Alignments for probes, raw WGS reads, and WGS assemblies

Ascidians (Phylum Chordata, Class Ascidiacea) are a large group of invertebrates which occupy a central role in the ecology of marine benthic communities.  Many ascidian species have become successfully introduced around the world via anthropogenic vectors.  The botryllid ascidians (Order Stolidobranchia, Family Styelidae) are a group of 53 colonial species, several of which are widespread throughout temperate or tropical and subtropical waters.  However, the systematics and biology of this group of ascidians is not well-understood.  To provide a systematic framework for this group, we have constructed a well-resolved phylogenomic tree using 200 novel loci and 55 specimens.  A Principal Components Analysis of all species described in the literature using 31 taxonomic characteristics revealed that some species occupy a unique morphological space and can be easily identified using characteristics of adult colonies.  For other species, additional information such as larval or life history ..., Anchored Hybrid Enrichment (AHE) Locus Identification and Probe Design

Our aim was to develop a resource for collecting hundreds of orthologous loci across the botryllid ascidians using Anchored Hybrid Enrichment (AHE) [70]. The pre-existing genomic resources included an assembled genome of Botryllus schlosseri [71], and two assembled transcriptomes: Botryllus schlosseri [72], and Botrylloides leachii [73], recently re-assigned to Botrylloides diegensis in [23].  In order to better represent the high diversity of the botryllid group, we collected low-coverage, whole genome data assemblies for seven additional species (details are given in Supplementary Table S2).  DNA extracts for these seven species were sent to the Center for Anchored Phylogenomics (http:www.anchoredphylogeny.com) for processing. In brief, after the quality/quantity of DNA was assessed using Qubit, Illumina libraries with single 8bp indexes were prepared following [74], with modifications described in [75]. Librari..., ,