Hongyu Ma

The complete mitochondrial genome of the swimming crab Charybdis natator (Herbst) (Decapoda: Brachyura: Portunidae) and its phylogeny

Abstract The complete mitochondrial genome of Charybdis natator (family Portunidae) was obtained using Illumina and Sanger dideoxy sequencing. This genome was a typically circular molecule with a length of 15,664u2009bp and encoded 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition of this mitogenome was 34.00% for A, 11.06% for G, 36.36% for T, and 18.58% for C, respectively, with a higher Au2009+u2009T content (70.36%). The gene composition and arrangement were accordant to the closely published species. The phylogenetic analysis suggested that C. natator had the closest relationship with C. japonica.

Genetic structure and historical demography of the blue swimming crab (Portunus pelagicus) from southeastern sea of China based on mitochondrial COI gene

Abstract In this study, the population genetic structure and historical demography of the blue swimming crab, Portunus pelagicus, from southeastern sea of China were investigated using cytochrome c oxidase subunit I (COI) gene of mitochondrion. A total of 889u2009bp segment of COI gene was sequenced, which showed a high haplotype diversity (0.6833–0.8142) and low nucleotide diversity (0.0021–0.0034). Among 30 haplotypes defined in this study, one (H1) was the most dominant (47.7%) and shared by each locality, while the majority (23) were rare and only existed in one individual. The AMOVA analysis revealed a limited population genetic structure, which suggested a high level of gene flow along the distribution areas of China. This conclusion was supported by the pairwise FST comparison values. The topology of the neighbour-joining tree constructed using 30 haplotypes from four localities presented two distinct clades (clade A and clade B). Meanwhile, three sequences of P. pelagicus downloaded from NCBI database showed a high-level divergence with the individuals collected in our study, which might form a new cryptical species. The individuals of clade B were cryptically embedded in the whole population, with a low frequency (7.7–24.2%), while clade A accounted for 75.8–92.3%. Neutrality tests and mismatch analyses suggested a late Pleistocene population expansion for both clade A (47,000–66,000 years ago) and clade B (74,000–100,000 years ago). This study should provide insight into phylogeny, population genetic structure, conservation genetics, and sustainable management of P. pelagicus.

Comparative Transcriptome Analysis Provides Insights into Differentially Expressed Genes and Long Non-Coding RNAs between Ovary and Testis of the Mud Crab (Scylla paramamosain)

The molecular mechanism underlying sex determination and gonadal differentiation of the mud crab (Scylla paramamosain) has received considerable attention, due to the remarkably biological and economic differences between sexes. However, sex-biased genes, especially non-coding genes, which account for these differences, remain elusive in this crustacean species. In this study, the first de novo gonad transcriptome sequencing was performed to identify both differentially expressed genes and long non-coding RNAs (lncRNAs) between male and female S. paramamosain by using Illumina Hiseq2500. A total of 79,282,758 and 79,854,234 reads were generated from ovarian and testicular cDNA libraries, respectively. After filtrating and de novo assembly, 262,688 unigenes were produced from both libraries. Of these unigenes, 41,125 were annotated with known protein sequences in public databases. Homologous genes involved in sex determination and gonadal development pathways (Sxl-Tra/Tra-2-Dsx/Fru, Wnt4, thyroid hormone synthesis pathway, etc.) were identified. Three hundred and sixteen differentially expressed unigenes were further identified between both transcriptomes. Meanwhile, a total of 233,078 putative lncRNAs were predicted. Of these lncRNAs, 147 were differentially expressed between sexes. qRT-PCR results showed that nine lncRNAs negatively regulated the expression of eight genes, suggesting a potential role in sex differentiation. These findings will provide fundamental resources for further investigation on sex differentiation and regulatory mechanism in crustaceans.

