Biology subjects

Hoerandl, E.

Publications and source records attributed to Hoerandl, E..

10 recordsLinked to original sources

bioRxiv2023

Sex determination system turnovers play important roles in the willows speciation

Almost all species in the genus Salix (willow) are dioecious, but some have male and some female heterogamety, and the chromosomal location of the sex-linked regions (termed SDSs) differs between different species. We first analyzed the SDSs of two species, Salix cardiophylla and S. interior, whose positions in the Salix phylogeny make them important species for understanding a sex chromosome turnover that has been detected in their relatives, and that changed the system from male to female heterogamety. We show that both species have male heterogamety, with XY-linked regions on chromosome 15 (termed a 15XY system). The sex-linked regions occupy 21.3% and 22.8% of the entire reference chromosome, respectively. By constructing phylogenetic trees of species with known SDSs, we determined the phylogenetic positions of all the species. Reconstruction of SDSs revealed that 15XY system is likely the ancestral of willows. Finally, we tested for both current and ancestral gene flow between different species with the same or different sex-determining systems, as the sex chromosomes can play important roles in reproductive isolation between species. We inferred lower gene flow between species with XY on chromosome 7 (7XY) and ZW on chromosome 15 (15ZW) systems, compared with gene flow either between species with XY on chromosome 15 (15XY) and 15ZW systems or between species with 7XY and 15XY systems. We argue that, although sex chromosomes turnovers in willows may not create complete reproductive barriers, gene flow may be reduced between species with different SDSs.

evolutionary biology↗

bioRxiv2023

Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes and reversion to autosomes

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid Salix dunnii using Hi-C and PacBio HiFi reads. We use phylogenomics of nuclear and plastid genomes to show that weeping willow arose from crosses between female ancestor from the Salix clade, having XY sex chromosomes on chromosome 7, with a male ancestor from the Vetrix clade, having ancestral XY sex chromosomes on chromosome 15. Our analysis reveals that weeping willow has one pair sex chromosomes, ZW on chromosome 15, that derive from the ancestral XY sex chromosomes in the Vetrix-clade male ancestor, and the X chromosomes on chromosome 7 from the Salix-clade female ancestor has reverted to an autosome. Taken together, our results point to rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow. Significance StatementWe assembled haplotype-resolved genomes and obtained gap-free sex chromosomes of a female allotetraploid weeping willow (Salix babylonica) and a male diploid Salix dunnii. The weeping willow arose from two dioecious ancestors, that have XY sex chromosomes on chromosome 7 and 15, respectively. The one pair sex chromosomes 15W and 15Z in weeping willow derived from ancestral 15X and 15Y, respectively. Inversions contributed to the evolutions of sex-linked regions (SLRs) of diploid and polyploid willows.

evolutionary biology↗

bioRxiv2023

Gap-free X and Y chromosomes of Salix arbutifolia reveal an evolutionary change from male to female heterogamety in willows, without a change in the sex-determining region

In the Vetrix clade of Salix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We used genome sequencing (with chromosome conformation capture (Hi-C) and PacBio HiFi high-fidelity reads) to study the evolutionary history of the sex-linked regions before and after the transition. We assembled chromosome level gap-free X and Y chromosomes of Salix arbutifolia, and distinguished the haplotypes in the 15X- and 15Y-linked regions. This revealed "micro-heteromorphism" differentiating the haplotypes of the Y- and X-linked regions, including insertions, deletions and duplications. Unusually, the X-linked region is considerably larger than the corresponding Y region, and we show that this primarily reflects extensive accumulation of repetitive sequences and gene duplications. The phylogenies of single-copy orthogroups within the sex-linked regions of S. arbutifolia (X and Y) and S. purpurea (Z and W) indicate that they possess a common ancestral sex-linked region that is physically small and located in a repeat-rich region near the chromosome 15 centromere. During the change in heterogamety, the W-linked region was derived from the X-linked one and the Z from the Y. The W may subsequently have evolved a region in which recombination became suppressed. We also detected accumulation of genes with opposite sex-biases in the sex-linked regions.

