Genetics, Neuchâtel, Switzerland
| | - Pei-Jun Xie
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Jason R. Grant
- University of Neuchâtel, Laboratory of Evolutionary Genetics, Neuchâtel, Switzerland
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Moore‐Pollard ER, Jones DS, Mandel JR. Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11568. [PMID: 38369976 PMCID: PMC10873820 DOI: 10.1002/aps3.11568] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/30/2023] [Accepted: 11/12/2023] [Indexed: 02/20/2024]
Abstract
Premise A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization. Methods We developed a Hyb-Seq probe set, Compositae-ParaLoss-1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 Packera taxa that were previously studied using Compositae-1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support. Results We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae-1061. Most notably, Compositae-ParaLoss-1272 recovered substantially fewer paralogous sequences than Compositae-1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae-1061. Discussion Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae-ParaLoss-1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.
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Affiliation(s)
- Erika R. Moore‐Pollard
- Department of Biological SciencesUniversity of Memphis3700 Walker Ave.MemphisTennessee38152USA
| | - Daniel S. Jones
- Department of Biological SciencesAuburn University101 Rouse Life SciencesAuburnAlabama36849USA
| | - Jennifer R. Mandel
- Department of Biological SciencesUniversity of Memphis3700 Walker Ave.MemphisTennessee38152USA
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Zhou W, Shi W, Soltis PS, Soltis DE, Xiang QY(J. Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation. FRONTIERS IN PLANT SCIENCE 2023; 14:1274746. [PMID: 38192694 PMCID: PMC10773735 DOI: 10.3389/fpls.2023.1274746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/27/2023] [Indexed: 01/10/2024]
Abstract
Introduction The well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these lineages. Here we compared foliar endophytic fungi and bacteria-archaea (FEF and FEB) in 17 EA-ENA disjunct species or clade pairs from genera representing conifers and 10 orders of five major groups of angiosperms and 23 species of Cornus from EA and North America. Methods Metagenomic sequencing of fungal ITS and bacterial-archaeal 16S rDNA was used to capture the foliar endophytic communities. Alpha and beta diversity of fungi and bacteria were compared at multiple scales and dimensions to gain insights into the relative roles of historical geographic isolation, host identity, phylogeny, and environment from samples at different sites in shaping endophytic diversity patterns. Results We found that beta diversity of endophytes varied greatly among plant individuals within species and between species among genera at the same sampling site, and among three sampling sites, but little variation between region-of-origin of all plant species (EA vs ENA) and between EA-ENA disjunct counterparts within genera. Various numbers of indicator fungal species differing in abundance were identified for each plant genus and Cornus species. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance of plants was detected among the disjunct genera but not among species of Cornus. However, significant correlations between beta diversities at different taxonomic scales of endophytes and phylogenetic distances of Cornus species were observed. Discussion Our results suggest important roles of host identity and environment (sampling sites), and a likely minor role of phylogenetic divergence and historical biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera and Cornus. The results lead to a hypothesis that the sister taxa in EA and ENA likely differ in FEF and FEB when growing in native habitats due to differences in local environments, which may potentially drive allopatric divergence of the functional features of species.
