Search for: All records

Abstract The relatively young and repeated evolutionary origins of dioecy (separate sexes) in flowering plants enable investigation of molecular dynamics occurring at the earliest stages of sex chromosome evolution. With two independently young origins of dioecy, Asparagus is a model genus for studying the genetics of sex-determination and sex chromosome evolution. Dioecy first evolved in Asparagus ∼3-4 million years ago (Ma) in the ancestor of a now widespread Eurasian clade including garden asparagus (Asparagus officinalis). A second origin occurred in a smaller, geographically restricted, Mediterranean Basin clade including Asparagus horridus. New haplotype-resolved reference genomes for garden asparagus and A. horridus, elucidate contrasting first steps in the origin of the sex chromosomes of the Eurasian and Mediterranean Basin clade ancestors. Analysis of the A. horridus genome revealed an XY system derived from different ancestral autosomes with different sex-determining genes than have been characterized for garden asparagus. We estimate that proto-XY chromosomes evolved 1-2 Ma in the Mediterranean Basin clade, following an ∼2.1-megabase inversion that now distinguishes the X and Y chromosomes. Recombination suppression and LTR retrotransposon accumulation drove the expansion of the male-specific region on the Y (MSY) that reaches ∼9.6-megabases in A. horridus. The garden asparagus genome revealed an MSY spanning ∼1.9-megabases. A segmental duplication and neofunctionalization of one duplicated gene (SOFF) drove the origin of dioecy in the Eurasian clade. These findings support previous inference based on phylogeographic analysis revealing two recent origins of dioecy in Asparagus and establish the genus as a model for investigating sex chromosome evolution. 

Abstract PremiseTarget sequence capture (Hyb‐Seq) is a cost‐effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low‐copy orthologs, Hyb‐Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726—a Hyb‐Seq probe set targeting 1726 low‐copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae—which will aid the often‐challenging delineation and resolution of evolutionary relationships within Asparagaceae. MethodsHere we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target‐enriched data sets. ResultsWe recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference. DiscussionAsparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family. 

Abstract PremiseDioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genusAsparagus(Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. MethodsWe use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genusAsparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. ResultsWe estimate that dioecy evolved once or twice approximately 2.78−3.78 million years ago inAsparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. ConclusionsOur findings support previous work implicating a young age and the possibility of two origins of dioecy inAsparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy inAsparagusapproximately 2.78−3.78 million years ago. 

Abstract The genus Asparagus arose ∼9 to 15 million years ago (Ma), and transitions from hermaphroditism to dioecy (separate sexes) occurred ∼3 to 4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying the early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1,726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus—first in a widely distributed Eurasian clade and then in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also reveal several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes. 

Abstract A phylogenomic analysis of the so far phylogenetically unresolved subfamily Bromelioideae (Bromeliaceae) was performed to infer species relationships as the basis for future taxonomic treatment, stabilization of generic concept, and further analyses of evolution and biogeography of the subfamily. A target‐enrichment approach was chosen, using the Angiosperms353 v.4 kit RNA‐baits and including 86 Bromelioideae species representing previously identified major evolutionary lineages. Phylogenetic analyses were based on 125 target nuclear loci, assembled off‐target plastome as well as mitogenome reads. A Bromelioideae phylogeny with a mostly well‐resolved backbone is provided based on nuclear (194 kbp), plastome (109 kbp), and mitogenome data (34 kbp). For the nuclear markers, a coalescent‐based analysis of single‐locus gene trees was performed as well as a supermatrix analysis of concatenated gene alignments. Nuclear and plastome datasets provide well‐resolved trees, which showed only minor topological incongruences. The mitogenome tree is not sufficiently resolved. A total of 26 well‐supported clades were identified. The generaAechmea,Canistrum,Hohenbergia,Neoregelia, andQuesneliawere revealed polyphyletic. In core Bromelioideae,Acanthostachysis sister to the remainder. Among the 26 recognized clades, 12 correspond with currently employed taxonomic concepts. Hence, the presented phylogenetic framework will serve as an important basis for future taxonomic revisions as well as to better understand the evolutionary drivers and processes in this exciting subfamily. 

