Abstract
Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome. Analysing genome size, gene number, repetitive elements, orthologs clustering and gene ontology terms show that B. leachii has a genomic architecture similar to that of most solitary tunicates, while other recently sequenced colonial ascidians have undergone genome expansion. In addition, ortholog clustering has identified groups of candidate genes for the study of colonialism and whole-body regeneration. By analysing the structure and composition of conserved gene linkages, we observed examples of cluster breaks and gene dispersions, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. We also found lineage-specific gene gain and loss within conserved cell-signalling pathways. Such examples of genetic changes within conserved cell-signalling pathways commonly associated with regeneration and development that may underlie some of the diverse regenerative abilities observed in tunicates. Overall, these results provide a novel resource for the study of tunicates and of colonial ascidians.
Highlights
Among the tunicate orthologous clusters that we obtained, we identified several groups of genes that are not shared by all the tunicate genomes (Fig. 2A)
Our assembly of the B. leachii genome provides an essential resource for the study of this colonial ascidian as well as a crucial point of comparison to gain further insights into the remarkable genetic diversity among tunicate species
The genome of B. leachii will be most useful for dissecting WBR in chordates; through comparison with B. schlosseri for understanding how the initiation of WBR can be blocked during specific periods of its life cycle
Summary
B. leachii colonies were collected from Nelson harbour (latitude 41.26°S, longitude 173.28°E) in New Zealand. To reduce the likelihood of contamination, embryos were dissected out of a colony and pooled before carrying out DNA extraction using E.Z.N.A SP Plant DNA Mini Kit (Omega Biotek). A total of 4 μg DNA was sent to New Zealand Genomics Limited (University of Otago, NZ) for two runs of library preparation and sequencing. Short read sequencing of Illumina TruSeq libraries in a HiSeq. 2500 generated 19,090,212 paired-end reads of 100 bp (average fragment size: 450 bp, adaptor length: 120 bp). A second sequencing (Illumina Nextera MiSeq Mate Pair), without size-selection, generated 31,780,788 paired-end sequences of 250 bp (fragment size: 1.5–15 kb, median size: ~3 kb, adaptor length: 38 bp)
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