Evidence map›Paper›PMID 30203240›Full record

ArticleMolecular biology reports2018

De novo assembly of genome and development of polymorphic microsatellite loci in the blue swimming crab (Portunus pelagicus) using RAD approach.

Qingyang Wu, Guidong Miao, Xincang Li, Wenhua Liu, Mhd Ikhwanuddin, Hongyu Ma

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Article in Molecular biology reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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5 · Who and what money

Authors and funding

6 authors.

Qingyang WuGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, China.
Guidong MiaoGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, China.
Xincang LiEast China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, 200090, China.
Wenhua LiuGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, China.
Mhd IkhwanuddinSTU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
Hongyu MaGuangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, 243 Daxue Road, Shantou, 515063, China. mahy@stu.edu.cn.ORCID http://orcid.org/0000-0003-2299-503X

Funding

the Program for Innovation and Enhancement of School of Department of Education of Guangdong Province 2017KCXTD014the STU Scientific Research Foundation for Talents NTF17006
6 · The paper itself

Abstract

The blue swimming crab (Portunus pelagicus) is a valuable marine fishery resource in Indo-West Pacific Ocean. So far, rare genetic resource of this species is available. In this report, the restriction-site associated DNA (RAD) approach was employed to mine the genomic information and identify molecular markers in P. pelagicus. A total of 0.82 Gbp clean data were generated from the genome of individual "X2A". De novo assembly produced 85,796 contigs with an average length of 339 bp. A total of 45,464 putative SNPs and 17,983 microsatellite loci were identified from the genomes of ten individuals. Furthermore, 31 pairs of primers were successfully designed, with 16 of them exhibiting polymorphism in a wild population. For these polymorphic loci, the expected and observed alleles per locus ranged from 1.064 to 7.314 and from 2 to 11, respectively. The expected and observed heterozygosity per locus ranged from 0.0615 to 0.819 and from 0.0626 to 1.000, respectively. Nine loci showed high informative with polymorphism information content (PIC) > 0.5. Five loci significantly deviated from Hardy-Weinberg equilibrium in the samples analyzed. No linkage disequilibrium was found among the 16 polymorphic microsatellite loci. This study provided massive genetic resource and polymorphic molecular markers that should be helpful for studies on conservation genetics, population dynamics and genetic diversity of P. pelagicus and related crab species.

Indexed as

AllelesAnimalsBrachyuraDNAGene FrequencyGenetic LociGenetics, PopulationGenetic VariationLinkage DisequilibriumMicrosatellite RepeatsPacific OceanPolymorphism, GeneticPolymorphism, Single NucleotideRestriction MappingSequence Analysis, DNADNAMolecular markerPolymorphic microsatellitesPortunus pelagicusRestriction-site associated DNA sequencing

Identifiers

PMID30203240

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