The phylogeny of Salix revealed by whole genome re-sequencing suggests different sex-determination systems in major groups of the genus

Abstract

Background and Aims The biggest genus of Salicaceae sensu lato (s.l.) Salix L. has been shown to consist of two main clades: clade Salix, in which species have XY sex determination systems (SDSs) on chromosome 7, and clade Vetrix including species with ZW SDSs on chromosome 15. Here, we test the utility of whole genome re-sequencing (WGR) for phylogenomic reconstructions of willows to infer changes between different SDSs. Methods We used more than 1 TB of whole genome re-sequencing (WGR) data from 70 Salix taxa to ascertain SNPs on the autosomes, the sex-linked regions (SLRs), and the chloroplast genomes, for phylogenetic and species tree analyses. To avoid bias, we chose reference genomes from both groups, Salix dunnii from clade Salix and S. purpurea from clade Vetrix. Key Results Two main largely congruent groups were recovered: the paraphyletic Salix grade and the Vetrix clade. The autosome dataset trees resolved four subclades (C1-C4) in Vetrix. C1 and C2 comprise species from the Hengduan Mountains and adjacent areas and Eurasia, respectively. Section Longifoliae (C3) grouped within the Vetrix clade but fell into the Salix clade in trees based on the chloroplast dataset analysis. Salix triandra from Eurasia (C4) was revealed as sister to the remaining species of clade Vetrix. In Salix, polyploid group C5 is paraphyletic to clade Vetrix and subclade C6 is consistent with Argus’s subgenus Protitea. Chloroplast datasets separated both Vetrix and Salix as monophyletic, and yielded C5 embedded in Salix. Using only diploid species, the SLR and autosomal datasets both yielded trees with Vetrix and Salix as well supported clades. Conclusion WGR data are useful for phylogenomic analyses of willows. The different sex determining systems may contribute to the isolation of the two major groups, but the reproductive barrier between them needs to be studied.

The male-heterogametic sex determination system on chromosome 15 of Salix triandra and Salix arbutifolia reveals ancestral male heterogamety and subsequent turnover events in the genus Salix

“…Clade 4 (the Salix clade) includes S. nigra and S. dunnii. This topology is consistent with previous conclusions(Wu et al 2015;Gulyaev et al 2022).…”

“…However, it is worth noting that in Salix group there are some polyploid species with just 2 stamens, eg. S. chienii (tetraploid) and S. matsudana (tetraploid) (Gulyaev et al 2022), whether such a pattern exists in polyploidy requires further investigation. Hence, the relationship between turnover events and biased sex ratios remains unclear.…”

“…Voucher specimens of these samples are deposited in the Beijing Forestry University herbarium (BJFC) and Shanghai Chenshan Botanical Garden (CSH). To estimate the phylogeny, we also downloaded whole genome sequencing data for six Salix species whose SDSs are known, covering the two main clades (Gulyaev et al 2022): Salix clade S. dunnii (SRR12893418) and S. nigra (SRR16018717); and Vetrix clade S. polyclona (SRR16018674), S. purpurea (SRR3927002), S. suchowensis (SRR10197854), and S. viminalis (ERR1558612). We chose Populus euphratica (SRR13324572) as outgroup.…”

“…The SDS of previously studied Vetrix clade species is on chromosome 15, while the Salix clade SDS is on chromosome 7 (Gulyaev et al 2022). Our analysis suggests an equivocal state for ancestors of S. triandra and S. arbutifolia, but a transition to the XY system on chromosome 15 that is the ancestral state to clade 1 (Fig.…”

The chloroplast genome of Salix floderusii and characterization of chloroplast regulatory elements

“…With the development of high-throughput sequencing technology and low sequencing cost, increasing amounts of cp genomic data have been accumulated (Hatmaker et al, 2020;Shidhi et al, 2021;Wei et al, 2021;Zhang et al, 2021). To date, the cp genome of Salix has been reported (Chen et al, 2019;Guo et al, 2021;Li et al, 2021;Gulyaev et al, 2022;Wang et al, 2022). The published cp genomic data of these species offer important references for related research (Lauron-Moreau et al, 2015;Zong et al, 2019;Meucci et al, 2021).…”