The complete mitochondrial genome and phylogenetic analysis of Matuta planipes (Decapoda: Brachyura: Matutidae)

Abstract The complete mitochondrial genome of Matuta planipes was obtained using long and conventional PCR method. The circular genome was 15,760u2009bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region. Of the 37 genes, 23 were encoded by the heavy strand, while the others were encoded by the light strand. The genome composition with Au2009+u2009T bias (70.82%) and gene arrangement were largely identical to those observed in most arthropods, such as the mud crab (Scylla paramamosain). The phylogenetic analysis suggested that M. planipes was closest to Ashtoret lunaris. The newly described mitochondrial genome may provide valuable data for phylogenetic analysis for Matutidae.

Transcriptome-seq provides insights into sex-preference pattern of gene expression between testis and ovary of the crucifix crab (Charybdis feriatus)

The crucifix crab, Charybdis feriatus, which mainly inhabits Indo-Pacific region, is regarded as one of the most high-potential species for domestication and incorporation into the aquaculture sector. However, the regulatory mechanisms of sex determination and differentiation of this species remain unclear. To identify candidate genes involved in sex determination and differentiation, high throughput sequencing of transcriptome from the testis and ovary of C. feriatus was performed by the Illumina platform. After removing adaptor primers, low-quality sequences and very short (<50 nt) reads, we obtained 80.9 million and 66.2 million clean reads from testis and ovary, respectively. A total of 86,433 unigenes were assembled, and ~43% (37,500 unigenes) were successfully annotated to the NR, NT, Swiss-Prot, KEGG, COG, GO databases. By comparing the testis and ovary libraries, we obtained 27,636 differentially expressed genes. Some candidate genes involved in the sex determination and differentiation of C. feriatus were identified, such as vasa, pgds, vgr, hsp90, dsx-f, fem-1, and gpr. In addition, 88,608 simple sequence repeats were obtained, and 61,929 and 77,473 single nucleotide polymorphisms from testis and ovary were detected, respectively. The transcriptome profiling was validated by quantitative real-time PCR in 30 selected genes, which showed a good consistency. The present study is the first high-throughput transcriptome sequencing of C. feriatus. These findings will be useful for future functional analysis of sex-associated genes and molecular marker-assisted selections in C. feriatus.

The complete mitochondrial genome of Varuna yui (Decapoda: Brachyura: Varunidae) and its phylogeny

Abstract The complete mitochondrial genome plays an important role in the research on phylogenetic relationship. Here, we reported the first complete mitochondrial genome sequence of Varuna yui Hwang & Takeda, 1986 (Varunidae). The complete mtDNA (15,915u2009bp in length) consisted of 13 protein-coding genes, 22 tRNAs, two rRNA genes, and a control region. The gene arrangement was identical to those observed in the Varunidae species. The phylogenetic analysis suggested that V. yui had close relationship with other Varunidae species (Helicetient sinensis, Eriocher sinesis, etc.). The newly described genome may facilitate further comparative mitogenomic analysis within Varunidae species.

C-type lectin B ( Sp CTL-B) regulates the expression of antimicrobial peptides and promotes phagocytosis in mud crab Scylla paramamosain

