Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequence and phylogenetic analysis of the complete mitochondrial genome for Hepu mitten crab (Eriocheir hepuensis) from Nanjiujiang River basin.

ABSTRACT: Taxonomic classification of Eriocheir hepuensis was ambiguous, and it has long been controversial. In this study, the whole mitochondrial genome of E. hepuensis was determined to be 16,397?bp, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. A total of 20 intergenic gaps were detected, and the AT content of whole mitochondrial genome was 71.78%. Phylogenetic analysis confirmed that the evolutionary relationship of E. hepuensis, E. sinensis, and E. japonica are most likely to be three species with the same taxonomic status. The whole mitogenome of this species will be useful for the future animal evolutionary, phylogenetic relationship, phylogeny and genomic studies in the genus Eriocheir.

SUBMITTER: Zhang C

PROVIDER: S-EPMC7707772 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Sequence and phylogenetic analysis of the complete mitochondrial genome for Hepu mitten crab (Eriocheir hepuensis) from Nanjiujiang River basin.

Zhang Cheng C Li Qingqing Q Meng Qingguo Q Wang Wen W Cheng Yongxu Y Wu XuGan X

Mitochondrial DNA. Part B, Resources 20191108 2

Taxonomic classification of Eriocheir hepuensis was ambiguous, and it has long been controversial. In this study, the whole mitochondrial genome of E. hepuensis was determined to be 16,397 bp, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. A total of 20 intergenic gaps were detected, and the AT content of whole mitochondrial genome was 71.78%. Phylogenetic analysis confirmed that the evolutionary relationship of E. hepuensi ...[more]

PMID: 33366237

Similar Datasets

Sustainable farming practices of the Chinese mitten crab (Eriocheir sinensis) around Hongze Lake, lower Yangtze River Basin, China.

Project description:Results of a survey of 156 Chinese mitten crab (Eriocheir sinensis) grow-out farms around Hongze Lake (118.48-118.72°E; 33.36-33.38°N) are reported. Area farmed has remained relatively unchanged but production (59 932 t in 2012) increased steadily over the last 7 years, indicative of the viability and sustainability of the farming system that has gradually replaced intensive Chinese major carp polyculture around Hongze Lake. Results showed that production range was 135-2400 kg ha(-1) cycle(-1) (mean 1144 ± 34). Crab yields correlated linearly to stocking density and conformed to a normal distribution curve, with 66.7 % of farms yielding 900 kg ha(-1) cycle(-1) or more. Yield was negatively correlated to pond size and capture size (p < 0.01), and farms with macrophyte coverage rate lower than 30 % of water surface were significantly (p < 0.05) lower than those exceeding 30 %.

| S-EPMC4815763 | biostudies-literature

Draft genome of the Chinese mitten crab, Eriocheir sinensis.

Project description:BackgroundThe Chinese mitten crab, Eriocheir sinensis, is one of the most studied and economically important crustaceans in China. Its transition from a swimming to a crawling method of movement during early development, anadromous migration during growth, and catadromous migration during breeding have been attractive features for research. However, knowledge of the underlying molecular mechanisms that regulate these processes is still very limited.FindingsA total of 258.8 gigabases (Gb) of raw reads from whole-genome sequencing of the crab were generated by the Illumina HiSeq2000 platform. The final genome assembly (1.12 Gb), about 67.5 % of the estimated genome size (1.66 Gb), is composed of 17,553 scaffolds (>2 kb) with an N50 of 224 kb. We identified 14,436 genes using AUGUSTUS, of which 7,549 were shown to have significant supporting evidence using the GLEAN pipeline. This gene number is much greater than that of the horseshoe crab, and the annotation completeness, as evaluated by CEGMA, reached 66.9 %.ConclusionsWe report the first genome sequencing, assembly, and annotation of the Chinese mitten crab. The assembled draft genome will provide a valuable resource for the study of essential developmental processes and genetic determination of important traits of the Chinese mitten crab, and also for investigating crustacean evolution.

| S-EPMC4730596 | biostudies-literature

Near-Full-Length Genome Sequence of a Novel Reovirus from the Chinese Mitten Crab, Eriocheir sinensis.

