Résumé
Ascidians or sea squirts form a diverse group within chordates, which
includes a few thousand members of marine sessile filter-feeding animals.
Their mitochondrial genomes are characterized by particularly high
evolutionary rates and rampant gene rearrangements. This extreme
variability complicates standard PCR-based techniques for molecular
characterization studies, and consequently only a few complete ascidian
mitochondrial genome sequences are available. Using the standard PCR and
Sanger sequencing approach, we produced the mitochondrial genome of
Ascidiella aspersa only after a great effort. In contrast, we produced
five additional mitogenomes (Botrylloides aff. leachii, Halocynthia
spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum)
with a novel strategy, consisting in sequencing the pooled total DNA
samples of these five species using one Illumina HiSeq 2000 flow cell
lane. Each mitogenome was efficiently assembled in a single contig using
de novo transcriptome assembly, as de novo genome assembly generally
performed poorly for this task. Each of the new six mitogenomes presents a
different and novel gene order, showing that no syntenic block has been
conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia).
Phylogenetic analyses support the paraphyly of both Ascidiacea and
Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the
deepest nodes of the Phlebobranchia-Thaliacea clade are not well resolved.
The strategy described here thus provides a cost-effective approach to
obtain complete mitogenomes characterized by a highly plastic gene order
and a fast nucleotide/amino-acid substitution rate.