File  Contents Ahor_pb32m_HAP1_v1.0.chrY_regions.bed.gz  Y chromosome nonrecombining region coordinatesAhor_pb32m_HAP1_v1.0.EDTA.TEanno.gff3.gz  All TE annotations by EDTAAhor_pb32m_HAP1_v1.0.EDTA.TEintact.fa.gz  Intact TE sequences by EDTAAhor_pb32m_HAP1_v1.0.EDTA.TEintact.gff3.gz  Intact TE annotations by EDTAAhor_pb32m_HAP1_v1.0.entap_results.tsv  Reciprocal functional gene annotations by EnTAPAhor_pb32m_HAP1_v1.0.fa.gz  Haplotype assembly fasta fileAhor_pb32m_HAP1_v1.0.ISOFORMS.bed.gz  Filtered gene annotations - all isoformsAhor_pb32m_HAP1_v1.0.ISOFORMS.CDS.fa.gz  Filtered gene annotations (protein coding nucleotides) - all isoformsAhor_pb32m_HAP1_v1.0.ISOFORMS.gff3.gz  Filtered gene annotations - all isoformsAhor_pb32m_HAP1_v1.0.ISOFORMS.peptides.fa.gz  Filtered gene annotations (protein sequences) - all isoformsAhor_pb32m_HAP1_v1.0.PRIMARY.bed.gz  Filtered gene annotations - longest isoforms onlyAhor_pb32m_HAP1_v1.0.PRIMARY.CDS.fa.gz  Filtered gene annotations (protein coding nucleotides) - longest isoforms onlyAhor_pb32m_HAP1_v1.0.PRIMARY.gff3.gz  Filtered gene annotations - longest isoforms onlyAhor_pb32m_HAP1_v1.0.PRIMARY.peptides.fa.gz  Filtered gene annotations (protein sequences) - longest isoforms onlyAhor_pb32m_HAP1_v1.0.RM.TE.gff.gz  All TE annotations by RepeatMaskerAhor_pb32m_HAP2_v1.0.chrX_regions.bed.gz  X chromosome nonrecombining region coordinatesAhor_pb32m_HAP2_v1.0.EDTA.TEanno.gff3.gz  All TE annotations by EDTAAhor_pb32m_HAP2_v1.0.EDTA.TEintact.fa.gz  Intact TE sequences by EDTAAhor_pb32m_HAP2_v1.0.EDTA.TEintact.gff3.gz  Intact TE annotations by EDTAAhor_pb32m_HAP2_v1.0.entap_results.tsv  Reciprocal functional gene annotations by EnTAPAhor_pb32m_HAP2_v1.0.fa.gz  Haplotype assembly fasta fileAhor_pb32m_HAP2_v1.0.ISOFORMS.bed.gz  Filtered gene annotations - all isoformsAhor_pb32m_HAP2_v1.0.ISOFORMS.CDS.fa.gz  Filtered gene annotations (protein coding nucleotides) - all isoformsAhor_pb32m_HAP2_v1.0.ISOFORMS.gff3.gz  Filtered gene annotations - all isoformsAhor_pb32m_HAP2_v1.0.ISOFORMS.peptides.fa.gz  Filtered gene annotations (protein sequences) - all isoformsAhor_pb32m_HAP2_v1.0.PRIMARY.bed.gz  Filtered gene annotations - longest isoforms onlyAhor_pb32m_HAP2_v1.0.PRIMARY.CDS.fa.gz  Filtered gene annotations (protein coding nucleotides) - longest isoforms onlyAhor_pb32m_HAP2_v1.0.PRIMARY.gff3.gz  Filtered gene annotations - longest isoforms onlyAhor_pb32m_HAP2_v1.0.PRIMARY.peptides.fa.gz  Filtered gene annotations (protein sequences) - longest isoforms onlyAhor_pb32m_HAP2_v1.0.RM.TE.gff.gz  All TE annotations by RepeatMaskerAoff_pb81m_HAP1_v1.0.chrX_regions.bed.gz  X chromosome nonrecombining region coordinatesAoff_pb81m_HAP1_v1.0.EDTA.TEanno.gff3.gz  All TE annotations by EDTAAoff_pb81m_HAP1_v1.0.EDTA.TEintact.fa.gz  Intact TE sequences by EDTAAoff_pb81m_HAP1_v1.0.EDTA.TEintact.gff3.gz  Intact TE annotations by EDTAAoff_pb81m_HAP1_v1.0.entap_results.tsv  Reciprocal functional gene annotations by EnTAPAoff_pb81m_HAP1_v1.0.fa.gz  Haplotype assembly fasta fileAoff_pb81m_HAP1_v1.0.ISOFORMS.bed.gz  Filtered gene annotations - all isoformsAoff_pb81m_HAP1_v1.0.ISOFORMS.CDS.fa.gz  Filtered gene annotations (protein coding nucleotides) - all isoformsAoff_pb81m_HAP1_v1.0.ISOFORMS.gff3.gz  Filtered gene annotations - all isoformsAoff_pb81m_HAP1_v1.0.ISOFORMS.peptides.fa.gz  Filtered gene annotations (protein sequences) - all isoformsAoff_pb81m_HAP1_v1.0.PRIMARY.bed.gz  Filtered gene annotations - longest isoforms onlyAoff_pb81m_HAP1_v1.0.PRIMARY.CDS.fa.gz  Filtered gene annotations (protein coding nucleotides) - longest isoforms onlyAoff_pb81m_HAP1_v1.0.PRIMARY.gff3.gz  Filtered gene annotations - longest isoforms onlyAoff_pb81m_HAP1_v1.0.PRIMARY.peptides.fa.gz  Filtered gene annotations (protein sequences) - longest isoforms onlyAoff_pb81m_HAP1_v1.0.RM.TE.gff.gz  All TE annotations by RepeatMaskerAoff_pb81m_HAP2_v1.0.chrY_regions.bed.gz  Y chromosome nonrecombining region coordinatesAoff_pb81m_HAP2_v1.0.EDTA.TEanno.gff3.gz  All TE annotations by EDTAAoff_pb81m_HAP2_v1.0.EDTA.TEintact.fa.gz  Intact TE sequences by EDTAAoff_pb81m_HAP2_v1.0.EDTA.TEintact.gff3.gz  Intact TE annotations by EDTAAoff_pb81m_HAP2_v1.0.entap_results.tsv  Reciprocal functional gene annotations by EnTAPAoff_pb81m_HAP2_v1.0.fa.gz  Haplotype assembly fasta fileAoff_pb81m_HAP2_v1.0.ISOFORMS.bed.gz  Filtered gene annotations - all isoformsAoff_pb81m_HAP2_v1.0.ISOFORMS.CDS.fa.gz  Filtered gene annotations (protein coding nucleotides) - all isoformsAoff_pb81m_HAP2_v1.0.ISOFORMS.gff3.gz  Filtered gene annotations - all isoformsAoff_pb81m_HAP2_v1.0.ISOFORMS.peptides.fa.gz  Filtered gene annotations (protein sequences) - all isoformsAoff_pb81m_HAP2_v1.0.PRIMARY.bed.gz  Filtered gene annotations - longest isoforms onlyAoff_pb81m_HAP2_v1.0.PRIMARY.CDS.fa.gz  Filtered gene annotations (protein coding nucleotides) - longest isoforms onlyAoff_pb81m_HAP2_v1.0.PRIMARY.gff3.gz  Filtered gene annotations - longest isoforms onlyAoff_pb81m_HAP2_v1.0.PRIMARY.peptides.fa.gz  Filtered gene annotations (protein sequences) - longest isoforms onlyAoff_pb81m_HAP2_v1.0.RM.TE.gff.gz  All TE annotations by RepeatMaskerAhorridus_MSY_CODEML.zip  CODEML M2a output for 11 MSY genes with evidence of positive selection in Asparagus horridus 