Project description:A novel Eriocheir sinensis reovirus (EsRV) was identified using deep-sequencing techniques in crabs afflicted with trembling disease (TD). Near-full-length genome sequences of 12 segments of EsRV were obtained. The genome of EsRV will facilitate further studies on the causative agent of TD.

| S-EPMC4440949 | biostudies-literature

A transcriptome analysis of mitten crab testes (Eriocheir sinensis).

Project description:The identification of expressed genes involved in sexual precocity of the mitten crab (Eriocheir sinensis) is critical for a better understanding of its reproductive development. To this end, we constructed a cDNA library from the rapid developmental stage of testis of E. sinensis and sequenced 3,388 randomly picked clones. After processing, 2,990 high-quality expressed sequence tags (ESTs) were clustered into 2,415 unigenes including 307 contigs and 2,108 singlets, which were then compared to the NCBI non-redundant (nr) protein and nucleotide (nt) database for annotation with Blastx and Blastn, respectively. After further analysis, 922 unigenes were obtained with concrete annotations and 30 unigenes were found to have functions possibly related to the process of reproduction in male crabs - six transcripts relevant to spermatogenesis (especially Cyclin K and RecA homolog DMC1), two transcripts involved in nuclear protein transformation, two heat-shock protein genes, eleven transcription factor genes (a series of zinc-finger proteins), and nine cytoskeleton protein-related genes. Our results, besides providing valuable information related to crustacean reproduction, can also serve as a base for future studies of reproductive and developmental biology.

| S-EPMC3085360 | biostudies-literature

Sixteen polymorphic simple sequence repeat markers from expressed sequence tags of the Chinese Mitten Crab Eriocheir sinensis.

Project description:The Chinese mitten crab (Eriocheir sinensis) is an economically important aquaculture species in China. In this study, we developed and evaluated simple sequence repeat markers from expressed sequence tags of E. sinensis. Among the 40 wild E. sinensis individuals tested, 16 loci were polymorphic. The number of alleles per locus ranged from two to ten. The observed heterozygosity ranged from 0.0667 to 0.9667, whereas the expected heterozygosity ranged from 0.0661 to 0.9051. These markers have the potential for use in genetic studies of population structure and intraspecific variation in E. sinensis.

| S-EPMC2996744 | biostudies-literature

The complete mitochondrial genome sequence of the Metschnikowia bicuspidata (Metschnikoff, 1884), an emerging pathogen of 'milky disease' in Chinese mitten crab.

Project description:The outbreak of milky disease of Chinese mitten crab caused by M. bicuspidata seriously restricted the development of the crab industry. In this study, the mitochondrial genome sequence of M. bicuspidata was assembled, annotated, and further analyzed. The results indicated that the complete mitochondrial genome of M. bicuspidata was 75,095 bp, which contained two rRNAs, 23 tRNAs, and 13 protein-coding genes. The phylogenetic tree of 13 yeasts based on the complete mitochondrial genome was constructed which showed that M. bicuspidata (accession number OK514652) and M. bicuspidata (accession number MW147605.1) were clustered in a clade. To sum up, our research results would further provide essential data for the systematics and evolution study of M. bicuspidata.

| S-EPMC9278424 | biostudies-literature

Characterization of the complete mitochondrial genome of Eriocheir leptognathus with phylogenetic analysis.

Project description:Eriocheir leptognathus is a dominant species in the Yangtze River estuary. In this study, we first determined the complete mitochondrial genome (mitogenome) of E. leptognathus. The mitogenome is 16,143 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one non-coding control region. Initiation codons ATG and ATT were identified in eight and four PCGs, respectively, while stop codons TAA or TAG were found in eleven genes except for two genes which use incomplete stop codon T-. The phylogenetic analysis indicated that three species (E. hepuensis, E.japonica, E. sinensis) and E. leptognathus are very closely related. The complete mitogenome of E. leptognathus can provide population genetics information to further explore the taxonomic status of this species.

| S-EPMC7510619 | biostudies-literature

Identification and characterization of thirty novel microsatellite DNA markers from the Chinese mitten crab Eriocheir sinensis expressed sequence tags.

