Cite this paper:
SONG Chenyu, FENG Ziyi, LI Chunhou, SUN Zhicheng, GAO Tianxiang, SONG Na, LIU Lu. Profile and development of microsatellite primers for Acanthogobius ommaturus based on high-throughput sequencing technology[J]. Journal of Oceanology and Limnology, 2020, 38(6): 1880-1890

Profile and development of microsatellite primers for Acanthogobius ommaturus based on high-throughput sequencing technology

SONG Chenyu1, FENG Ziyi1, LI Chunhou2, SUN Zhicheng1, GAO Tianxiang3, SONG Na1, LIU Lu1
1 Fisheries College, Ocean University of China, Qingdao 266003, China;
2 South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China;
3 National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China
Abstract:
Acanthogobius ommaturus, a fish species of the Family Gobiidae, is a marine commercial fish perched on the bottom of seawater. In this study, Illumina high-throughput sequencing technology was applied to obtain the candidate microsatellite markers of A. ommaturus. A total of 4 746 microsatellite-rich fragments were found, of which 4 542 microsatellites are with primer fragments, containing 971 dinucleotide sequences, 2 643 trinucleotide sequences, 569 tetranucleotide sequences, 406 pentanucleotide sequences, and 212 hexanucleotide sequences. Based on the results of high-throughput sequencing, a total of 141 pairs of the microsatellite primers were designed and screened. And then 24 polymorphic primers were finally obtained by polyacrylamide gel electrophoresis. In total, 271 alleles were detected in the 24 pairs of primers. The number of alleles for different primers ranged from 5 to 19. The average number of effective alleles (Na) was 11.292; the average observed heterozygosity (Ho) of the 24 pairs of primers was 0.665, the average expected heterozygosity (He) was 0.880, and the average polymorphic information content was 0.846. All sites were highly polymorphic (PIC>0.50).
Key words:    microsatellite|Acanthogobius ommaturus|high-throughput sequencing|polymorphic sites   
Received: 2019-06-04   Revised: 2019-09-23
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Articles by SONG Chenyu
Articles by FENG Ziyi
Articles by LI Chunhou
Articles by SUN Zhicheng
Articles by GAO Tianxiang
Articles by SONG Na
Articles by LIU Lu
References:
Arens P, Bugter R, Van't Westende W, Zollinger R, Stronks J, Vos C, Smulders M J M. 2006. Microsatellite variation and population structure of a recovering tree frog (Hyla arborea L.) metapopulation. Conservation Genetics, 7(6):825-835.
Bai C C, Liu S F, Zhuang Z M, Yuan Y J, Liu H B, Dai F Q. 2012. Seventeen polymorphic microsatellite markers developed for the Javelin goby, Synechogobius hasta(Gobiidae). Genetics and Molecular Research, 11(2):1 465-1 468.
Barbará T, Palma-Silva C, Paggi G M, Bered F, Fay M F, Lexer C. 2007. Cross-species transfer of nuclear microsatellite markers:potential and limitation. Molecular Ecology, 16(18):3 759-3 767.
Bergh M O, Getz W M. 1989. Stability and harvesting of competing populations with genetic variation in life history strategy. Theoretical Population Biology, 36(1):77-124.
Botstein D, White R L, Skolnick M, Davis R W. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphism. American Journal of Human Genetics, 32(3):314-331.
Castoe T A, Poole A W, Gu W J, De Koning A P J, Daza J M, Smith E N, Pollock D D. 2010. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources, 10(2):341-347.
Chen M, Tan Z Y, Zeng G M, Peng J. 2010. Comprehensive analysis of simple sequence repeats in pre-miRNAs. Molecular Biology and Evolution, 27(10):2 227-2 232.
Chistiakov D A, Hellemans B, Volckaert F A M. 2006. Microsatellites and their genomic distribution, evolution, function and applications:a review with special reference to fish genetics. Aquaculture, 255(1-4):1-29.