&NA; As pattern recognition receptors, C‐type lectins (CTLs) play important roles in immune system of crustaceans through identifying and binding to the conservative pathogen‐associated molecular patterns (PAMPs) on pathogen surfaces. In this study, a new CTL, SpCTL‐B, was identified from the hemocytes of mud crab Scylla paramamosain. The full‐length of SpCTL‐B cDNA was 1278 bp with an open reading frame (ORF) of 348 bp. The predicted SpCTL‐B protein contains a single carbohydrate‐recognition domain (CRD). SpCTL‐B transcripts were distributed in all examined tissues with the highest levels in hepatopancreas. After challenged with Vibrio parahaemolyticus, LPS, polyI:C and white spot syndrome virus (WSSV), the mRNA levels of SpCTL‐B in hemocytes and hepatopancreas were up‐regulated. The recombinant SpCTL‐B (rSpCTL‐B) purified by Ni‐affinity chromatography showed stronger binding activities with Staphylococcus aureus, &bgr;‐hemolytic Streptococcus, Escherichia coli, Aeromonas hydrophila, Vibrio alginolyticus than those with V. parahaemolyticus and Saccharomyces cerevisiae. rSpCTL‐B exhibited a broad spectrum of microorganism‐agglutination activities against Gram‐positive bacteria (S. aureus, &bgr;‐hemolytic Streptococcus) and Gram‐negative bacteria (E. coli, V. parahaemolyticus, A. hydrophila, V. alginolyticus) in a Ca2+‐dependent manner. The agglutination activities of rSpCTL‐B could be inhibited by D‐mannose and LPS, but not by D‐fructose and galactose. The antimicrobial assay showed that rSpCTL‐B exhibited the growth inhibition against all examined gram‐positive bacteria and gram‐negative bacteria. When SpCTL‐B was silenced by RNAi, the bacterial clearance ability in mud crab was decreased and the transcript levels of five antimicrobial peptides (AMPs) (SpCrustin, SpHistin, SpALF4 (anti‐lipopolysaccharide factor), SpALF5 and SpALF6) were significantly decreased in hemocytes. In our study, knockdown of SpCTL‐B could down‐regulate the expression of SpSTAT at mRNA transcriptional level and protein translational level in mud crab. Meantime, the phagocytosis rate and the expression of three phagocytosis related genes were declined after RNAi of SpCTL‐B in hemocytes in mud crab. Collectively, our results suggest that SpCTL‐B might play its roles as a pattern recognition receptor (PRR) in immune response towards pathogens infection through influencing the expression of AMPs and the phagocytosis of hemocytes in mud crab S. paramamosain.

The complete mitochondrial genome sequence and gene organization of Ambassis gymnocephalus (Perciformes, Ambassidae)

Abstract In this study, we firstly obtained the complete mitochondrial genome DNA sequence of the Ambassis gymnocephalus. Its length is 17,388u2009bp, containing 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a large noncoding region. The overall length of protein coding genes is 11,448u2009bp, including A (26.75%), G (15.20%), T (26.44%) and C (31.61%). The Au2009+u2009T content of control region (1555u2009bp) is 60.45%. The protein-coding gene COI is started by GTG and ended by AGA. From the phylogenetic tree, we find A. gymnocephalus and Oreochromis niloticus has the closest relationship among 21 related species. This work will provide some valuable information for further studies on A. gymnocephalus and the family Ambassidae.

The complete mitochondrial genome of Stolephorus commersonii

Abstract In this study, the complete mitochondrial genome of Stolephorus commersonii is determined. It is 16,734u2009bp in length and consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. Phylogenetic tree was constructed based on the complete mitogenome of S. commersonii and closely related 17 other species to assess its phylogenic relationship and evolution. The findings of the study will contribute to the phylogenetic classification and the genetic conservation management of S. commersonii.

On Types of Sexual Maturity in Brachyurans, with Special Reference to Size at the Onset of Sexual Maturity

ABSTRACT n Sexual maturity is an important phase of brachyurans life cycle as it marks the transition of becoming an adult and the ability to reproduce. This article discussed on the types of sexual maturity found in brachyurans and the implication and application of size at the onset of sexual maturity (SOM) in general. In addition, data on the estimates of SOM of brachyurans were collected on a global scale for the period 1971–2015. The 220 maturity data were representative of 133 brachyuran stocks from 23 families and 55 species. The effect of sampling methods and indicators used for the estimation of SOM were highlighted as well. Variation in the carapace width at which 50% of the population reaches maturity (CW50) was apparent between families, species, sexes, and populations within the same species, in addition to latitudinal and temporal variation. The CW50 was in a positive linear relationship with the maximum size (CWmax) for males (logCW50 = -0.28 + 1.01logCWmax; R2 = 0.85, P < 0.001), females (logCW50 = -0.35 + 1.08logCWmax; R2 = 0.96, P < 0.001), and specifically Portunidae (logCW50 =-0.88 + 1.32logCWmax; R2 = 0.69, P < 0.001). The size at maturity data in this review serve as guidelines for stock assessment and sustainable population management of brachyuran species.