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Affiliation(s)
- Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Wei Shi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Douglas E. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
- Department of Biology, University of Florida, Gainesville, FL, United States
| | - Qiu-Yun (Jenny) Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Yang LH, Shi XZ, Wen F, Kang M. Phylogenomics reveals widespread hybridization and polyploidization in Henckelia (Gesneriaceae). ANNALS OF BOTANY 2023; 131:953-966. [PMID: 37177810 PMCID: PMC10332401 DOI: 10.1093/aob/mcad047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/12/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS Hybridization has long been recognized as an important process for plant evolution and is often accompanied by polyploidization, another prominent force in generating biodiversity. Despite its pivotal importance in evolution, the actual prevalence and distribution of hybridization across the tree of life remain unclear. METHODS We used whole-genome shotgun (WGS) sequencing and cytological data to investigate the evolutionary history of Henckelia, a large genus in the family Gesneriaceae with a high frequency of suspected hybridization and polyploidization events. We generated WGS sequencing data at about 10× coverage for 26 Chinese Henckelia species plus one Sri Lankan species. To untangle the hybridization history, we separately extracted whole plastomes and thousands of single-copy nuclear genes from the sequencing data, and reconstructed phylogenies based on both nuclear and plastid data. We also explored sources of both genealogical and cytonuclear conflicts and identified signals of hybridization and introgression within our phylogenomic dataset using several statistical methods. Additionally, to test the polyploidization history, we evaluated chromosome counts for 45 populations of the 27 Henckelia species studied. KEY RESULTS We obtained well-supported phylogenetic relationships using both concatenation- and coalescent-based methods. However, the nuclear phylogenies were highly inconsistent with the plastid phylogeny, and we observed intensive discordance among nuclear gene trees. Further analyses suggested that both incomplete lineage sorting and gene flow contributed to the observed cytonuclear and genealogical discordance. Our analyses of introgression and phylogenetic networks revealed a complex history of hybridization within the genus Henckelia. In addition, based on chromosome counts for 27 Henckelia species, we found independent polyploidization events occurred within Henckelia after different hybridization events. CONCLUSIONS Our findings demonstrated that hybridization and polyploidization are common in Henckelia. Furthermore, our results revealed that H. oblongifolia is not a member of the redefined Henckelia and they suggested several other taxonomic treatments in this genus.
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Affiliation(s)
- Li-Hua Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Xi-Zuo Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wen
- Gesneriad Conservation Center of China, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin 541006, China
| | - Ming Kang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
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13
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Gao Y, Zhu J, Zhai H, Xu K, Zhu X, Wu H, Zhang W, Wu S, Chen X, Xia Z. Dysfunction of an Anaphase-Promoting Complex Subunit 8 Homolog Leads to Super-Short Petioles and Enlarged Petiole Angles in Soybean. Int J Mol Sci 2023; 24:11024. [PMID: 37446203 DOI: 10.3390/ijms241311024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Plant height, petiole length, and the angle of the leaf petiole and branch angles are crucial traits determining plant architecture and yield in soybean (Glycine max L.). Here, we characterized a soybean mutant with super-short petioles (SSP) and enlarged petiole angles (named Gmssp) through phenotypic observation, anatomical structure analysis, and bulk sequencing analysis. To identify the gene responsible for the Gmssp mutant phenotype, we established a pipeline involving bulk sequencing, variant calling, functional annotation by SnpEFF (v4.0e) software, and Integrative Genomics Viewer analysis, and we initially identified Glyma.11G026400, encoding a homolog of Anaphase-promoting complex subunit 8 (APC8). Another mutant, t7, with a large deletion of many genes including Glyma.11G026400, has super-short petioles and an enlarged petiole angle, similar to the Gmssp phenotype. Characterization of the t7 mutant together with quantitative trait locus mapping and allelic variation analysis confirmed Glyma.11G026400 as the gene involved in the Gmssp phenotype. In Gmssp, a 4 bp deletion in Glyma.11G026400 leads to a 380 aa truncated protein due to a premature stop codon. The dysfunction or absence of Glyma.11G026400 caused severe defects in morphology, anatomical structure, and physiological traits. Transcriptome analysis and weighted gene co-expression network analysis revealed multiple pathways likely involved in these phenotypes, including ubiquitin-mediated proteolysis and gibberellin-mediated pathways. Our results demonstrate that dysfunction of Glyma.11G026400 leads to diverse functional consequences in different tissues, indicating that this APC8 homolog plays key roles in cell differentiation and elongation in a tissue-specific manner. Deciphering the molecular control of petiole length and angle enriches our knowledge of the molecular network regulating plant architecture in soybean and should facilitate the breeding of high-yielding soybean cultivars with compact plant architecture.
