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Complete Mitochondrial DNA Genome Sequences for Two Lineages in Coilia mystus (Clupeiformes: Engraulididae): Mitogenomic Perspective on the Phylogenetic Relationships of Genus Coilia

Complete Mitochondrial DNA Genome Sequences for Two Lineages in Coilia mystus (Clupeiformes: Engraulididae): Mitogenomic Perspective on the Phylogenetic Relationships of Genus Coilia

Ai Guo1,2,3, Jiaguang Xiao4, Binbin Shan4, Tianxiang Gao5 and Yongdong Zhou3,*

1College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China
2State Key Laboratory of Satellite Ocean Environment Dynamics, The Second Institute of Oceanography, State Oceanic Administration, Hangzhou 310012, China
3Marine Fisheries Research Institute of Zhejiang Province, Zhoushan 316021, China
4Fishery College, Ocean University of China, Qingdao 266003, China
5Fishery College, Zhejiang Ocean University, Zhoushan 316022, China

Ai Guo and Jiaguang Xiao contributed equally to this study.

*      Corresponding author: zyd511@126.com

 

Fig. 1.

Gene organization for the mitochondrial genomes of the Coilia mystus N and Coilia mystus S. (C. mystus N and C. mystus S shared the same structural organization and gene arrangement, so only gene organization of C. mystus N were shown).

Fig. 2.

H-strand comparison of frequencies of codons ending with the same nucleotide. Values on the y-axis represent the sum of relative synonymous codon usage (RSCU) values of codons ending with the same nucleotide across all codon families (x-axis).

Fig. 3.

Complete nucleotide sequences of mitochondrial control region of Coilia. Termination associated sequence (TAS), central conserved sequences (CSB-F, -E, -D) and sequence blocks (CSB-1, -2, -3). VNTRs were embellished in the same times for sequences alignment.

Fig. 4.

Plot of divergences among mtDNA sequences excluding non-coding regions. The sliding window analysis calculates the divergence of C. mystus N and C. mystus S (A), C. mystus N and C. mystus (KJ710625) (B), respectively. The bar at the top illustrates the position of protein-coding genes, rRNAs and tRNAs are represented as black boxes.

Fig. 5.

Inferred phylogenetic relationships among Coilia based on the concatenated nucleotide sequences of 13 mitochondrial protein-coding genes using maximum likelihood (ML) and Bayesian Inference (BI). Numbers on branches are bootstrap percentages and Bayesian posterior probabilities. Engraulis japonicas (NC_003097) and Engraulis encrasicolus (NC_009581) are used as outgroups.

Pakistan Journal of Zoology

October

Vol. 50, Iss. 5, Pages 1601-1998

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