Shotgun assembly of the mitochondrial genome from Fenneropenaeus penicillatus with phylogenetic consideration

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• 作者：Dianchang Zhang^a ; ^{zhangdch@163.com" class="auth_mail" title="E-mail the corresponding author} ; Fahui Gong^a ; ^b ; Tiantian Liu^a ; ^b ; Huayang Guo^a ; Nan Zhang^a ; Kecheng Zhu^a ; Shigui Jiang^a ; ^{jiangsg@21cn.com" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Penaeidae ; Shrimp ; Mitochondrial genome ; Phylogenetic relationship ; Shotgun assembly
• 刊名：Marine Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：24
• 期：part_P3
• 页码：379-386
• 全文大小：880 K

文摘

The complete mitochondrial genome is of great importance for better understanding of the genome-level characteristics and phylogenetic relationships among related species. In this study, Fenneropenaeus penicillatus mitochondrial genome sequence was determined by next-generation sequencing. The complete genome DNA was 16,040 bp in length and consisted of a typical set of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a putative control region (CR). The gene arrangement is identical to the pancrustacean pattern. The overall base composition of its mitochondrial genome is estimated to be 34.1% for A, 34.1% for T, 12.5% for G and 19.3% for C with a high A + T content (68.2%). The analysis of the average Ka/Ks in the 13 mitochondrial protein-coding genes of penaeid shrimps indicated a strong purifying selection within this group. The phylogenetic analysis based on mitochondrial sequences and 13 concatenated protein-coding genes showed strong statistic support for the following relationship among the five genera ((Penaeus s.s + Fenneropenaeus) + (Litopenaeus + Farfantepenaeus)) + Marsupenaeus. The sequence data of F. penicillatus can provide useful information for the studies on molecular systematics, population structure, stock evaluation and conservation genetics.