plant biology↗

bioRxiv2023

Efficient hybrid strategies for assembling the plastome, mitochondriome, and large nuclear genome of diploid Ranunculus cassubicifolius (Ranunculaceae)

Currently, it is still a challenge - in terms of laboratory effort and cost, as well as assembly quality - to unravel the sequence of large and complex genomes from non-model plants. This often hampers the study of evolutionarily intricate species groups. The species-rich genus Ranunculus (Ranunculaceae) is an angiosperm model system for the study of polyploidy, apomixis, reticulate evolution, and biogeography. However, neither mitochondrial, nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) or PacBio/HiFi long-read, and hybrid-read assembly strategies. We used the diploid progenitor species R. cassubicifolius (R. auricomus complex), and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome, we favored a PacBio-based assembly three-times polished with filtered reads and subsequently scaffolded into 8 pseudochromosomes by chromatin conformation data (Hi-C) as the representative sequence. We obtained a haploid genome sequence with 2.69 Gbp, 94.5% complete BUSCO embryophyta_odb10 genes found, and 31,322 annotated genes. The genomic information presented here will improve phylogenomic analyses in this species complex, and will enable advanced functional, evolutionary, and biogeographic analyses for the genus and beyond Ranunculaceae in the future. Significance StatementThe genus Ranunculus is a model system in flowering plants for polyploidy, apomixis, evolution, and biogeography research. We present the first nuclear and mitochondrial genome sequence, and the plastid evolution of Ranunculaceae. Using Illumina, ONT, and PacBio data, we developed an efficient assembly strategy that can be applied to other non-model plants. Results presented here are useful for improving population genomic and phylogenomic analyses, and enable better functional analyses at species, genus and family level.

genomics↗

bioRxiv2021

Unraveling phylogenetic relationships, reticulate evolution, and genome composition of polyploid plant complexes by RAD-Seq and Hyb-Seq

Complex genome evolution of young polyploid complexes is poorly understood. Besides challenges caused by hybridization, polyploidization, and incomplete lineage sorting, bioinformatic analyses are often exacerbated by missing information on progenitors, ploidy, and reproduction modes. By using a comprehensive, self-developed bioinformatic pipeline integrating phylogenetic, structure, network, and SNP-origin analyses, we for the first time unraveled polyploid phylogenetic relationships and genome evolution within the large Eurasian Ranunculus auricomus species complex comprising more than 840 taxa. Our results rely on 97,312 genomic RAD-Seq loci, target enrichment of 576 nuclear genes (48 phased), and 71 plastid regions (Hyb-Seq; OMICS-data) derived from the 75 most widespread polyploid apomictic taxa and four di- and one tetraploid potential sexual progenitor species. Phylogenetic tree and structure analyses consistently showed 3-5 supported polyploid groups, each containing sexual progenitor species. In total, analyses revealed four diploid sexual progenitors and a one unknown, probably extinct progenitor, contributing to the genome composition of R. auricomus polyploids. Phylogenetic network, structure, and SNP-origin analyses based on RAD-Seq loci and phased nuclear genes completed by plastid data demonstrated predominantly allopolyploid origins, each involving 2-3 different diploid sexual subgenomes. Allotetraploid genomes were characterized by subgenome dominance and large proportions of interspecific, non-hybrid SNPs, indicating an enormous degree of post-origin evolution (i.e., Mendelian segregation of the diploid hybrid generations, back-crossings, and gene flow due to facultative sexuality of apomicts), but only low proportions of lineage-specific SNPs. The R. auricomus model system is the first large European polyploid species complex studied with reduced representation OMICS data. Our bioinformatic pipeline underlines the importance of combining different approaches and datasets to successfully unveil how reticulate evolution and post-origin processes shape the diversity of polyploid plant complexes.

