Phylomitogenomics of Malacostraca(Arthropoda: Crustacea)

Along with the sequencing technology development and continual enthusiasm of researchers on the mitochondrial genomes, the number of metazoan mitochondrial genomes reported has a tremendous growth in the past decades. Phylomitogenomics—reconstruction of phylogenetic relationships based on mitochondrial genomic data—is now possible across large animal groups. Crustaceans in the class Malacostraca display a high diversity of body forms and include large number of ecologically and commercially important species. In this study, comprehensive and systematic analyses of the phylogenetic relationships within Malacostraca were conducted based on 86 mitochondrial genomes available from Gen Bank. Among 86 malacostracan mitochondrial genomes, 54 species have identical major gene arrangement（excluding t RNAs） to pancrustacean ground pattern,including six species from Stomatopoda, three species from Amphipoda, two krill, seven species from Dendrobranchiata（Decapoda）, and 36 species from Pleocyemata（Decapoda）. However, the other 32 mitochondrial genomes reported exhibit major gene rearrangements. Phylogenies based on Bayesian analyses of nucleotide sequences of the protein-coding genes produced a robust tree with 100% posterior probability at almost all nodes. The results indicate that Amphipoda and Isopoda cluster together（Edriophthalma）（BPP=100）.Phylomitogenomic analyses strong support that Euphausiacea is nested within Decapoda, and closely related to Dendrobranchiata, which is also consistent with the evidence from developmental biology. Yet the taxonomic sampling of mitochondrial genome from Malacostraca is very biased to the order Decapoda, with no complete mitochondrial genomes reported from 11 of the 16 orders. Future researches on sequencing the mitochondrial genomes from a wide variety of malacostracans are necessary to further elucidate the phylogeny of this important group of animals. With the increase in mitochondrial genomes available, phylomitogenomics will emerge as an important component in the Tree of Life researches.

Characterization of mitochondrial genome of sea cucumber Stichopus horrens:A novel gene arrangement in Holothuroidea

The complete mitochondrial DNA sequence contains useful information for phylogenetic analyses of metazoa. In this study, the complete mitochondrial DNA sequence of sea cucumber Stichopus horrens （Holothuroidea： Sdchopodidae： Stichopus） is presented. The complete sequence was determined using normal and long PCRs. The mitochondrial genome of Stichopus horrens is a circular molecule 16257 bps long, composed of 13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes. Most of these genes are coded on the heavy strand except for one protein-coding gene （had6） and five tRNA genes （tRNAser（UcN）, tRNAGtn, tRNAAla, tRNA val, tRNAASp） which are coded on the light strand. The composition of the heavy strand is 30.8% A, 23.7% C, 16.2% G, and 29.3% T bases （AT skew=0.025; GC skew=-0.188）. A non-coding region of 675 bp was identified as a putative control region because of its location and AT richness. The intergenic spacers range from 1 to 50 bp in size, totaling 227 bp. A total of 25 overlapping nucleotides, ranging from 1 to 10 bp in size, exist among 11 genes. All 13 protein-coding genes are initiated with an ATG. The TAA codon is used as the stop codon in all the protein coding genes ex- cept nad3 and nad4 that use TAG as their termination codon. The most frequently used amino acids are Leu （16.29%）, Ser （10.34%） and Phe （8.37%）. All of the tRNA genes have the potential to fold into typical cloverleaf secondary structures. We also compared the order of the genes in the mitochondrial DNA from the five holothurians that are now available and found a novel gene arrangement in the mitochondrial DNA of Stichopus horrens.

Characterization of the first mitochondrial genome of Aclerdidae (Hemiptera: Coccoidea) with a novel gene arrangement

Scale insects comprise a diverse group of insects within superfamily Coccoidea in the suborder Sternorrhyncha,many of them are important pests of economic crops.The advent in next-generation sequencing(NGS)technologies has revolutionized conventional phylogenomic researches,causing a rapid accumulation of sequenced insect mitochondrial genomes.However,there have been few studies on the mitochondrial genome of diverse scale insect groups.By using NGS methods,the complete mitochondrial genome of Nipponaclerda biwakoensis was obtained in this study,representing the first mtDNA of the family Aclerdidae.The whole mitochondrial genome is 16,654 bp in length with an A+T content of 81.3%,including 13 protein-coding genes(PCGs),2 ribosomal RNAs,17 transfer RNAs and a control region.All PCGs begin with typical ATN codons and use standard TAA as their termination codons,except nad1 gene stopping with TAG.Meanwhile,this mitochondrial genome shows a unique gene rearrangement with a long fragment(trnP-trnC-trnI-nad2-trnY-trnT)insertion in the conserved region nad6-cob,which is novel to Hemiptera,even Insecta.The phylogeny reconstruction of Sternorrhyncha based on 13 PCGs and 2 rRNAs under Bayesian Inference method support a robust topology that Aleyrodoidea is the earliest branch of Sternorrhyncha,with Psylloidea as the sister group of the(Aphidoidea+Coccoidea)clade.

The complete mitochondrial genome of Cervaphis quercus （Insecta： Hemiptera： Aphididae： Greenideinae）

The mitochondrial genome of Cervaphis quercus has been sequenced and annotated. The entire genome of 15 272 bp encodes two ribosomal RNA genes （rrnL and rrnS）, 22 transfer RNA （tRNA） genes, 13 protein-coding genes and a control region. The genome has the same gene order as that found in the inferred ancestral insect. Nucleotide composition is highly A＋T biased. All protein-coding genes use standard mitochondrial initiation codons. Secondary structure models of the two ribosomal RNA genes ofC. quercus are similar to those proposed for other insects. All tRNAs have the classic clover-leaf structure, except for the dihydrouridine （DHU） arm of trnS （AGN）, which forms a simpleloop. The presence of structural elements in the control region is also discussed, with an emphasis on the possible regulation of replication and/or transcription. Comparison withmitochondrial genomes of other aphid species shows their gene arrangements are conserved; however, the variety of repeat regions in species from a different aphid subfamily,Aphidinae, suggests that they resulted from independent evolutionary events.

Revaluation of deuterostome phylogeny and evolutionary relationships among chordate subphyla using mitogenome data

The traditional knowledge in textbooks indicated that cephalochordates were the closest relatives to vertebrates among all extant organisms. However, this opinion was challenged by several recent phylogenetic studies using hundreds of nuclear genes. The researchers suggested that urochordates, but not cephalochordates, should be the closest living relatives to vertebrates. In the present study, by using data generated from hundreds of mtDNA sequences, we revalue the deuterostome phylogeny in terms of whole mitochondrial genomes （mitogenomes）. Our results firmly demonstrate that each of extant deuterostome phyla and chordate subphyla is monophyletic. But the results present several alternative phylogenetic trees depending on different sequence datasets used in the analysis. Although no clear phylogenetic relationships are obtained, those trees indicate that the ancient common ancestor diversified rapidly soon after their appearance in the early Cambrian and generated all major deuterostome lineages during a short historical period, which is consistent with ＂Cambrian explosion＂ revealed by paleontologists. It was the 520-million-year＇s evolution that obscured the phylogenetic relationships of extant deuterostomes. Thus, we conclude that an integrative analysis approach rather than simply using more DNA sequences should be employed to address the distant evolutionary relationship.