A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

UnlabelledPremise of the studyThe Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. •Methods and resultsWe designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. •ConclusionsThese methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families

Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. • We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. • These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families

The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements

Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (Helianthus annuus L.), especially given its large genome size (?3.5 Gb) and the well-documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain-containing Gypsy LTR retrotransposons (‘chromoviruses’), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.<br/

COS_sequence_length&number_of_sequences

List of COS sequences with alignment length and number of sequences in each alignment

tree file in newick format for the concatenation of all COS loci, as run in Garli

tree file in newick format for the concatenation of all COS loci, as run in Garl

COS alignment files

Alignments from all COS loc

Concatenation_of_all_763_ COS_alignments

Concatenated alignment file

Massive haplotypes underlie ecotypic differentiation in sunflowers.

Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2-4. Here, by resequencing 1,506&nbsp;wild sunflowers from 3&nbsp;species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37&nbsp;large (1-100&nbsp;Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H.&nbsp;argophyllus (probably through deletion of a homologue of FLOWERING&nbsp;LOCUS&nbsp;T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation

Massive haplotypes underlie ecotypic differentiation in sunflowers

Species often include multiple ecotypes that are adapted to different environments 1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations 2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation. Local adaptation is common in species that experience different environments across their range, often resulting in the formation of ecotypes-ecological races with distinct morphological and/or physiological characteristics that provide an environment-specific fitness advantage. Despite the prevalence of ecotypic differentiation, much remains to be understood about the genetic basis and evolutionary mechanisms that underlie its establishment and maintenance. In particular , a longstanding evolutionary question-dating to criticisms of Darwin's theories by his contemporaries 4-concerns how such ecological divergence can occur when challenged by hybridization with non-adapted populations 2. Local adaptation typically requires alleles at multiple loci that contribute to increased fitness in the same environment ; however, different ecotypes are often geographically close and interfertile, and hybridization between them should break up adaptive allelic combinations 3. To better understand the genetic basis of local adaptation and ecotypic differentiation, we conducted an in-depth study of genetic, phenotypic and environmental variation in three annual sunflower species, each of which includes multiple reproductively compatible ecotypes. Two species (H. annuus and H. petiolaris) have broad, overlapping distributions across North America. Helianthus annuus, the common sunflower, is generally found on mesic soils, but can grow in a variety of disturbed or extreme habitats, including semi-desert or frequently flooded areas. An especially well-characterized ecotype (formally known as H. annuus subsp. texanus) is adapted to the higher temperatures and herbivore pressures in Texas (USA) 5. Helianthus petiolaris, the prairie sunflower, prefers sandier soils; ecotypes of this species are adapted to sand sheets and dunes 6. The third species-H. argophyllus, the silverleaf sunflower-is endemic to southern Texas and includes both an early-flowering, coastal-island ecotype and a late-flowering inland ecotype 7. Population structure of wild sunflowers In a common garden experiment, we grew 10 plants from each of 151 populations of the 3 species, selected from across their native range (Fig. 1a); for each of these populations, we collected corresponding soil samples. We generated extensive records of developmental and morphological traits, and resequenced the genomes of 1,401 individual plants. We resequenced an additional 105 H. annuus plants to fill gaps in geographical coverage, as well as 12 outgroup taxa (Supplementary Table 1). Sunflower genomes are relatively large (H. annuus, 3.5 Gbp; https://doi