Abstract
BackgroundThe basally divergent phylogenetic position of amphioxus (Cephalochordata), as well as its conserved morphology, development and genetics, make it the best proxy for the chordate ancestor. Particularly, studies using the amphioxus model help our understanding of vertebrate evolution and development. Thus, interest for the amphioxus model led to the characterization of both the transcriptome and complete genome sequence of the American species, Branchiostoma floridae. However, recent technical improvements allowing induction of spawning in the laboratory during the breeding season on a daily basis with the Mediterranean species Branchiostoma lanceolatum have encouraged European Evo-Devo researchers to adopt this species as a model even though no genomic or transcriptomic data have been available. To fill this need we used the pyrosequencing method to characterize the B. lanceolatum transcriptome and then compared our results with the published transcriptome of B. floridae.ResultsStarting with total RNA from nine different developmental stages of B. lanceolatum, a normalized cDNA library was constructed and sequenced on Roche GS FLX (Titanium mode). Around 1.4 million of reads were produced and assembled into 70,530 contigs (average length of 490 bp). Overall 37% of the assembled sequences were annotated by BlastX and their Gene Ontology terms were determined. These results were then compared to genomic and transcriptomic data of B. floridae to assess similarities and specificities of each species.ConclusionWe obtained a high-quality amphioxus (B. lanceolatum) reference transcriptome using a high throughput sequencing approach. We found that 83% of the predicted genes in the B. floridae complete genome sequence are also found in the B. lanceolatum transcriptome, while only 41% were found in the B. floridae transcriptome obtained with traditional Sanger based sequencing. Therefore, given the high degree of sequence conservation between different amphioxus species, this set of ESTs may now be used as the reference transcriptome for the Branchiostoma genus.
Highlights
The Mediterranean amphioxus, Branchiostoma lanceolatum, belongs to the subphylum Cephalochordata, one of the three extant chordate groups with the urochordates and the vertebrates
The cDNA library was constructed with total RNA extracted from eight different developmental stages as well as from adult tissues of the Mediterranean amphioxus, B. lanceolatum (Table 1; sequencing performed by GATC Biotech AG)
The strategy used here, combining the construction of a normalized cDNA library with RNAs extracted from nine key developmental stages with a high throughput GS FLX sequencing, resulted in the achievement of high quality results
Summary
The Mediterranean amphioxus, Branchiostoma lanceolatum, belongs to the subphylum Cephalochordata, one of the three extant chordate groups with the urochordates and the vertebrates. Amphioxus is considered ‘vertebrate-like’, but simpler and characterized by a dorsal hollow nerve cord, dorsal notochord, ventral digestive tract, and pharynx perforated with gill slits This relative simplicity is found in its genome because cephalochordates diverged from the other chordates before the two whole genome duplication events that occurred at the base of the vertebrate diversification [4,5]. Recent technical improvements allowing induction of spawning in the laboratory during the breeding season on a daily basis with the Mediterranean species Branchiostoma lanceolatum have encouraged European Evo-Devo researchers to adopt this species as a model even though no genomic or transcriptomic data have been available. To fill this need we used the pyrosequencing method to characterize the B. lanceolatum transcriptome and compared our results with the published transcriptome of B. floridae
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