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Affiliation(s)
- Yi Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinlong Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Xiaobin Zhu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Wenjing Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
| | - Shihao Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin 150081, China
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14
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Pezzini FF, Ferrari G, Forrest LL, Hart ML, Nishii K, Kidner CA. Target capture and genome skimming for plant diversity studies. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11537. [PMID: 37601316 PMCID: PMC10439825 DOI: 10.1002/aps3.11537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 06/16/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections, which often have degraded DNA. The need to fast-freeze newly collected living samples to conserve high-quality DNA can be complicated when plants are only found in remote areas. Therefore, short-read reduced-genome representations, such as target capture and genome skimming, remain important for evolutionary studies. Here, we review the pros and cons of each technique for non-model plant taxa. We provide guidance related to logistics, budget, the genomic resources previously available for the target clade, and the nature of the study. Furthermore, we assess the available bioinformatic analyses, detailing best practices and pitfalls, and suggest pathways to combine newly generated data with legacy data. Finally, we explore the possible downstream analyses allowed by the type of data generated using each technique. We provide a practical guide to help researchers make the best-informed choice regarding reduced genome representation for evolutionary studies of non-model plants in cases where whole-genome sequencing remains impractical.
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Affiliation(s)
| | - Giada Ferrari
- Royal Botanic Garden EdinburghEdinburghUnited Kingdom
| | | | | | - Kanae Nishii
- Royal Botanic Garden EdinburghEdinburghUnited Kingdom
| | - Catherine A. Kidner
- Royal Botanic Garden EdinburghEdinburghUnited Kingdom
- School of Biological SciencesUniversity of EdinburghEdinburghUnited Kingdom
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15
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Ma’ruf M, Fadli JC, Mahendra MR, Irham LM, Sulistyani N, Adikusuma W, Chong R, Septama AW. A bioinformatic approach to identify pathogenic variants for Stevens-Johnson syndrome. Genomics Inform 2023; 21:e26. [PMID: 37704211 PMCID: PMC10326529 DOI: 10.5808/gi.23010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 07/08/2023] Open
Abstract
Stevens-Johnson syndrome (SJS) produces a severe hypersensitivity reaction caused by Herpes simplex virus or mycoplasma infection, vaccination, systemic disease, or other agents. Several studies have investigated the genetic susceptibility involved in SJS. To provide further genetic insights into the pathogenesis of SJS, this study prioritized high-impact, SJS-associated pathogenic variants through integrating bioinformatic and population genetic data. First, we identified SJS-associated single nucleotide polymorphisms from the genome-wide association studies catalog, followed by genome annotation with HaploReg and variant validation with Ensembl. Subsequently, expression quantitative trait locus (eQTL) from GTEx identified human genetic variants with differential gene expression across human tissues. Our results indicate that two variants, namely rs2074494 and rs5010528, which are encoded by the HLA-C (human leukocyte antigen C) gene, were found to be differentially expressed in skin. The allele frequencies for rs2074494 and rs5010528 also appear to significantly differ across continents. We highlight the utility of these population-specific HLA-C genetic variants for genetic association studies, and aid in early prognosis and disease treatment of SJS.
