Restriction‐site associated DNA sequencing data reveal a radiation of willow species (<i>Salix</i>L., Salicaceae) in the Hengduan Mountains and adjacent areas

He, Li; Wagner, Natascha; Hörandl, Elvira

doi:10.1111/jse.12593

Cited by 30 publications

(50 citation statements)

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“…Our findings support the suitability of RAD sequencing for interspecific phylogenetic inference and are in accordance with many studies on different levels of divergence (e.g. Hipp et al, 2014;Eaton et al, 2017;Wagner et al, 2018;He et al, 2020). The allelic information of the polyploid samples can be condensed to a single consensus sequence to circumvent the challenges of dealing with more than two alleles for phylogenetic approaches.…”

Section: Rad Sequencing Data and Analysis Pipelines For Polyploidssupporting

confidence: 89%

“…The ploidy levels of seven species (23 samples) with unknown chromosome counts were estimated using flow cytometric analyses based on DAPI (4', 6-diamidino-2-phenylindole) fluorochrome applying a modified protocol of Suda and Travnıćěk (2006) as described in He et al (2020). Salix caprea with known ploidy level (2x=2n=38) was used as an external standard.…”

Section: Ploidy Determination Using Flow Cytometrymentioning

confidence: 99%

“…The huge amount of biallelic SNPs is well suited to study evolutionary processes, resolve reticulate relationships, reconstruct species trees, and to analyze polyploid species in a phylogenetic framework (Bryant et al, 2012;Dufresne et al, 2014;Clevenger et al, 2015;Clevenger et al, 2018). However, there are only few studies using RAD sequencing data when dealing with polyploid non-model plants (Chen et al, 2013;Mastretta-Yanes et al, 2014;Qi et al, 2015;Brandrud et al, 2020;He et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…RAD sequencing (Baird et al, 2008) was recently used to overcome the lack of phylogenetic information within the genus Salix (Gramlich et al, 2018;Wagner et al, 2018;He et al, 2020). Wagner et al (2018) published the first well-resolved phylogeny of diploid European members of the Chamaetia/Vetrix clade, while He et al (2020) recognized a recent adaptive radiation of willows in the Hengduan mountains. Gramlich et al (2018) successfully used RAD sequencing to analyze recent homoploid hybridization patterns and introgression between two Salix species on alpine glacier forefields.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data

Wagner

Hörandl

2020

Front. Plant Sci.

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Polyploidy is common in the genus Salix. However, little is known about the origin, parentage and genomic composition of polyploid species because of a lack of suitable molecular markers and analysis tools. We established a phylogenomic framework including species of all described sections of Eurasian shrub willows. We analyzed the genomic composition of seven polyploid willow species in comparison to putative diploid parental species to draw conclusions on their origin and the effects of backcrossing and post-origin evolution. We applied recently developed programs like SNAPP, HyDe, and SNiPloid to establish a bioinformatic pipeline for unravelling the complexity of polyploid genomes. RAD sequencing revealed 23,393 loci and 320,010 high quality SNPs for the analysis of relationships of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/ Vetrix). Polyploid willow species appear to be predominantly of allopolyploid origin. More ancient allopolyploidization events were observed for two hexaploid and one octoploid species, while our data suggested a more recent allopolyploid origin for the included tetraploids and identified putative parental taxa. SNiPloid analyses disentangled the different genomic signatures resulting from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid species. Our RAD sequencing data demonstrate that willow genomes are shaped by ancient and recent reticulate evolution, polyploidization, and post-origin divergence of species.

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Section: Rad Sequencing Data and Analysis Pipelines For Polyploidssupporting

confidence: 89%

Section: Ploidy Determination Using Flow Cytometrymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data

Wagner

Hörandl

2020

Front. Plant Sci.

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“…Although Salix is the largest genus in the family Salicaceae sensu lato, with ~450 species (reviewed in He et al 2020), fewer Salix than Populus genomes have been assembled, and assemblies include only the cushion shrub S. brachista and the shrub willows S. purpurea, S. suchowensis, and S. viminalis (Chen et al 2019;Almeida et al 2020;Wei et al 2020;Zhou et al 2020). Shrub stature is a derived character, and the tree habit is ancestral , and is usual in poplars.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale assembly of the genome ofSalix dunniireveals a male-heterogametic sex determination system on chromosome 7

Jia

Zhang³

et al. 2020

Preprint

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Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads, and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 contigs, and includes 31,501 genes. We inferred a male heterogametic sex determining factor on chromosome 7, suggesting that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii X-linked region occupies about 3.21 Mb of chromosome 7, and is probably in a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for studying sex chromosome evolution in Salicaceae family.

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Challenge accepted: Evolutionary lineages versus taxonomic classification of North American shrub willows (Salix)

Marinček,

Léveillé‐Bourret,

Heiduk

et al. 2024

American J of Botany

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PremiseThe huge diversity of Salix subgenus Chamaetia/Vetrix clade in North America and the lack of phylogenetic resolution within this clade has presented a difficult but fascinating challenge for taxonomists to resolve. Here we tested the existing taxonomic classification with molecular tools.MethodsIn this study, 132 samples representing 46 species from 22 described sections of shrub willows from the United States and Canada were analyzed and combined with 67 samples from Eurasia. The ploidy levels of the samples were determined using flow cytometry and nQuire. Sequences were produced using a RAD sequencing approach and subsequently analyzed with ipyrad, then used for phylogenetic reconstructions (RAxML, SplitsTree), dating analyses (BEAST, SNAPPER), and character evolution analyses of 14 selected morphological traits (Mesquite).ResultsThe RAD sequencing approach allowed the production of a well‐resolved phylogeny of shrub willows. The resulting tree showed an exclusively North American (NA) clade in sister position to a Eurasian clade, which included some North American endemics. The NA clade began to diversify in the Miocene. Polyploid species appeared in each observed clade. Character evolution analyses revealed that adaptive traits such as habit and adaxial nectaries evolved multiple times independently.ConclusionsThe diversity in shrub willows was shaped by an evolutionary radiation in North America. Most species were monophyletic, but the existing sectional classification could not be supported by molecular data. Nevertheless, monophyletic lineages share several morphological characters, which might be useful in the revision of the taxonomic classification of shrub willows.

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Restriction‐site associated DNA sequencing data reveal a radiation of willow species (SalixL., Salicaceae) in the Hengduan Mountains and adjacent areas

Cited by 30 publications

References 69 publications

Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data

Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data

Chromosome-scale assembly of the genome ofSalix dunniireveals a male-heterogametic sex determination system on chromosome 7

Challenge accepted: Evolutionary lineages versus taxonomic classification of North American shrub willows (Salix)

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