Binlun Yan

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 GenBank. Among 86 malacostracan mitochondrial genomes, 54 species have identical major gene arrangement (excluding tRNAs) 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.

Mitogenomics reveals two subspecies in Coelomactra antiquata (Mollusca: Bivalvia)

The mitochondrial genome sequence of Coelomactra antiquata (Mollusca: Bivalvia) in Zhangzhou (zz-mtDNA) was fully sequenced and compared with that in Rizhao (rz-mtDNA) in this study. A tRNA (tRNA Met ) located between tRNA Ala and cox1 genes was identified in zz-mtDNA but not in rz-mtDNA. The largest non-coding region (NCR; MNR) contained 11 copies 99nt tandem repeat sequences exclusively in rz-mtDNA, while the second largest NCR with 400 bp between tRNA Ala and tRNA Met in zz-mtDNA was absent in rz-mtDNA. Secondary structures of ZZ and RZ C. antiquata rRNAs are significantly different. The mitochondrial genomic characteristics clearly indicate that there are at least two subspecies in C. antiquata.

The complete mitochondrial genome of the clam Mactra veneriformis (Bivalvia: Mactridae): Has a unique non-coding region, missing atp8 and typical tRNASer

Mactra veneriformis (Bivalvia: Mactridae) is one commonly cultured bivalve species in the western Pacific Ocean. In the current study, the complete mitrochondrial DNA (mtDNA) of the clam M. veneriformis was determined. The M. veneriformis mt genome is 16,854 bp in length and encodes 34 genes on the same strand, including 12 protein-coding genes (PCGs), 2 ribosomal RNA genes and 20 transfer RNA genes. The length of 12 PCGs is 11,358 bp, which accounts for 67.4% in whole mt genome. The proportion is similar to other clams mt genomes and within those of bivalves mt genomes. Gene order (which is the same as that of RZ C. antiquata) of M. veneriformis mt genome is compared with that of other veneroids. Compared with the typical gene content of animal mt genomes, atp8 and two tRNA Ser genes are missing in the mt genome. All non-coding regions are 1978 bp in length, among them the longest one is speculated as the control region, which is located between the tRNA His and tRNA Arg . The secondary largest non-coding region (NCR664) between the tRNA Gln and tRNA Thr in the M. veneriformis mt genome contains one section of tandem repeats (125 nt × 5.2 or 249 nt × 2.6). The tandem repeats account for 97.89% (650/664) of the NCR664, which is a unique characteristic of the M. veneriformis mt non-coding regions compared with those of other veneroids.

A new heat shock protein 70 gene (HSC70) and its expression profiles in response to cadmium stress and after different post-moulting times in Exopalaemon carinicauda (Holthuis, 1950) (Decapoda, Palaemonidae)

In this study, the full-length cDNA sequence (GenBank accession number AGF80339.1) encoding a novel heat shock protein HSP70 family member (Heat shock cognate 70, EcHSC70) was cloned from the ridgetail white prawn, Exopalaemon carinicauda (Holthuis, 1950) [currently also as: Palaemon carinicauda Holthuis, 1950]. EcHSC70 full-length cDNA consists of 2452xa0bp, containing an open reading frame (ORF) of 1935xa0bp, and it encodes a 650-amino-acid protein with a theoretical size of about 71xa0kDa and a predicted isoelectric point of 5.32. Phylogenetic analysis showed that EcHSC70 can be categorized together with the known HSP70 family members reported in other crustaceans. Tissue-expression analysis revealed that EcHSC70 was constitutively expressed in all of the tested tissues, with a significantly increased expression in the gill post-moulting. Moreover, the relative mRNA level of EcHSC70 tended to increase in the early stages of post-moulting (from 0 to 5xa0min), suggesting that EcHSC70 might take part in the recovery of E. carinicauda after moulting. In addition, under different levels of cadmium stress, EcHSC70 tended to be significantly expressed only after 24xa0h of cadmium exposure, and was more inducible by low concentrations of cadmium, as opposed to high concentrations.

Cloning of the ANT gene and its expression profiles at different developmental stages and post-molting times in the ridgetail white prawn Exopalaemon carinicauda

To investigate the roles of the ANT gene, which codes for adenine nucleotide translocase (ANT) during crustacean development, a full-length cDNA sequence of EcANT in the ridgetail white prawn Exopalaemon carinicauda, was cloned, and its expression profile was analyzed at different developmental stages and post-molting times. The EcANT gene (GenBank accession number: KP892663) contained an open reading frame of 924xa0bp encoding a 307 amino acid protein with a theoretical size of about 33.42xa0kDa and a predicted isoelectric point of 9.77. Tissue expression analysis revealed that EcANT was mainly expressed in muscle and its expression level tended to increase with the developmental stages. In addition, the expression level of EcANT after molting increased following the lengthening of post-molting time. Our results suggest that EcANT is an important gene related to the growth and development of E. carinicauda.