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Affiliation(s)
- Muhammad Ma’ruf
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
| | | | | | - Lalu Muhammad Irham
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
- Center for Vaccine and Drugs, Research Organization for Health, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
| | - Nanik Sulistyani
- Faculty of Pharmacy, Universitas Ahmad Dahlan, Yogyakarta 55164, Indonesia
| | - Wirawan Adikusuma
- Departement of Pharmacy, University of Muhammadiyah Mataram, Mataram 83127, Indonesia
- Center for Vaccine and Drugs, Research Organization for Health, National Research and Innovation Agency (BRIN), South Tangerang 15314, Indonesia
| | - Rockie Chong
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, CA, USA
| | - Abdi Wira Septama
- Departement of Pharmacy, University of Muhammadiyah Mataram, Mataram 83127, Indonesia
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16
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Pouchon C, Boluda CG. REFMAKER: make your own reference to target nuclear loci in low coverage genome skimming libraries. Phylogenomic application in Sapotaceae. Mol Phylogenet Evol 2023:107826. [PMID: 37257798 DOI: 10.1016/j.ympev.2023.107826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/24/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
Genome skimming approach is widely used in plant systematics to infer phylogenies mostly from organelle genomes. However, organelles represent only 10% of the produced libraries, and the low coverage associated with these libraries (< 3X) prevents the capture of nuclear sequences, which are not always available in non-model organisms or limited to the ribosomal regions. We developed REFMAKER, a user-friendly pipeline, to create specific sets of nuclear loci that can next be extracted directly from the genome skimming libraries. For this, a catalogue is built from the meta-assembly of each library contigs and cleaned by selecting the nuclear regions and removing duplicates from clustering steps. Libraries are next mapped onto this catalogue and consensus sequences are generated to produce a ready-to-use phylogenetic matrix following different filtering parameters aiming at removing putative errors and paralogous sequences. REFMAKER allowed us to infer a well resolved phylogeny in Capurodendron (Sapotaceae) on 67 nuclear loci from low-coverage libraries (<1X). The resulting phylogeny is concomitant with one previously inferred on 638 nuclear genes from target enrichment libraries. While it remains preliminary because of this low sequencing depth, REFMAKER therefore opens perspectives in phylogenomics by allowing nuclear phylogeny reconstructions with genome skimming datasets.
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Affiliation(s)
- Charles Pouchon
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland; PhyloLab, Department of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland.
| | - Carlos G Boluda
- Conservatoire et Jardin botaniques de la Ville de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland; PhyloLab, Department of Plant Sciences, Université de Genève, Chemin de l'Impératrice 1, 1292 Chambésy, Geneva, Switzerland
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17
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Walden N, Schranz ME. Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae. Genome Biol Evol 2023; 15:7059155. [PMID: 36848527 PMCID: PMC10016055 DOI: 10.1093/gbe/evad034] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/27/2023] [Accepted: 02/17/2023] [Indexed: 03/01/2023] Open
Abstract
Large genomic data sets are becoming the new normal in phylogenetic research, but the identification of true orthologous genes and the exclusion of problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with ortholog detection through genomic synteny in a data set of 11 representative diploid Brassicaceae whole-genome sequences spanning the entire phylogenetic space. Then, we evaluated the resulting gene sets regarding gene number, functional annotation, and gene and species tree resolution. Finally, we used the syntenic gene sets for comparative genomics and ancestral genome analysis. The use of synteny resulted in considerably more orthologs and also allowed us to reliably identify paralogs. Surprisingly, we did not detect notable differences between species trees reconstructed from syntenic orthologs when compared with other gene sets, including the Angiosperms353 set and a Brassicaceae-specific target enrichment gene set. However, the synteny data set comprised a multitude of gene functions, strongly suggesting that this method of marker selection for phylogenomics is suitable for studies that value downstream gene function analysis, gene interaction, and network studies. Finally, we present the first ancestral genome reconstruction for the Core Brassicaceae which predating the Brassicaceae lineage diversification ∼25 million years ago.
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Affiliation(s)
- Nora Walden
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands.,Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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18
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Omeershffudin UNM, Kumar S. Antibiotic resistance in Neisseria gonorrhoeae: broad-spectrum drug target identification using subtractive genomics. Genomics Inform 2023; 21:e5. [PMID: 37037463 PMCID: PMC10085745 DOI: 10.5808/gi.22066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 04/03/2023] Open
Abstract
Neisseria gonorrhoeae is a Gram-negative aerobic diplococcus bacterium that primarily causes sexually transmitted infections through direct human sexual contact. It is a major public health threat due to its impact on reproductive health, the widespread presence of antimicrobial resistance, and the lack of a vaccine. In this study, we used a bioinformatics approach and performed subtractive genomic methods to identify potential drug targets against the core proteome of N. gonorrhoeae (12 strains). In total, 12,300 protein sequences were retrieved, and paralogous proteins were removed using CD-HIT. The remaining sequences were analyzed for non-homology against the human proteome and gut microbiota, and screened for broad-spectrum analysis, druggability, and anti-target analysis. The proteins were also characterized for unique interactions between the host and pathogen through metabolic pathway analysis. Based on the subtractive genomic approach and subcellular localization, we identified one cytoplasmic protein, 2Fe-2S iron-sulfur cluster binding domain-containing protein (NGFG RS03485), as a potential drug target. This protein could be further exploited for drug development to create new medications and therapeutic agents for the treatment of N. gonorrhoeae infections.
