Genome-Wide Identification, Characterization and Phylogenetic Analysis of 50 Catfish ATP-Binding Cassette (ABC) Transporter Genes

<div><p>Background</p><p>Although a large set of full-length transcripts was recently assembled in catfish, annotation of large gene families, especially those with duplications, is still a great challenge. Most often, complexities in annotation cause mis-identification and thereby much confusion in the scientific literature. As such, detailed phylogenetic analysis and/or orthology analysis are required for annotation of genes involved in gene families. The ATP-binding cassette (ABC) transporter gene superfamily is a large gene family that encodes membrane proteins that transport a diverse set of substrates across membranes, playing important roles in protecting organisms from diverse environment.</p><p>Methodology/Principal Findings</p><p>In this work, we identified a set of 50 ABC transporters in catfish genome. Phylogenetic analysis allowed their identification and annotation into seven subfamilies, including 9 ABCA genes, 12 ABCB genes, 12 ABCC genes, 5 ABCD genes, 2 ABCE genes, 4 ABCF genes and 6 ABCG genes. Most ABC transporters are conserved among vertebrates, though cases of recent gene duplications and gene losses do exist. Gene duplications in catfish were found for ABCA1, ABCB3, ABCB6, ABCC5, ABCD3, ABCE1, ABCF2 and ABCG2.</p><p>Conclusion/Significance</p><p>The whole set of catfish ABC transporters provide the essential genomic resources for future biochemical, toxicological and physiological studies of ABC drug efflux transporters. The establishment of orthologies should allow functional inferences with the information from model species, though the function of lineage-specific genes can be distinct because of specific living environment with different selection pressure.</p></div

Development of Molecular Resources for an Intertidal Clam, <i>Sinonovacula constricta</i>, Using 454 Transcriptome Sequencing

<div><p>Background</p><p>The razor clam <i>Sinonovacula constricta</i> is a benthic intertidal bivalve species with important commercial value. Despite its economic importance, knowledge of its transcriptome is scarce. Next generation sequencing technologies offer rapid and efficient tools for generating large numbers of sequences, which can be used to characterize the transcriptome, to develop effective molecular markers and to identify genes associated with growth, a key breeding trait.</p><p>Results</p><p>Total RNA was isolated from the mantle, gill, liver, siphon, gonad and muscular foot tissues. High-throughput deep sequencing of <i>S. constricta</i> using 454 pyrosequencing technology yielded 859,313 high-quality reads with an average read length of 489 bp. Clustering and assembly of these reads produced 16,323 contigs and 131,346 singletons with average lengths of 1,376 bp and 458 bp, respectively. Based on transcriptome sequencing, 14,615 sequences had significant matches with known genes encoding 147,669 predicted proteins. Subsequently, previously unknown growth-related genes were identified. A total of 13,563 microsatellites (SSRs) and 13,634 high-confidence single nucleotide polymorphism loci (SNPs) were discovered, of which almost half were validated.</p><p>Conclusion</p><p>De novo sequencing of the razor clam <i>S. constricta</i> transcriptome on the 454 GS FLX platform generated a large number of ESTs. Candidate growth factors and a large number of SSRs and SNPs were identified. These results will impact genetic studies of <i>S. constricta</i>.</p></div

Distribution of simple sequence repeats (SSR) and other nucleotide repeats in the transcriptome.

<p>(A) Distribution of five nucleotide repeat types (di-, tri-, tetra-, penta-, and hexa-nucleotide repeats). (B) Distribution of tri-nucleotide repeats. (C) Distribution of di-nucleotide repeats. SSRs had at least six di-nucleotide repeats and five other repeats (tri-, tetra-, penta-, and hexa-nucleotide repeats).</p

NJ phylogenetic tree based on Mt-COI protein sequences from four Veneridae species (<i>S. constricta</i>, <i>C. gallina</i>, <i>M. meretrix</i>, and <i>R. philippinarum</i>).

<p>NJ phylogenetic tree based on Mt-COI protein sequences from four Veneridae species (<i>S. constricta</i>, <i>C. gallina</i>, <i>M. meretrix</i>, and <i>R. philippinarum</i>).</p

Species matched to the annotated sequences of <i>S. constricta</i> by BLASTx.

<p>Species matched to the annotated sequences of <i>S. constricta</i> by BLASTx.</p

Comparison of gene ontology (GO) in transcriptomes from <i>C. gallina</i>, <i>M. meretrix, R. philippinarum</i> and <i>S. constricta</i>.

<p>Comparison of gene ontology (GO) in transcriptomes from <i>C. gallina</i>, <i>M. meretrix, R. philippinarum</i> and <i>S. constricta</i>.</p

Length distribution of total reads and contigs from the <i>S. constricta</i> transcriptome.

<p>Length distribution of total reads and contigs from the <i>S. constricta</i> transcriptome.</p

Gene ontology (GO) terms for the transcriptome sequences of <i>S. constricta</i>.

<p>Gene ontology (GO) terms for the transcriptome sequences of <i>S. constricta</i>.</p

Comparison of experiment conditions and analysis results among <i>Sinonovacula constricta</i>, <i>Ruditapes philippinarum, Chamelea gallina</i> and <i>Meretrix meretrix</i>.

<p>Comparison of experiment conditions and analysis results among <i>Sinonovacula constricta</i>, <i>Ruditapes philippinarum, Chamelea gallina</i> and <i>Meretrix meretrix</i>.</p

Bivalve species matched to the annotated sequences of <i>S. constricta</i>.

<p>Bivalve species matched to the annotated sequences of <i>S. constricta</i>.</p