The first representative of Coelomactra antiquata mitochondrial genome from Liaoning (China) and phylogenetic consideration

Abstract Coelomactra antiquata is a famous delicacy and a promising new candidate for aquaculture, which belongs to the family Mactridae (Mollusca: Veneroida). The complete mitochondrial genome of C. antiquata (Liao Ning province, in China, LN) was finished, which is the first representative from this province. The results showed that the total length of LN-mtDNA sequence is 16,797u2009bp and the content of Au2009+u2009T is 65.01%. It encodes 35 genes, including 12 protein-coding genes, 21 transfer RNA genes and two ribosomal RNA genes. All coding genes are encoded on the heavy strand. Compared with the typical gene content of animal mitochondrial genomes, atp8 and trnSer(UCN) genes are missing in the mitochondrial genome. The complete mitochondrial genome contains 26 non-coding regions (1598u2009bp), one major non-coding region consists of 1046u2009bp in which 4.9 tandem repeat sequences (99bp per sequence) was observed. The phylogenetic tree showed that Liaoning population was clustered into one clade with Shandong (Rizhao, Jiaonan and Jimo) and Guangxi (Beihai) populations, meanwhile all of them are far from the Fujian populations (Pingtan, Zhangzhou and Changle). So, Liaoning, Shandong and Guangxi populations have a close relationship. Actually, Fujian is located between Liaoning, Shandong and Guangxi. So, the result challenges the previously assumed relevance between geographic distance and genetic distance. The genetic distance of Liaoning C. antiquata and Fujian (Changle, Zhangzhou and Pingtan) C. antiquata (0.176–0.177) is greater than the genetic distance between Mytilus galloprovincialis and Mytilus trossulus (0.160). The genetic difference of Liaoning population and Fujian populations has reached species level.

The complete mitochondrial genome of the Japanese threadfin bream, Nemipterus japonicus (Teleostei, Nemipteridae)

Abstract The complete mitochondrial sequence of the Japanese threadfin bream, Nemipterus japonicus has been determined. The circle genome is 16,995u2009bp in size, and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of N. japonicus was similar to that of most other teleosts. The base composition of H-strand is 28.11% (A), 28.02% (T), 16.64 % (G) and 27.24 % (C), with an AT content of 56.12%. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of N. japonicus presented will be in favor of resolving phylogenetic relationships within the family Nemipteridae and the Perciformes.

The complete mitochondrial genome of the redeye mullet Liza haematocheila (Teleostei, Mugilidae).

Abstract The complete mitochondrial sequence of the redeye mullet Liza haematocheila has been determined. The circle genome is 16,822u2009bp in size, and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of L. haematocheila was similar to that of most other teleosts. The base composition of H-strand is 26.42% (A), 26.38% (T), 16.72% (G) and 30.47% (C), with an AT content of 52.8%. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of L. haematocheila presented will be in favor of resolving phylogenetic relationships within the family Scatophagidae and the Mugiliformes.

Complete mitochondrial genome of the spotted scat Scatophagus argus (Teleostei, Scatophagidae).

Abstract The spotted scat, Scatophagus argus (Perciformes, Scatophagidae), is a recreational and commercial fish in China. In this paper, the complete mitochondrial genome of S. argus was firstly determined. It is 16,783u2009bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. Except for the eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the heavy strand. The mitochondrial DNA information would be useful in species identification and natural resources conservation.

cDNA cloning and expression characterization of serum transferrin gene from oriental weatherfish Misgurnus anguillicaudatus

In this study, the cDNA coding serum transferrin (stf) of Misgurnus anguillicaudatus (mastf) was cloned. mastf cDNA is composed of 2326 bp with a 2007 bp open reading frame encoding 668 amino acids. The deduced Mastf protein consists of a signal peptide, two lobes (N and C-lobes) and signature motifs of transferrin (Tf) family. The results of tissue distribution indicated that mastf mRNA was predominantly expressed in the liver. The results indicate that the mastf expression increased significantly in liver, blood, spleen and head kidney after the challenge with Aeromonas sobria, acting as a positive acute protein, suggesting that mastf is related to the immune response. The cloning and expression analysis of mastf further demonstrates the evolutionary conservation of Stf and immune function in vertebrates.