Sequencing and Analysis of the Mediterranean Amphioxus (Branchiostoma lanceolatum) Transcriptome

BACKGROUND: The 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. RESULTS: Starting 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. CONCLUSION: We 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

Adsorption of cellulose onto cellulose fibres. II: the effect of pH on silane

International audienc

Sequence and assembly statistics.

<p>Sequence and assembly statistics.</p

Size distribution of annotated (blue) and non-annotated (red) contigs.

<p>Non-annotated contigs are highly present within the shorter contigs (less than 500 bp).</p

Biological Process.

<p>Gene Ontology (GO) assignment of the <i>Branchiostoma lanceolatum</i> transcriptome for the Biological Process category (total of 54,218 terms).</p

Molecular Function.

<p>Gene Ontology (GO) assignment of the <i>B. lanceolatum</i> transcriptome for the Molecular Function category (total of 85,213 terms).</p

Scatter plot representing the number of reads per contig for each contig length.

<p>Scatter plot representing the number of reads per contig for each contig length.</p

Cellular Component.

<p>Gene Ontology (GO) assignment of the <i>B. lanceolatum</i> transcriptome for the Cellular Component category (total of 48,754 terms).</p

Genomic and transcriptomic comparisons between <i>B. floridae</i> and <i>B. lanceolatum</i>.

<p>BlastN were performed between each database in both directions. The arrow indicates the sense of the blast, from the query to the database. Databases used: (1) transcriptomic data of <i>B. lanceolatum</i> presented here; (2) genomic data of <i>B. floridae</i> published by Putnam et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036554#pone.0036554-Putnam1" target="_blank">[10]</a>; (3) transcriptomic data of <i>B. floridae</i> published by Yu et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036554#pone.0036554-Yu1" target="_blank">[11]</a>.</p