DOI: 10.5061/dryad.73n5tb2z7
title: A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

description: Understanding the genetic changes associated with the evolution of
 biological diversity is of fundamental interest to molecular ecologists.
 The assessment of genetic variation at hundreds or thousands of unlinked
 genetic loci forms a sound basis to address questions ranging from micro-
 to macro-evolutionary timescales, and is now possible thanks to advances
 in sequencing technology. Major difficulties are associated with i) the
 lack of genomic resources for many taxa, especially from tropical
 biodiversity hotspots, ii) scaling the numbers of individuals analyzed and
 loci sequenced, and iii) building tools for reproducible bioinformatic
 analyses of such datasets. To address these challenges, we developed a set
 of target capture probes for phylogenomic studies of the highly diverse,
 pantropically distributed and economically significant rosewoods
 (Dalbergia spp.), explored the performance of an overlapping probe set for
 target capture across the legume family (Fabaceae), and built a
 general-purpose bioinformatics pipeline. Phylogenomic analyses of
 Dalbergia species from Madagascar yielded highly resolved and well
 supported hypotheses of evolutionary relationships. Population genomic
 analyses identified differences between closely related species and
 revealed the existence of a potentially new species, suggesting that the
 diversity of Malagasy Dalbergia species has been underestimated. Analyses
 at the family level corroborated previous findings by the recovery of
 monophyletic subfamilies and many well-known clades, as well as high
 levels of gene tree discordance, especially near the root of the family.
 The new genomic and bioinformatics resources will hopefully advance
 systematics and ecological genetics research in legumes, and promote
 conservation of the highly diverse and endangered Dalbergia rosewoods.
description: We produced a transcriptome
 assembly of a cultivated individual of <em>Dalbergia
 madagascariensis </em>subsp. <em>antongilensis</em>
 Bosser & R. Rabev., based on 63 million paired-end sequencing
 reads generated on an Illumina® HiSeq<sup>TM </sup>2000
 platform. We performed <em>de novo</em> assembly of the
 transcriptome using Trinity release 2012-01-25 (Grabherr et al., 2011),
 resulting in 146,484 scaffolds, which were between 201 and 17,129 bp long,
 with a mean length of 815 bp (see Supplementary Methods). We then pairwise
 aligned the <em>Dalbergia</em> transcriptome with reference
 genomes of five legume species available in public databases to generate a
 set of 12,049 probes from 6,555 conserved target regions (see
 Supplementary Methods). This probe set was used for synthesis of
 hybridizing probes at myBaits® Custom Target Capture Kits (Arbor
 Biosciences; https://arborbiosci.com). Motivated by the need for genomic resources to inform a reliable taxonomy and foster conservation practice for endangered rosewood species (<em>Dalbergia</em> spp., Fabaceae), we introduce a target capture approach for anchored phylogenomic analyses in <em>Dalbergia</em> (Dalbergia2396 set). We further explored the applicability of our approach for analyses across the entire legume family, which resulted in a second probe set (Fabaceae1005 set).
description: Target capture sequencing data has been uploaded here: https://www.ebi.ac.uk/ena/browser/view/PRJEB41848 The accompanying bioinformatics pipeline CaptureAl was used for data analysis. It is available and documented here: https://github.com/scrameri/CaptureAl