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Affiliation(s)
| | - Suresh Kumar
- Faculty of Health and Life Sciences, Management and Science University, Seksyen 13, 40100, Shah Alam, Selangor, Malaysia
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19
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Du ZY, Jenny Xiang QY, Cheng J, Zhou W, Wang QF, Soltis DE, Soltis PS. An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data. AMERICAN JOURNAL OF BOTANY 2023; 110:e16116. [PMID: 36480351 DOI: 10.1002/ajb2.16116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
PREMISE A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group. METHODS We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis. RESULTS A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode. CONCLUSIONS Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.
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Affiliation(s)
- Zhi-Yuan Du
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jin Cheng
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Wenbin Zhou
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Qing-Feng Wang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611 FL, USA
- Department of Biology, University of Florida, Gainesville, 32611 FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611 FL, USA
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20
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Guo C, Luo Y, Gao LM, Yi TS, Li HT, Yang JB, Li DZ. Phylogenomics and the flowering plant tree of life. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:299-323. [PMID: 36416284 DOI: 10.1111/jipb.13415] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 11/22/2022] [Indexed: 06/16/2023]
Abstract
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations, describes the baseline methodology of experimental and analytical procedures, and summarizes recent progress in flowering plant phylogenomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors, and underlying biological factors, such as whole-genome duplication, hybridization/introgression, and incomplete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Yang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Lian-Ming Gao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650201, China
- Lijiang Forest Diversity National Observation and Research Station, Kunming Institute of Botany, Chinese Academy of Sciences, Lijiang, 674100, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
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21
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Reginato M. A pipeline for assembling low copy nuclear markers from plant genome skimming data for phylogenetic use. PeerJ 2022; 10:e14525. [PMID: 36523475 PMCID: PMC9745922 DOI: 10.7717/peerj.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Background Genome skimming is a popular method in plant phylogenomics that do not include a biased enrichment step, relying on random shallow sequencing of total genomic DNA. From these data the plastome is usually readily assembled and constitutes the bulk of phylogenetic information generated in these studies. Despite a few attempts to use genome skims to recover low copy nuclear loci for direct phylogenetic use, such endeavor remains neglected. Causes might include the trade-off between libraries with few reads and species with large genomes (i.e., missing data caused by low coverage), but also might relate to the lack of pipelines for data assembling. Methods A pipeline and its companion R package designed to automate the recovery of low copy nuclear markers from genome skimming libraries are presented. Additionally, a series of analyses aiming to evaluate the impact of key assembling parameters, reference selection and missing data are presented. Results A substantial amount of putative low copy nuclear loci was assembled and proved useful to base phylogenetic inference across the libraries tested (4 to 11 times more data than previously assembled plastomes from the same libraries). Discussion Critical aspects of assembling low copy nuclear markers from genome skims include the minimum coverage and depth of a sequence to be used. More stringent values of these parameters reduces the amount of assembled data and increases the relative amount of missing data, which can compromise phylogenetic inference, in turn relaxing the same parameters might increase sequence error. These issues are discussed in the text, and parameter tuning through multiple comparisons tracking their effects on support and congruence is highly recommended when using this pipeline. The skimmingLoci pipeline (https://github.com/mreginato/skimmingLoci) might stimulate the use of genome skims to recover nuclear loci for direct phylogenetic use, increasing the power of genome skimming data to resolve phylogenetic relationships, while reducing the amount of sequenced DNA that is commonly wasted.
