Dataset Information

Complete mitochondrial genome of the Loligo japonica.

ABSTRACT: In this study, we determined the complete mitochondrial genome of Loligo japonica. The genome was 17,232?bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The overall base composition of L. japonica is A 39.60%, C 18.22%, T33.38% and G 8.80%, with a highly A?+?T bias of 72.98%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. Here, we describe a phylogenetic analysis of 11 species Cephalopoda based on the complete mitochondrial genome, and the result showed that the Loligo Beka and Loligo uyii are most closely related to L. japonica. This mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Cephalopoda.

SUBMITTER: Jiang L

PROVIDER: S-EPMC7800932 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Complete mitochondrial genome of the Loligo japonica.

Jiang Lihua L Kang Lisen L Wu Changwen C

Mitochondrial DNA. Part B, Resources 20170809 2

In this study, we determined the complete mitochondrial genome of Loligo japonica. The genome was 17,232 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 3 main non-coding regions. The overall base composition of L. japonica is A 39.60%, C 18.22%, T33.38% and G 8.80%, with a highly A + T bias of 72.98%. All of the three control regions (CR) contain termination-associated sequences and conserved sequence blocks. Here, we describe a ...[more]

PMID: 33473874

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Project description:Sophora japonica L. (Faboideae, Leguminosae) is an important traditional Chinese herb with a long history of cultivation. Its flower buds and fruits contain abundant flavonoids, and therefore, the plants are cultivated for the industrial extraction of rutin. Here, we determined the complete nucleotide sequence of the mitochondrial genome of S. japonica 'JinhuaiJ2', the most widely planted variety in Guangxi region of China. The total length of the mtDNA sequence is 484,916 bp, with a GC content of 45.4%. Sophora japonica mtDNA harbors 32 known protein-coding genes, 17 tRNA genes, and three rRNA genes with 17 cis-spliced and five trans-spliced introns disrupting eight protein-coding genes. The gene coding and intron regions, and intergenic spacers account for 7.5%, 5.8% and 86.7% of the genome, respectively. The gene profile of S. japonica mitogenome differs from that of the other Faboideae species by only one or two gene gains or losses. Four of the 17 cis-spliced introns showed distinct length variations in the Faboideae, which could be attributed to the homologous recombination of the short repeats measuring a few bases located precisely at the edges of the putative deletions. This reflects the importance of small repeats in the sequence evolution in Faboideae mitogenomes. Repeated sequences of S. japonica mitogenome are mainly composed of small repeats, with only 20 medium-sized repeats, and one large repeat, adding up to 4% of its mitogenome length. Among the 25 pseudogene fragments detected in the intergenic spacer regions, the two largest ones and their corresponding functional gene copies located in two different sets of medium-sized repeats, point to their origins from homologous recombinations. As we further observed the recombined reads associated with the longest repeats of 2,160 bp with the PacBio long read data set of just 15 × in depth, repeat mediated homologous recombinations may play important role in the mitogenomic evolution of S. japonica. Our study provides insightful knowledge to the genetic background of this important herb species and the mitogenomic evolution in the Faboideae species.

Dataset Information

Complete mitochondrial genome of the Loligo japonica.

Publications

Complete mitochondrial genome of the <i>Loligo japonica</i>.

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