Additional file 2: Table S2. of Model-based clustering with certainty estimation: implication for clade assignment of influenza viruses

Cluster ID from Mclust of the influenza A (H7) HA sequences. (DOCX 29 kb

Stellaria fenzlii Regel

原著和名: エゾフスマ シラオイハコベ科名: ナデシコ科 = Caryophyllaceae採集地: 北海道 広尾郡 広尾町 海岸岩地 (北海道 十勝 広尾町 海岸岩地)採集日: 1985/8/29採集者: 萩庭丈壽整理番号: JH032758国立科学博物館整理番号: TNS-VS-98275

Analysis of the Skin Transcriptome in Two Oujiang Color Varieties of Common Carp

<div><p>Background</p><p>Body color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (<i>Cyprinus carpio</i> var. <i>color</i>), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding.</p><p>Methodology/Principal Findings</p><p>In this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW.</p><p>Conclusions</p><p>The transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.</p></div

The distribution of SNP types in the common carp transcriptome.

<p>* indicates single nucleotide polymorphisms other than single nucleotide substitution, including deletion.</p

The number of common carp transcripts (isotigs and singletons) and enzymes found in each KEGG pathway.

<p>Shown only the top 20 pathways and see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090074#pone.0090074.s002" target="_blank">Table S2</a> for the complete list of 134 pathways.</p

Venn diagram of the number of isotigs found in the skin transcriptome of Oujiang color varieties of common carp (RB and WW) and gynogenic transcriptome of common carp (CC).

<p>RB - red with big black spots, WW - whole white.</p

Summary statistics of common carp skin transcriptomic sequencing and assembly.

<p>* Oujiang color varieties of common carp: RB - red with big black spots, WW - whole white;</p><p>** CC reads are from a gynogenic common carp from 12 tissues downloaded from NCBI (SRA 050545).</p

Analysis pipeline of Oujiang color varieties of common carp (RB - red with big black spots and WW – whole white) and gynogenic common carp (CC) transcriptomes, with the number of raw 454 reads, singletons and isotigs denoted.

<p>The pictures of RB, WW and CC are shown at the top panel. CC raw sequencing reads were downloaded from NCBI SRA database (SRA 050545).</p

Putative color pattern-specific SNP markers found in Oujiang color varieties of common carp isotig sequences generated from the skin transcriptome^*.

<p>* See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090074#pone.0090074.s003" target="_blank">Table S3</a> for the complete list of candidate SNP markers.</p><p>** RB - red with big black spots, WW - whole white.</p

The number of common carp transcripts in each level-2 Gene Ontology category.

<p>The transcriptome was assembled from Oujiang color varieties of common carp (RB - red with big black spots and WW – whole white) and gynogenic common carp (CC).</p