Complete Mitochondrial Genomes Of Two Caenorhabditis

Compared with nuclear geneome, mitochondrial genomes have many advantages, such as high copy number, small size, absence of recombination, conserved structure, faster mutation rates and presumed maternal inheritance. These features make mitochondrial genome (mitogeonme) to be not only the powerful instrument on studying phylogeny, but also the unique molecular genetic markers on the basis of genome. Since the genome sequences of C. elegans and the other eight sister species have been completed, Caenorhabditis have become not only one of the best modal organisms, but also the best experimental subject for comparative genomics and evolution research. So far, only two complete mitogeonme have been reported in the genus of Caenorhabditis. These results are too few for a genus which owned twenty-seven kinds of species.In order to deeply learn and summarize the characteristics of Caenorhabditis mitogeonme, and reconstruct the phylogenetic relationship of Caenorhabditis based on complete mitogeonme, the amplification of complete mitogeonme in C. tropicalis n. sp. and C. remanei were carried out by means of long PCR, general PCR and primer walking. Referring to the mitogeonme of C. elegans, C. briggsae and C. sp.5, the annotation and analysis were made. In addition, we used the mitogeonme of these five species to conclude the characteristics and build the phylogenetic relationship of Caenorhabditis. The concrete results are as following:1. The complete mitogeonme of C. tropicalis n. sp. and C. remaneiThe complete mitogeonme of C.tropicalis n. sp. and C. remanei were 13,874 bp and 13,977 bp in size, respectively, including 12 protein-coding genes (PCGs),22 transfer RNA genes (tRNAs),2 ribosomal RNA genes (rRNAs), an AT-rich region and a non-coding region located between nad4 and coxl. All these genes were located on the heavy strand. There had a other non-coding region (130bp) located between trnR and trnQin C. tropicalis n. sp..(A+T)%in C. tropicalis n.sp. and C.remanei were 75.69% and 77.46%, separately, exhibiting obvious preference. Among the constituent parts of mitogeonme, (A+T)% in AT-rich region was the highest. The nucleotide composition of codons in different sites also had bias, among which the third site was the highest.ATT and TTG were the initiation codons in the mitogeonme of C. tropicalis n. sp. and C. remanei, and C. tropicalis n.sp. also used ATA as their initiation codons. The most frequently used termination condon for these two species was TAA followed by TAG. Of the 12 PCGs, NNU and NNA were the dominant codons, among which UUU(F), UUA(L) and AUU(I) had the highest frequency in usage.Twenty-two tRNAs couldn't fold into the typical structure of clover leaf.In 20 of the tRNA, the T?C arm and variable loop were together replaced with the TV-replacement loop. While the DHU arm was replaced with a loop in trnS. In these secondary structures, there existed mismatches in which G-U mismatch was dominating.The AT-rich region of C. tropicalis n. sp. and C. remanei was 410 bp and 655 bp in length, respectively. They were separately the shortest and the longest in the corresponding regions of Caenorhabditis. These two AT-rich regions all consisted of AT dinucleotide repeat units, direct repeat sequences and inverted repeat sequences, but these two species were different on the length and copy numbers. The non-coding region located between nad4 and coxl could fold into three stem-loops on the secondary structure where some poly T were existed in the some loops.2. Characteristics in the mitogeonme of CaenorhabditisThe mitogeonme of Caenorhabditis had the following features:(1) The complete mitogeonme were 13,874-14,420 bp in size; (2) The percentage of variable sites in PCGs were far more than rRNAs; (3) coxl, cox2 and cox3 were the most conservative genes in PCGs; (4) All PCGs were under strong purity selection; (5) The AT-rich regions were composed of AT dinucleotide repeat units, direct repeat sequences and inverted repeat sequences composed in which there had conservative fragments; (6) The non-coding region which located between nad4 and coxl could fold into three stem-loops in the secondary structure; (7) There had a other long non-coding region in the mitogeonme of C. briggsae, C. sp.5 and C. tropicalis n. sp., but these regions were not found in the mitogeonme of C. remanei and C. elegans. We preliminarily summarized the length of AT-rich region and the existence of inconstant non-coding region were two of the main reasons for which making the mitogenome of Caenorhabditis species different in size.3. Phylogenetic relationship based on mtDNAWe used the mtDNA of five Caenorhabditis species to rebuild the phylogenetic relationship of this genus. The result showed that using the amino acid sequence of PCGs to construct NJ tree, ML tree and BI tree could effectively reveal the phylogenetic relationship of Caenorhabditis. This result was consistent with the conclusion drew from the research on morphology and molecular biology.The completion of this research could not only enrich the mitochondrial genomic database and offer a new way for authenticating numerous species of Caenorhabditis, but also be a reference model for studying other nematodes mitogeonmes.