Project description:BackgroundThe Chinese mitten crab Eriocheir sinensis is an economically important decapod crustacean in China. Despite a widespread distribution and production in China, the resources of E. sinensis have experienced a dramatic decline in the past decades. Here we describe a new set of novel polymorphic microsatellite loci to facilitate the investigation of genetic structure and artificial breeding.ResultsIn this study, a set of 30 novel polymorphic microsatellite markers for E. sinensis was developed from EST databases. The number of alleles per locus ranged from three to twenty. The observed and expected heterozygosities ranged from 0.047 to 0.932 and from 0.047 to 0.935, respectively.ConclusionsThese informative microsatellite markers will be useful in studies of genetics, genomics and marker-assisted selection breeding in E. sinensis.

| S-EPMC4756445 | biostudies-literature

Effects of dietary lipids on the hepatopancreas transcriptome of Chinese mitten crab (Eriocheir sinensis).

Project description:Fish oil supplies worldwide have declined sharply over the years. To reduce the use of fish oil in aquaculture, many studies have explored the effects of fish oil substitutions on aquatic animals. To illustrate the effects of dietary lipids on Chinese mitten crab and to improve the use of vegetable oils in the diet of the crabs, 60 male juvenile Chinese mitten crabs were fed one of five diets for 116 days: fish oil (FO), soybean oil (SO), linseed oil (LO), FO + SO (1:1, FSO), and FO + LO (1:1, FLO). Changes in the crab hepatopancreas transcriptome were analyzed using RNA sequencing. There were a total 55,167 unigenes obtained from the transcriptome, of which the expression of 3030 was significantly altered in the FLO vs. FO groups, but the expression of only 412 unigenes was altered in the FSO vs. FO groups. The diets significantly altered the expression of many enzymes involved in lipid metabolism, such as pancreatic lipase, long-chain acyl-CoA synthetases, carnitine palmitoyltransferase I, acetyl-CoA carboxylase, fatty acid synthase, and fatty acyl ?9-desaturase. The dietary lipids also affected the Toll-like receptor and Janus activated kinase-signal transducers and activators of transcription signaling pathways. Our results indicate that substituting fish oil with vegetable oils in the diet of Chinese mitten crabs might decrease the digestion and absorption of dietary lipids, fatty acids biosynthesis, and immunologic viral defense, and increase ?-oxidation by altering the expression of the relevant genes. Our results lay the foundation for further understanding of lipid nutrition in Chinese mitten crab.

| S-EPMC5533325 | biostudies-literature

Functional Analysis of KIF3A and KIF3B during Spermiogenesis of Chinese Mitten Crab Eriocheir sinensis.

Project description:BackgroundSpermatogenesis represents the transformation process at the level of cellular development. KIF3A and KIF3B are believed to play some roles in the assembly and maintenance of flagella, intracellular transport of materials including organelles and proteins, and other unknown functions during this process. During spermatogenesis in Eriocheir sinensis, if the sperm shaping machinery is dependent on KIF3A and KIF3B remains unknown.Methodology/principal findingsThe cDNA of KIF3A and KIF3B were obtained by designing degenerate primers, 3'RACE, and 5'RACE. We detected the genetic presence of kif3a and kif3b in the heart, muscle, liver, gill, and testis of E. sinensis through RT-PCR. By western blot analysis, the protein presence of KIF3A and KIF3B in heart, muscle, gill, and testis reflected the content in protein level. Using in situ hybridization and immunofluorescence, we could track the dynamic location of KIF3A and KIF3B during different developmental phases of sperm. KIF3A and KIF3B were found surrounding the nucleus in early spermatids. In intermediate spermatids, these proteins expressed at high levels around the nucleus and extended to the final phase. During the nuclear shaping period, KIF3A and KIF3B reached their maximum in the late spermatids and were located around the nucleus and concentrated in the acrosome to some extent.Conclusions/significanceOur results revealed that KIF3A and KIF3B were involved in the nuclear and cellular morphogenesis at the levels of mRNA and protein. These proteins can potentially facilitate the intracellular transport of organelles, proteins, and other cargoes. The results represent the functions of KIF3A and KIF3B in the spermatogenesis of Crustacea and clarify phylogenetic relationships among the Decapoda.

| S-EPMC4037190 | biostudies-literature