Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next-generation sequencing yields the complete mitogenome of red-crowned crane (G. japonensis).

ABSTRACT: In this study, the complete mitogenome sequence of red-crowned crane (G. japonensis) has been decoded by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 16,727?bp, has unique 14 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for red-crowned crane phylogeny.

SUBMITTER: Hua R

PROVIDER: S-EPMC7799631 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Next-generation sequencing yields the complete mitogenome of red-crowned crane (G. japonensis).

Hua Rong R Cui Duoying D Liu Jia J You Yuyan Y Jia Ting T

Mitochondrial DNA. Part B, Resources 20180428 2

In this study, the complete mitogenome sequence of red-crowned crane (G. japonensis) has been decoded by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 16,727 bp, has unique 14 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for red-crowned crane phylogeny. ...[more]

PMID: 33474238

Similar Datasets

Next-generation sequencing yields the complete mitogenome of wattled crane (Bugeranus carunculatus).

Project description:In this study, the complete mitogenome sequence of wattled crane (Bugeranus carunculatus) has been decoded by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 16,679?bp, has unique 14 protein-coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for wattled crane phylogeny.

| S-EPMC7799669 | biostudies-literature

Virome characterization of diarrheic red-crowned crane (G. japonensis).

Project description:BackgroundThe red-crowned crane is one of the vulnerable bird species. Although the captive population has markedly increased over the last decade, infectious diseases can lead to the death of young red-crowned cranes while few virological studies have been conducted.MethodsUsing a viral metagenomics approach, we analyzed the virome of tissues of the dead captive red-crowned crane with diarrhea symptoms in Dongying Biosphere Reserve, Shandong Province, China and feces of individual birds breeding at the corresponding captive breeding center, which were pooled separately.ResultsThere is much more DNA and RNA viruses in the feces than that of the tissues. RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Parvoviridae, associated with enteric diseases were detected in the tissues and feces. Genomes of the picornavirus, genomovirus, and parvovirus identified in the study were fully characterized, which further suggested that infectious viruses of these families were possibly presented in the diseased red-crowned crane.ConclusionRNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Genomoviridae and Parvoviridae were possibly the causative agent for diarrhea of red-crowned crane. This study has expanded our understanding of the virome of red-crowned crane and provides a baseline for elucidating the etiology for diarrhea of the birds.

| S-EPMC10902971 | biostudies-literature

Mitochondrial Genome Sequence of Echinostoma revolutum from Red-Crowned Crane (Grus japonensis).

Project description:Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.

| S-EPMC7066449 | biostudies-literature

Breeding range shift of the red-crowned crane (Grus japonensis) under climate change.

Project description:The red-crowned crane (Grus japonensis) is an endangered species listed by International Union for Conservation of Nature (IUCN) HARRIS J (2013). The largest population of this species is distributed mainly in China and Russia, which is called continental population SU L (2012)-Curt D (1996). This population is migratory, which migrates from its breeding range located in Northeast China and Southern Russia, to the wintering range in the south of China to spend the winter every year. The breeding range of this species is critical for red-crowned crane to survive and maintain its population. Previous studies showed the negative effects of habitat loss and degradation on the breeding area of red-crowned crane Ma Z (1998), Claire M (2019). Climate change may also threat the survival of this endangered species. Previous studies investigated the impacts of climate change on the breeding range or wintering range in China Wu (2012), [1]. However, no study was conducted to assess the potential impacts of climate change on the whole breeding range of this species. Here, we used bioclimatic niche modeling to predict the potential breeding range of red-crowned crane under current climate conditions and project onto future climate change scenarios. Our results show that the breeding range of the continental population of red-crowned crane will shift northward over this century and lose almost all of its current actual breeding range. The climate change will also change the country owning the largest portion of breeding range from China to Russia, suggesting that Russia should take more responsibility to preserve this endangered species in the future.

| S-EPMC7067427 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of the Shaw's sea-snake (Squamata: Elapidae).