evolutionary biology↗

bioRxiv2020

Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7

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.

genomics↗

bioRxiv2020

RAD sequencing data reveal a radiation of willow species (Salix L., Salicaceae) in the Hengduan Mountains and adjacent areas

The Hengduan Mountains (HDM) in South West China are an important hotspot of plant diversity and endemism and considered to be a secondary diversification center for the woody plant genus Salix (Salicaceae). This study aimed to reconstruct the spatio-temporal evolution of the Salix Chamaetia-Vetrix clade in the HDM and to test for the occurrence of a radiation. We inferred phylogenetic relationships based on more than 34,000 RAD loci of 27 species. Phylogenetic analyses recovered a well-resolved tree topology with two major clades, the Eurasian and the HDM clade and a divergence time of c. 23.9 Ma. The HDM clade comprises two subclades. The species of the HDM clade originated in north HDM and adjacent areas and then dispersed into the south HDM, westwards to the Himalayas and eastwards to the Qinling Mountains. Niche modelling analyses revealed that during the last glacial maximum, range contractions were observed in the northern areas, while southward expansions resulted in range overlaps. The reconstruction of putative adaptive character evolution of plant height, inflorescence and flower morphology indicate that adaptations to altitudinal distribution contributed to the diversification of the HDM willows. Our data indicate that a radiation occurred in HDM within the Salix Chamaetia-Vetrix clade. Dispersal within the mountain system and to adjacent regions as well as survival in glacial refugia have shaped the biogeographical history of the clade. Differentiation along altitudinal zonation concomitant to morphological adaptations to colder climates may be important ecological factors for the high species diversity of Salix in this area.

evolutionary biology↗

bioRxiv2020

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomictic Ranunculus auricomus complex (Ranunculaceae)

Species are the basic units of biodiversity and evolution. Nowadays, they are widely considered as ancestor-descendant lineages. Their definition remains a persistent challenge for taxonomists due to lineage evolutionary role and circumscription, i.e., persistence in time and space, ecological niche or a shared phenotype of a lineage. Recognizing and delimiting species is particularly methodically challenging in fast-evolving, evolutionary young species complexes often characterized by low genetic divergence, hybrid origin, introgression and incomplete lineage sorting (ILS). Ranunculus auricomus is a large Eurasian apomictic polyploid complex that probably has arisen from the hybridization of a few sexual progenitor species. However, even delimitation and relationships of diploid sexual progenitors have been unclearly ranging from two to twelve species. Here, we present an innovative workflow combining phylogenomic methods based on 86,782 parameter-optimized RADseq loci and target enrichment of 663 nuclear genes together with geometric morphometrics to delimit sexual species in this evolutionary young complex (< 1 Mya). For the first time, we revealed a fully resolved and well-supported maximum likelihood (ML) tree phylogeny congruent to neighbor-net network and STRUCTURE results based on RADseq data. In a few clades, we found evidence of discordant patterns indicated by quartet sampling (QS) and reticulation events in the neighbor-net network probably caused by introgression and ILS. Together with coalescent-based species delimitation approaches based on target enrichment data, we found five main genetic lineages, with an allopatric distribution in Central and Southern Europe. A concatenated geometric morphometric data set including basal and stem leaves, as well as receptacles, revealed the same five main clusters. We accept those five morphologically differentiated, geographically isolated, genetic main lineages as species: R. cassubicifolius s.l. (incl. R. carpaticola), R. flabellifolius, R. envalirensis s.l. (incl. R. cebennensis), R. marsicus and R. notabilis s.l. (incl. R. austroslovenicus, R. calapius, R. mediocompositus, R. peracris and R. subcarniolicus). Our comprehensive workflow combing phylogenomic methods supported by geometric morphometrics proved to be successful in delimiting closely related sexual taxa and applying an evolutionary species concept, which is also transferable to other evolutionarily young species complexes.

