Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
PLoS One. 2013 Jul 16;8(7):e69909. doi: 10.1371/journal.pone.0069909. Print 2013.
Gracilariopsis lemaneiformis has a high economic value and is one of the most important aquaculture species in China. Despite it is economic importance, it has remained largely unstudied at the genomic level. In this study, we conducted a genome survey of Gp. lemaneiformis using next-generation sequencing (NGS) technologies. In total, 18.70 Gb of high-quality sequence data with an estimated genome size of 97 Mb were obtained by HiSeq 2000 sequencing for Gp. lemaneiformis. These reads were assembled into 160,390 contigs with a N50 length of 3.64 kb, which were further assembled into 125,685 scaffolds with a total length of 81.17 Mb. Genome analysis predicted 3490 genes and a GC% content of 48%. The identified genes have an average transcript length of 1,429 bp, an average coding sequence size of 1,369 bp, 1.36 exons per gene, exon length of 1,008 bp, and intron length of 191 bp. From the initial assembled scaffold, transposable elements constituted 54.64% (44.35 Mb) of the genome, and 7737 simple sequence repeats (SSRs) were identified. Among these SSRs, the trinucleotide repeat type was the most abundant (up to 73.20% of total SSRs), followed by the di- (17.41%), tetra- (5.49%), hexa- (2.90%), and penta- (1.00%) nucleotide repeat type. These characteristics suggest that Gp. lemaneiformis is a model organism for genetic study. This is the first report of genome-wide characterization within this taxon.
秀丽白虾具有很高的经济价值，是中国最重要的水产养殖物种之一。尽管它具有重要的经济意义，但在基因组水平上的研究仍然很大程度上未被探索。在本研究中，我们使用下一代测序（NGS）技术对秀丽白虾进行了基因组调查。通过 HiSeq 2000 测序，共获得了 18.70 Gb 的高质量序列数据，估计基因组大小为 97 Mb。这些reads 被组装成 160,390 个 contigs，N50 长度为 3.64 kb，进一步组装成 125,685 个 scaffolds，总长度为 81.17 Mb。基因组分析预测了 3490 个基因和 48%的 GC%含量。鉴定出的基因平均转录长度为 1429 bp，平均编码序列大小为 1369 bp，每个基因有 1.36 个外显子，外显子长度为 1008 bp，内含子长度为 191 bp。从初始组装的支架中，转座元件构成了基因组的 54.64%（44.35 Mb），并鉴定出 7737 个简单重复序列（SSR）。在这些 SSR 中，三核苷酸重复类型最为丰富（占总 SSR 的 73.20%），其次是二核苷酸（17.41%）、四核苷酸（5.49%）、六核苷酸（2.90%）和五核苷酸（1.00%）重复类型。这些特征表明秀丽白虾是遗传研究的模式生物。这是该分类群中首次进行全基因组特征描述的报告。
