scispace - formally typeset
Search or ask a question
Institution

Chinese Academy of Fishery Sciences

NonprofitBeijing, China
About: Chinese Academy of Fishery Sciences is a nonprofit organization based out in Beijing, China. It is known for research contribution in the topics: Population & Gene. The organization has 8107 authors who have published 7929 publications receiving 92095 citations. The organization is also known as: Zhōngguó shuǐchǎn Kēxuéyánjiūyuàn & Chinese Academy of Fishery Sciences.
Topics: Population, Gene, Shrimp, Mitochondrial DNA, Genome


Papers
More filters
Journal ArticleDOI
19 Mar 2013-PLOS ONE
TL;DR: This study reports the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data, and provides a high-resolution strategy for large-scale genotyping that can be generally applicable to various species and populations.
Abstract: Large-scale genotyping plays an important role in genetic association studies. It has provided new opportunities for gene discovery, especially when combined with high-throughput sequencing technologies. Here, we report an efficient solution for large-scale genotyping. We call it specific-locus amplified fragment sequencing (SLAF-seq). SLAF-seq technology has several distinguishing characteristics: i) deep sequencing to ensure genotyping accuracy; ii) reduced representation strategy to reduce sequencing costs; iii) pre-designed reduced representation scheme to optimize marker efficiency; and iv) double barcode system for large populations. In this study, we tested the efficiency of SLAF-seq on rice and soybean data. Both sets of results showed strong consistency between predicted and practical SLAFs and considerable genotyping accuracy. We also report the highest density genetic map yet created for any organism without a reference genome sequence, common carp in this case, using SLAF-seq data. We detected 50,530 high-quality SLAFs with 13,291 SNPs genotyped in 211 individual carp. The genetic map contained 5,885 markers with 0.68 cM intervals on average. A comparative genomics study between common carp genetic map and zebrafish genome sequence map showed high-quality SLAF-seq genotyping results. SLAF-seq provides a high-resolution strategy for large-scale genotyping and can be generally applicable to various species and populations.

621 citations

Journal ArticleDOI
TL;DR: It is found that massive gene loss occurred in the wake of sex-chromosome 'birth' in Cynoglossus semilaevis, and the sex chromosomes of these fish are derived from the same ancestral vertebrate protochromosome as the avian W and Z chromosomes.
Abstract: Genetic sex determination by W and Z chromosomes has developed independently in different groups of organisms. To better understand the evolution of sex chromosomes and the plasticity of sex-determination mechanisms, we sequenced the whole genomes of a male (ZZ) and a female (ZW) half-smooth tongue sole (Cynoglossus semilaevis). In addition to insights into adaptation to a benthic lifestyle, we find that the sex chromosomes of these fish are derived from the same ancestral vertebrate protochromosome as the avian W and Z chromosomes. Notably, the same gene on the Z chromosome, dmrt1, which is the male-determining gene in birds, showed convergent evolution of features that are compatible with a similar function in tongue sole. Comparison of the relatively young tongue sole sex chromosomes with those of mammals and birds identified events that occurred during the early phase of sex-chromosome evolution. Pertinent to the current debate about heterogametic sex-chromosome decay, we find that massive gene loss occurred in the wake of sex-chromosome 'birth'.

618 citations

Journal ArticleDOI
TL;DR: A draft genome of domesticated C. carpio (strain Songpu) is presented, whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100).
Abstract: The common carp, Cyprinus carpio, is one of the most important cyprinid species and globally accounts for 10% of freshwater aquaculture production. Here we present a draft genome of domesticated C. carpio (strain Songpu), whose current assembly contains 52,610 protein-coding genes and approximately 92.3% coverage of its paleotetraploidized genome (2n = 100). The latest round of whole-genome duplication has been estimated to have occurred approximately 8.2 million years ago. Genome resequencing of 33 representative individuals from worldwide populations demonstrates a single origin for C. carpio in 2 subspecies (C. carpio Haematopterus and C. carpio carpio). Integrative genomic and transcriptomic analyses were used to identify loci potentially associated with traits including scaling patterns and skin color. In combination with the high-resolution genetic map, the draft genome paves the way for better molecular studies and improved genome-assisted breeding of C. carpio and other closely related species.

515 citations

Journal ArticleDOI
TL;DR: The results highlight the ingestion and accumulation of MPs in different tissues of freshwater fish, which lead to perturbations in fish biological systems and should be considered in environmental risk assessment.

410 citations

Journal ArticleDOI
TL;DR: It is suggested that most lineages of living fishes were already established in the Mesozoic Period, more than 65 million years ago, and genome-scale data support the structure of the fish phylogeny.
Abstract: Our understanding of phylogenetic relationships among bony fishes has been transformed by analysis of a small number of genes, but uncertainty remains around critical nodes. Genome-scale inferences so far have sampled a limited number of taxa and genes. Here we leveraged 144 genomes and 159 transcriptomes to investigate fish evolution with an unparalleled scale of data: >0.5 Mb from 1,105 orthologous exon sequences from 303 species, representing 66 out of 72 ray-finned fish orders. We apply phylogenetic tests designed to trace the effect of whole-genome duplication events on gene trees and find paralogy-free loci using a bioinformatics approach. Genome-wide data support the structure of the fish phylogeny, and hypothesis-testing procedures appropriate for phylogenomic datasets using explicit gene genealogy interrogation settle some long-standing uncertainties, such as the branching order at the base of the teleosts and among early euteleosts, and the sister lineage to the acanthomorph and percomorph radiations. Comprehensive fossil calibrations date the origin of all major fish lineages before the end of the Cretaceous.

384 citations


Authors

Showing all 8142 results

NameH-indexPapersCitations
Yu Huang136149289209
Meilin Liu11782752603
Lin Li104202761709
Jian Xu94136652057
Xiaolong Wang8196631455
Sheng Luan7627221253
Peng Xu75115125005
Qiang Li7385630598
Deliang Chen6846116966
Chao Li6456117253
Min Du6132611328
Lei Wang5998814887
Quan Chen5215416697
Jun Li5056212002
James P. Barry4916210687
Network Information
Related Institutions (5)
Ocean University of China
27.8K papers, 440.1K citations

91% related

IFREMER
12.3K papers, 468.8K citations

87% related

Huazhong Agricultural University
23.5K papers, 500.1K citations

86% related

Nanjing Agricultural University
27.3K papers, 546.5K citations

85% related

Norwegian University of Life Sciences
13.5K papers, 442.2K citations

85% related

Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202311
2022147
2021894
2020763
2019734
2018653