Studies On Complete Mitochondrial Genomes Of Genus Coilia And Lota Lota

Genus Coilia are widely distributed in the Indo-West Pacific Ocean inhabiting mainly along the coast as well as the estuarine waters. Majority of them are the short distance migration fish between the river and the sea. There is a longstanding controversy about the classification of genus Coilia in China and it has been also found obvious geographic structure among Coilia nasus and Coilia mystus. Lota lota is the only fresh-water species from the family Gadidae. As a benthic and cold adapted carnivore, it mainly lives in slow-running rivers and oligotrophic lakes in Eurasia and North America, southward to about 40°N. In the present study, mitochondrial genome sequences of three Coilia nasus, two Coilia mystus and Coilia grayii were determined with the genomic organization and structure being analyzed and compared. The phylogenetic and taxonomic analysis of Coilia in China was probed based on mitochondrial genome sequences. Meanwhile, the genetic divergence level among Lota lota was probed based on mitochondrial genome sequences. The main results are presented as follows:1. Characterisation of the mitogenomes of genus CoiliaThe complete mitogenomes of three lineages of Coilia nasus is a typical circular molecule of 16896bp,16900 bp and 16896bp in length, respectively. So are two lineages of Coilia mystus with 16964bp and 17075bp in length and Coilia grayii with 16851bp in length. It was the variable number tandem repeats in control region that mainly resulted in the differences of length among three Coilia species. All the six mitogenomes carry set of 22 tRNAs,2 rRNAs,13 protein-coding genes as well as a putative control region and OL, the gene order of which is identical to those of canonical vertebrate mitogenomes. The nucleotide composition of the six mitogenomes is characterized by a strong excess of C relative to G but a slight excess of A relative to T on the H-strand. Anti-G bias and anti-C bias were found at the third codon positions of H- and L-strand, respectively, ultimately reflected in the codon usage on each strand. The protein-coding genes in all six mitogenomes employed the same start codon ATG except for COI gene being started with GTG. Three stop codons (TAA, TA-, and T--) were used in the six mitogenomes. All tRNA genes could putatively form typical cloverleaf secondary structures with the exception of tRNASer (AGY). Apart from the conserved blocks TAS and CSB-1,-2, and -3, three putative central conserved sequences blocks (CSB-D to CSB-F) could be recognized. The high sequence divergence could be detected between the mitogenomic sequences of the two lineages of Coilia mystus. While, the low level of sequence divergence was observed within three lineages of Coilia nasus.2. Probe into phylogenetic and taxonomic relationships of genus Coilia based on mitogenomic sequencesA molecular phylogenetic analysis of genus Coilia was conducted using Bayesian inferences multiple models and ML methods based on the complete mitogenomes excluding the ND6 genes and control region. Well-resolved phylogenies constructed in the present study strongly supported the two major branches. One branch consisted of Coilia nasus, Coilia grayii and Coilia lindamani. Coilia nasus and Coilia grayii had the closest genetic relationship, then they clustered with Coilia lindamani. The three lineages of Coilia nasus definitely existed genetic divergence, but it didn’t reach the inter-specific or inter-subspecific level. The net genetic distance among three lineages of Coilia nasus were only 0.003-0.004. Another branch consisted of two lineages of Coilia mystus. However, the two lineages of Coilia mystus were obviously divergent from each other. The result confirmed that the south and north lineage of Coilia mystus were genetically distinct as having been different species. The net genetic distance between two lineages of Coilia nasus were as high as 0.063.3. Characterisation of the mitogenomes and the genetic divergence level of Lota lotaThe complete mitogenomes of three specimens of Lota lota is a typical circular molecule of 16547 bp,16519bp and 16534bp in length, respectively. It was the NC non-coding region that mainly resulted in the differences of length of three Lota lota. All the three mitogenomes carry set of 22 tRNAs,2 rRNAs,13 protein-coding genes as well as a putative control region, NC non-coding region and OL, the gene order of which is identical to those of canonical vertebrate mitogenomes. The nucleotide composition of the three mitogenomes is characterized by a strong excess of C relative to G but a slight excess of A relative to T on the H-strand. Anti-G bias and anti-C bias were found at the third codon positions of H- and L-strand, respectively, ultimately reflected in the codon usage on each strand. The protein-coding genes in all three mitogenomes employed the same start codon ATG except for COI gene being started with GTG. Three stop codons (TAA, TA-, and T--) were used in the three mitogenomes. All tRNA genes could putatively form typical cloverleaf secondary structures with the exception of tRNASer(AGY). Apart from the conserved blocks TAS and CSB-1,-2, and -3, only two putative central conserved sequences blocks (CSB-D and CSB-F) could be recognized. The low level of sequence divergence was observed within three lineage specimens of Lota lota. A molecular phylogenetic analysis of Lota lota was conducted using Bayesian inferences multiple models and ML methods based on the complete mitogenomes excluding the ND6 genes and control region. The two methods showed the different results. It is unclear of the phylogenetic relationships of three specimens of Lota lota. However, the results also revealed there was significant genetic difference among three specimens of Lota lota and Lota lota IM from the Amur basin as a distinct lineage was separated clearly from the lineage XJ and lineage NA.