Sex chromosomes have evolved hundreds of times across the flowering plant tree of life; their recent origins in some members of this clade can shed light on the early consequences of suppressed recombination, a crucial step in sex chromosome evolution. Amborella trichopoda, the sole species of a lineage that is sister to all other extant flowering plants, is dioecious with a young ZW sex determination system. Here we present a haplotype-resolved genome assembly, including highly contiguous assemblies of the Z and W chromosomes. We identify a ~3-megabase sex-determination region (SDR) captured in two strata that includes a ~300-kilobase inversion that is enriched with repetitive sequences and contains a homologue of the Arabidopsis METHYLTHIOADENOSINE NUCLEOSIDASE (MTN1-2) genes, which are known to be involved in fertility. However, the remainder of the SDR does not show patterns typically found in non-recombining SDRs, such as repeat accumulation and gene loss. These findings are consistent with the hypothesis that dioecy is derived in Amborella and the sex chromosome pair has not significantly degenerated. 

Dataset and result files from phylogenomic analysis and ancestral biogeography estimation across the genus Asparagus using the Asparagaceae1726 bait set.  Contents of this version replaces Quartet_Sampling.zip in the previous version. Contents: Quartet_Sampling_FINAL.zip = input dataset and final results from Quartet Sampling (i.e., 1000 quartet replicates sampled per node)  

Introgression can produce novel genetic variation in organisms that hybridize. Sympatric species pairs in the carnivorous plant genusSarraceniaL. frequently hybridize, and all known hybrids are fertile. Despite being a desirable system for studying the evolutionary consequences of hybridization, the extent to which introgression occurs in the genus is limited to a few species in only two field sites. Previous phylogenomic analysis ofSarraceniaestimated a highly resolved species tree from 199 nuclear genes, but revealed a plastid genome that is highly discordant with the species tree. Such cytonuclear discordance could be caused by chloroplast introgression (i.e. chloroplast capture) or incomplete lineage sorting (ILS). To better understand the extent to which introgression is occurring inSarracenia, the chloroplast capture and ILS hypotheses were formally evaluated. Plastomes were assembledde-novofrom sequencing reads generated from 17 individuals in addition to reads obtained from the previous study. Assemblies of 14 whole plastomes were generated and annotated, and the remaining fragmented assemblies were scaffolded to these whole-plastome assemblies. Coding sequence from 79 homologous genes were aligned and concatenated for maximum-likelihood phylogeny estimation. The plastome tree is extremely discordant with the published species tree. Plastome trees were simulated under the coalescent and tree distance from the species tree was calculated to generate a null distribution of discordance that is expected under ILS alone. A t-test rejected the null hypothesis that ILS could cause the level of discordance seen in the plastome tree, suggesting that chloroplast capture must be invoked to explain the discordance. Due to the extreme level of discordance in the plastome tree, it is likely that chloroplast capture has been common in the evolutionary history ofSarracenia.