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Zhang Z, Xie P, Guo Y, Zhou W, Liu E, Yu Y. Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research. Mol Biol Evol 2022; 39:6862883. [PMID: 36458838 PMCID: PMC9757696 DOI: 10.1093/molbev/msac261] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/28/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
The Angiosperms353 gene set (AGS) consists of a set of 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These genes can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover Angiosperms353 genes efficiently and accurately from high-throughput sequences. Here, we developed Easy353, a reference-guided assembly tool to recover the AGS from high-throughput sequencing (HTS) data (including genome skimming, RNA-seq, and target enrichment). Easy353 is an open-source user-friendly assembler for diverse types of high-throughput data. It has a graphical user interface and a command-line interface that is compatible with all widely-used computer systems. Evaluations, based on both simulated and empirical data, suggest that Easy353 yields low rates of assembly errors.
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Affiliation(s)
- Zhen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, P. R. China
| | - Pulin Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, P. R. China
| | - Yongling Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, P. R. China
| | - Wenbin Zhou
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Enyan Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610065, P. R. China
| | - Yan Yu
- Corresponding author: E-mail:
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Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop—Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan. PLoS One 2022; 17:e0272680. [PMID: 36178903 PMCID: PMC9524695 DOI: 10.1371/journal.pone.0272680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/10/2022] [Indexed: 11/23/2022] Open
Abstract
‘Breadfruit’ is a common tree species in Taiwan. In the indigenous Austronesian Amis culture of eastern Taiwan, ‘breadfruit’ is known as Pacilo, and its fruits are consumed as food. On Lanyu (Botel Tobago) where the indigenous Yami people live, ‘breadfruit’ is called Cipoho and used for constructing houses and plank-boats. Elsewhere in Taiwan, ‘breadfruit’ is also a common ornamental tree. As an essential component of traditional Yami culture, Cipoho has long been assumed to have been transported from the Batanes Island of the Philippines to Lanyu. As such, it represents a commensal species that potentially can be used to test the hypothesis of the northward Austronesian migration ‘into’ Taiwan. However, recent phylogenomic studies using target enrichment show that Taiwanese ‘breadfruit’ might not be the same as the Pacific breadfruit (Artocarpus altilis), which was domesticated in Oceania and widely cultivated throughout the tropics. To resolve persistent misidentification of this culturally and economically important tree species of Taiwan, we sampled 36 trees of Taiwanese Artocarpus and used the Moraceae probe set to enrich 529 nuclear genes. Along with 28 archived Artocarpus sequence datasets (representing a dozen taxa from all subgenera), phylogenomic analyses showed that all Taiwanese ‘breadfruit’ samples, together with a cultivated ornamental tree from Hawaii, form a fully supported clade within the A. treculianus complex, which is composed only of endemic Philippine species. Morphologically, the Taiwanese ‘breadfruit’ matches the characters of A. treculianus. Within the Taiwanese samples of A. treculianus, Amis samples form a fully supported clade derived from within the paraphyletic grade composed of Yami samples, suggesting a Lanyu origin. Results of our target enrichment phylogenomics are consistent with the scenario that Cipoho was transported northward from the Philippines to Lanyu by Yami ancestors, though the possibility that A. treculianus is native to Lanyu cannot be ruled out completely.
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Thureborn O, Razafimandimbison SG, Wikström N, Rydin C. Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:967456. [PMID: 36160958 PMCID: PMC9493367 DOI: 10.3389/fpls.2022.967456] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.