Project description:We report the complete mitogenome of Hydrophis curtus, which is 17,702?bp in size and includes 13 protein-coding (PCGs), two rRNA genes, 22 tRNA genes, and two control regions. PCGs, with 13 genes, are 11,261?bp in length. All PCGs use as the start codon ATN except ND1 (CTA) and COX1 (GTG); ATP8, ATP6, ND4L, ND5, and Cytb use the typical stop codon TAA; but COX2 and ND4 with a single T-. Phylogeny recon-structed using the Bayesian inference (BI) method with 13 PCGs indicates that H. curtus at the root of Laticaudinae.

| S-EPMC7707276 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of stony coral (Favites abdita).

Project description:In this study, the complete mitogenome sequence of stony coral, Favites abdita (Scleractinia), has been decoded for the first time by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 17,825?bp, has unique 13 protein-coding genes (PCGs), 2 transfer RNAs and 3 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral phylogeny.

| S-EPMC7800620 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of Niya chicken (Gallus gallus).

Project description:In this study, the complete mitochondrial genome sequence of Niya chicken (Gallus gallus) was obtained by using the next-generation sequencing technology for the first time. The complete mitogenome sequence of Niya chicken is 16,784 bp in length, containing 2 ribosomal RNAs, 13 protein-coding genes, 22 transfer RNA genes and a D-loop region. Our work provides a valuable source of data for phylogenetic studies and helps us to understand the maternal origins of the native chickens.

| S-EPMC7782777 | biostudies-literature

Next generation sequencing yields the complete mitogenome of Smith's zokor (Eospalax smithii).

Project description:Sequencing analysis of mitochondrial genomes is useful for understanding the genome structures. In this study, complete mitochondrial genomes of the Eospalax smithii was obtained by using next generation sequencing method. The complete mitogenome of E. smithii was 16,350 bp long, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding control region (D-loop). The overall base composition of the heavy strand is A (33.65%), C (23.80%), T (30.31%), and G (12.24%). The base compositions present highly biased toward A + T nucleotides. The result of phylogenetic analysis showed the five Eospalax species formed a monophyly with the high bootstrap value and as a sister group of the genus Myospalax. This is the first report of the complete mitochondrial genomes of E. smithii and the mitogenome is potentially important for evolutionary biology, population genetics, and species diagnosis studies of the Mysopalacinae.

| S-EPMC7510577 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of the blue-banded sea-snake (Squamata: Elapidae).

Project description:We report the complete mitogenome of Hydrophis cyanocinctus, which is 17,750 bp in size and includes 13 protein-coding (PCGs), 2 rRNA genes, 22 tRNA genes, and 2 control regions. PCGs, with 13 genes, is 11,427 bp in length. All PCGs use ATN as the typical start codon except COX1 with GTG; the TAG was found as the stop codon in ND1 and ND2, the AGA was found as the stop codon in COI and ND6, the TAA was found as the stop codon in ATP8, ATP6, ND4L, ND5 and Cytb; while other 3 PCGs stop with a single T. Phylogeny reconstructed using the Bayesian inference (BI) method with 13 PCGs indicates the presence of H. cyanocinctus at the root of Laticaudinae.

| S-EPMC7687521 | biostudies-literature

Next-generation sequencing yields the complete mitogenome of Caridina multidentata and phylogenetic analysis.

Project description:In this study, the complete mitochondrial genome (mitogenome) of Caridina multidentata is reported for the first time. These data demonstrate that the C. multidentata mitochondrial genome is a 15,825 bp circular molecule and encodes the typical 37 metazoan mitochondrial genes [13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs)] and an A + T-rich control region. The genome composition was highly A + T biased 63.45% and showed negative AT-skew (-0.131) and slightly possitive GC-skew (0.018). The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for shrimps.

| S-EPMC7799520 | biostudies-literature