evolutionary biology↗

bioRxiv2020

Phylogenomics unravels speciation patterns in temperate-montane plant species: a case study on the recently radiating Ranunculus auricomus species complex

The time frame and geographical patterns of diversification processes in European temperate-montane herbs are still not well understood. We used the sexual species of the Ranunculus auricomus complex as a model system to understand how vicariance vs. dispersal processes in the context of Pleistocene climatic fluctuations have triggered speciation in temperate-montane plant species. We employed Target Enrichment sequence data from about 600 nuclear genes and coalescent-based species tree inference methods to resolve phylogenetic relationships among the sexual taxa of the complex. We estimated absolute divergence times and, using ancestral range reconstruction, we tested if speciation was rather enhanced by vicariance or dispersal processes. Phylogenetic relationships among taxa were fully resolved. Incongruence among species trees mainly concerned the intraspecific relationships in R. notabilis s.l., R. cassubicifolius s.l., and the position of the tetraploid R. marsicus. Speciation events took place in a very short time at the end of the Mid-Pleistocene Transition (830-580 ka). A second wave of intraspecific geographical differentiation within and around the European mountain systems happened between 200-100 ka. Ancestral range reconstruction supports the existence of a widespread European ancestor of the R. auricomus complex. Vicariance processes have triggered allopatric speciation in temperate-montane plant species during the climatic deterioration occurred in the last phase of the Mid-Pleistocene Transition. Vegetation restructuring from forest into tundra could have confined these forest species into isolated glacial refugia. During subsequent warming periods, range expansions of these locally distributed species could have been hampered by congeneric competitors in the same habitat.

evolutionary biology↗

bioRxiv2019

Relationships and genome evolution of polyploid Salix species revealed by RAD sequencing data

AO_SCPLOWBSTRACTC_SCPLOWDespite the general progress in using next generation sequencing techniques for evolutionary research questions, the analysis of polyploid species is still hampered by the lack of suitable analytical tools and the statistical difficulties of dealing with more than two alleles per locus. Polyploidization and especially allopolyploidy leads to new combinations of traits by combining genomes of two or more parental species. This enhances the adaptive potential and often results in speciation. However, multiple origins of polyploids, backcrossing to the parental species and post-origin evolution can strongly influence the genome composition of polyploid species. Here, we used RAD sequencing, which revealed 23,393 loci and 320,010 high quality SNPs, to analyze the relationships and origin of seven polyploid species of the diverse genus Salix by utilizing a phylogenomic and a network approach, as well as analyzing the genetic structure and composition of the polyploid genome in comparison to putative parental species. We adapted the SNiPloid pipeline that was originally developed to analyse SNP composition of recently established allotetraploid crop lineages to RAD sequencing data by using concatenated RAD loci as reference. Our results revealed a well-resolved phylogeny of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix), including 28 diploid and 7 polyploid species. Polyploidization in willows appears to be predominantly connected to hybridization, i.e. to an allopolyploid origin of species. More ancient allopolyploidization events involving hybridization of more distantly related, ancestral lineages were observed for two hexaploid and one octoploid species. Our data suggested a more recent allopolyploid origin for the included tetraploids within the major subclades and identified putative parental taxa that appear to be plausible in the context of geographical, morphological and ecological patterns. SNiPloid and HyDe analyses disentangled the different genomic signatures resulting from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid species. All tetraploids showed a considerable post-origin, species-specific proportion of SNPs. The amount of extant hybridization appears to be related to the degree of geographical and ecological isolation of species. Our data demonstrate that high-quality RAD sequencing data are suitable and highly informative for the analysis of the origin and relationships of polyploid species. The combination of the traditional tools RAxML, STRUCTURE, SplitsTree and recently developed programs like SNAPP, HyDe and SNiPloid established a bioinformatic pipeline for unraveling the complexity of polyploid genomes.

evolutionary biology↗