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Affiliation(s)
- Olle Thureborn
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | | | - Niklas Wikström
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Bergius Foundation, Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Catarina Rydin
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Bergius Foundation, Royal Swedish Academy of Sciences, Stockholm, Sweden
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Zhou W, Jenny Xiang QY. Phylogenomics and Biogeography of Castanea (Chestnut) and Hamamelis (Witch-hazel) - Choosing between RAD-seq and Hyb-Seq Approaches. Mol Phylogenet Evol 2022; 176:107592. [DOI: 10.1016/j.ympev.2022.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 06/18/2022] [Accepted: 07/20/2022] [Indexed: 10/31/2022]
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Ufimov R, Gorospe JM, Fér T, Kandziora M, Salomon L, van Loo M, Schmickl R. Utilizing paralogs for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data. Mol Ecol Resour 2022; 22:3018-3034. [PMID: 35796729 DOI: 10.1111/1755-0998.13684] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/28/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022]
Abstract
The analysis of target enrichment data in phylogenetics lacks optimization toward using paralogs for phylogenetic reconstruction. We developed a novel approach of detecting paralogs and utilizing them for phylogenetic tree inference, by retrieving both ortho- and paralogous copies and creating orthologous alignments, from which the gene trees are built. We implemented this approach in ParalogWizard and demonstrate its performance in plant groups that underwent a whole genome duplication relatively recently: the subtribe Malinae (family Rosaceae), using Angiosperms353 as well as Malinae481 probes, the genus Oritrophium (family Asteraceae), using Compositae1061 probes, and the genus Amomum (family Zingiberaceae), using Zingiberaceae1180 probes. Discriminating between orthologs and paralogs reduced gene tree discordance and increased the species tree support in the case of the Malinae, but not for Oritrophium and Amomum. This may relate to the difference in the proportion of paralogous loci between the datasets, which was highest for the Malinae. Overall, retrieving paralogs for phylogenetic reconstruction following ParalogWizard has the potential to increase the species tree support and reduce gene tree discordance in target enrichment data, particularly if the proportion of paralogous loci is high.
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Affiliation(s)
- Roman Ufimov
- Department of Forest Growth, Silviculture and Genetics, Austrian Research Centre for Forests, Seckendorff-Gudent-Weg 8, 1130, Vienna, Austria.,Komarov Botanical Institute, Russian Academy of Sciences, ul. Prof. Popova 2, 197376, St. Petersburg, Russian Federation
| | - Juan Manuel Gorospe
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czech Republic
| | - Tomáš Fér
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czech Republic
| | - Martha Kandziora
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czech Republic
| | - Luciana Salomon
- Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czech Republic
| | - Marcela van Loo
- Department of Forest Growth, Silviculture and Genetics, Austrian Research Centre for Forests, Seckendorff-Gudent-Weg 8, 1130, Vienna, Austria
| | - Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43, Průhonice, Czech Republic.,Department of Botany, Faculty of Science, Charles University, Benátská 2, 128 01, Prague, Czech Republic
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Pouchon C, Boyer F, Roquet C, Denoeud F, Chave J, Coissac E, Alsos IG, Lavergne S. ORTHOSKIM: in silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications. Mol Ecol Resour 2022; 22:2018-2037. [PMID: 35015377 DOI: 10.1111/1755-0998.13584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 12/08/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Abstract
Low-coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost-effective method for acquiring genomic data in non-model organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over-represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: 1) global sequence assembly, 2) mapping against reference sequences, and 3) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and non-coding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g. ultra-conserved elements) or collections of single-copy ortholog genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome-skimming libraries and 4 RNAseq libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well-known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL-3 license and is available at: https://github.com/cpouchon/ORTHOSKIM.
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Affiliation(s)
- Charles Pouchon
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Frédéric Boyer
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Cristina Roquet
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France.,Systematics and Evolution of Vascular Plants (UAB) - Associated Unit to CSIC, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057, Evry, France
| | - Jérome Chave
- Laboratoire Évolution et Diversité Biologique (EDB), UMR CNRS-IRD-UPS 5174, 31062, Toulouse Cedex, France
| | - Eric Coissac
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
| | - Inger Greve Alsos
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
| | | | | | - Sébastien Lavergne
- Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Laboratoire d'Ecologie Alpine (LECA), 38000, Grenoble, France
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