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BMC Genomics
2023 Jan 16;241:25. doi: 10.1186/s12864-023-09113-x.
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Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus.
Guo C
,
Zhang X
,
Li Y
,
Xie J
,
Gao P
,
Hao P
,
Han L
,
Zhang J
,
Wang W
,
Liu P
,
Ding J
,
Chang Y
.
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BACKGROUND: Apostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. japonicus, mainly harvested in the Vladivostok region, exhibits significant phenotypic differentiation, including in many economically important traits, compared with Chinese A. japonicus owing to differences in their habitat. However, both the genetic basis for the phenotypic divergence and the population genetic structure of Russian and Chinese A. japonicus are unknown.
RESULT: In this study, 210 individuals from seven Russian and Chinese A. japonicus populations were sampled for whole-genome resequencing. The genetic structure analysis differentiated the Russian and Chinese A. japonicus into two groups. Population genetic analyses indicated that the Russian population showed a high degree of allelic linkage and had undergone stronger positive selection compared with the Chinese populations. Gene ontology terms enriched among candidate genes with group selection analysis were mainly involved in immunity, such as inflammatory response, antimicrobial peptides, humoral immunity, and apoptosis. Genome-wide association analysis yielded eight single-nucleotide polymorphism loci significantly associated with parapodium number, and these loci are located in regions with a high degree of genomic differentiation between the Chinese and Russia populations. These SNPs were associated with five genes. Gene expression validation revealed that three of these genes were significantly differentially expressed in individuals differing in parapodium number. AJAP08772 and AJAP08773 may directly affect parapodium production by promoting endothelial cell proliferation and metabolism, whereas AJAP07248 indirectly affects parapodium production by participating in immune responses.
CONCLUSIONS: This study, we performed population genetic structure and GWAS analysis on Chinese and Russian A. japonicus, and found three candidate genes related to the number of parapodium. The results provide an in-depth understanding of the differences in the genetic structure of A. japonicus populations in China and Russia, and provide important information for subsequent genetic analysis and breeding of this species.
Alexander,
Fast model-based estimation of ancestry in unrelated individuals.
2009, Pubmed
Alexander,
Fast model-based estimation of ancestry in unrelated individuals.
2009,
Pubmed
Alm Rosenblad,
Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.
2021,
Pubmed
Blair,
Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.).
2018,
Pubmed
Burgarella,
The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns.
2021,
Pubmed
Cantalapiedra,
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale.
2021,
Pubmed
Cingolani,
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
2012,
Pubmed
Cui,
High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis.
2015,
Pubmed
Danecek,
The variant call format and VCFtools.
2011,
Pubmed
Das,
Modulation of the arginase pathway in the context of microbial pathogenesis: a metabolic enzyme moonlighting as an immune modulator.
2010,
Pubmed
Epand,
Mechanisms for the modulation of membrane bilayer properties by amphipathic helical peptides.
1995,
Pubmed
Hoekstra,
Novel insights into the echinoderm nervous system from histaminergic and FMRFaminergic-like cells in the sea cucumber Leptosynapta clarki.
2012,
Pubmed
,
Echinobase
Jia,
Diversification of the aquaporin family in geographical isolated oyster species promote the adaptability to dynamic environments.
2022,
Pubmed
Jin,
Deep Learning: Individual Maize Segmentation From Terrestrial Lidar Data Using Faster R-CNN and Regional Growth Algorithms.
2018,
Pubmed
Khotimchenko,
Pharmacological Potential of Sea Cucumbers.
2018,
Pubmed
,
Echinobase
Li,
Fast and accurate long-read alignment with Burrows-Wheeler transform.
2010,
Pubmed
Li,
Genomic analyses of an extensive collection of wild and cultivated accessions provide new insights into peach breeding history.
2019,
Pubmed
Liao,
Amphidromous but endemic: Population connectivity of Rhinogobius gigas (Teleostei: Gobioidei).
2021,
Pubmed
Liu,
Antioxidant and antihyperlipidemic activities of polysaccharides from sea cucumber Apostichopus japonicus.
2012,
Pubmed
,
Echinobase
Liyanage,
Molecular cloning, expression analysis of interleukin 17D (cysteine knot cytokine) from Amphiprion clarkii and their functional characterization and NFκB pathway activation using FHM cells.
2022,
Pubmed
Loeuille,
Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera.
2021,
Pubmed
Marquet,
Chemicals released by male sea cucumber mediate aggregation and spawning behaviours.
2018,
Pubmed
,
Echinobase
McKenna,
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
2010,
Pubmed
Purcell,
PLINK: a tool set for whole-genome association and population-based linkage analyses.
2007,
Pubmed
Sadanandam,
Semaphorin 5A promotes angiogenesis by increasing endothelial cell proliferation, migration, and decreasing apoptosis.
2010,
Pubmed
Saif,
Detection of whole genome selection signatures of Pakistani Teddy goat.
2021,
Pubmed
Sandoval-Castillo,
Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus).
2022,
Pubmed
Shai,
Molecular recognition between membrane-spanning polypeptides.
1995,
Pubmed
Shao,
Cloning and comparative analysis the proximal promoter activities of arginase and agmatinase genes in Apostichopus japonicus.
2016,
Pubmed
,
Echinobase
Valenza-Troubat,
Unraveling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus).
2022,
Pubmed
VandenSpiegel,
Fine structure of the dorsal papillae in the holothurioid Holothuria forskali (Echinodermata).
1995,
Pubmed
,
Echinobase
Varshney,
Next-generation sequencing technologies and their implications for crop genetics and breeding.
2009,
Pubmed
Waples,
Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon.
2022,
Pubmed
Weir,
ESTIMATING F-STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE.
1984,
Pubmed
Wu,
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.
2021,
Pubmed
Yamazaki,
Comparing the genetic diversity and population structure of sister marine snails having contrasting habitat specificity.
2022,
Pubmed
Yang,
Genome-wide complex trait analysis (GCTA): methods, data analyses, and interpretations.
2013,
Pubmed
Yang,
Concepts, estimation and interpretation of SNP-based heritability.
2017,
Pubmed
Yina,
The first description of complete invertebrate arginine metabolism pathways implies dose-dependent pathogen regulation in Apostichopus japonicus.
2016,
Pubmed
,
Echinobase
Zhang,
The sea cucumber genome provides insights into morphological evolution and visceral regeneration.
2017,
Pubmed
,
Echinobase
Zhang,
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files.
2019,
Pubmed
Zhou,
Genome-wide efficient mixed-model analysis for association studies.
2012,
Pubmed