Duan Y F, Zhang Z, Li J T, Li J, Liu P. 2016. Bioinformatics and microsatellite sequences analysis of EST Sequence in ridge tail shrimp Exopalaemon carinicauda. Fisheries Science, 35(5):562-567. (in Chinese with English abstract)
Fan H Y, Ji Y P, Zhang S H, Yuan C T, Gao T X. 2005. Research of fishery biology of the neritic fish Synechogobius ommaturus in the area of the Huanghe delta. Periodical of Ocean University of China, 35(5):733736. (in Chinese with English abstract)
Feng J, Zu J Q, Zheng Z M, Chen Y C. 2004. Studies on the individual fecundity of Synechogobius hasta. Journal of Zhejiang Ocean University (Natural Science), 23(4):302-314. (in Chinese with English abstract)
Gao F T, Shao C W, Cui Z K, Wang S P, Wei M, Chen S L, Yang G P. 2017. Development and population genetic diversity analysis of microsatellite markers in Epinephelus awoara. Periodical of Ocean University of China, 47(4):52-57. (in Chinese with English abstract)
Gao S H, Yu H Y, Wu S Y, Wang S, Geng J N, Luo Y F, Hu S N. 2018. Advances of sequencing and assembling technologies for complex genomes. Hereditas (Beijing), 40(11):944-963. (in Chinese with English abstract)
Gu C P, Gao P, Chen Y J. 2013. DNA barcoding Acanthogobius ommaturus of Zhejiang coast. Journal of Zhejiang Ocean University (Natural Science), 32(6):488-493. (in Chinese with English abstract)
Guo Z Y. 2014. Tandem Repeats Analysis of Yesso scallop Genome. Ocean University of China, Qingdao. (in Chinese with English abstract)
Han D Y, Xue Y, Ji Y P, Xu B D, Liu H, Ma Q Y. 2013. Trophic and spatial niche of five Gobiid fishes in Jiaozhou Bay. Journal of Fishery Sciences of China, 20(1):148-156. (in Chinese with English abstract)
Holt R A, Jones S J. 2008. The new paradigm of flow cell sequencing. Genome Research, 18(6):839-846.
Kashi Y, King D G. 2006. Simple sequence repeats as advantageous mutators in evolution. Trends in Genetics, 22(5):253-259.
Katti M V, Ranjekar P K, Gupta V S. 2001. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Molecular Biology and Evolution, 18(7):1 161-1 167.
Kong X L, Chen Z Z, Lin L, Li C H, Xu S N, Liu Y. 2014. Polymorphic microsatellite loci isolated from the yellowbelly threadfin bream, Nemipterus bathybius. Genetics and Molecular Research, 13(3):5 254-5 257.
Leberg P L. 2002. Estimating allelic richness:effects of sample size and bottlenecks. Molecular Ecology, 11(11):2 445-2 449.
Li Q. 2004. Advances in studies on microsatellite markers in the Pacific abalone. Periodical of Ocean University of China, 34(3):365-370. (in Chinese with English abstract)
Li Y C, Korol A B, Fahima T, Nevo E. 2004. Microsatellites within genes:structure, function, and evolution. Molecular Biology and Evolution, 21(6):991-1 007.
Li Z F, Feng Z L, Zhao L H, Shi Y Q, Li C H, Wang L F, Liu Y J, Zhu H Q. 2013. Frequency and distribution of microsatellites in the whole genome of Verticillium alboatrum. Cotton Science, 25(2):135-141. (in Chinese with English abstract)
Lin L, Zhu L, Liu S F, Su Y Q, Zhung Z M. 2011. Polymorphic microsatellite loci for the Japanese anchovy Engraulis japonicus (Engraulidae). Genetics and Molecular Research, 10(2):764-768.
Lin L, Li C H, Chen Z Z, Xu S S, Liu Y. 2015. Development and characterization of twenty-three microsatellite markers for the purpleback flying squid (Symplectoteuthis oualaniensis). Conservation Genetics Resources, 7(1):161-163.
Liu L, Li C Y, Yang J, Ye Y F, Li J B, Zhou X G, Wang Y Y, Zhu Y Y. 2006. Analysis of microsatellite sequences in the genome of basidiomycetes fungus, Coprinus cinereus. Southwest China Journal of Agricultural Sciences, 19(1):131-135. (in Chinese with English abstract)
Lu Y X, Di M Y, Li Y F, Zhou Z C, Hou H M, He C B, Wang S Z, Gao M L. 2017. Microsatellite analysis of genetic diversity in wild and cultured populations of jellyfish Rhopilema esculentum. Fisheries Science, 36(4):472-479. (in Chinese with English abstract)
Ma H Y, Chen S L. 2009. Isolation and characterization of 31 polymorphic microsatellite markers in barfin flounder(Verasper moseri) and the cross-species amplification in spotted halibut (Verasper variegatus). Conservation Genetics, 5(10):1 591-1 595.
Nei M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89(3):583-590.
Primmer C R, Møller A P, Ellegren H. 1995. Resolving genetic relationships with microsatellite markers:a parentage testing system for the swallow Hirundo rustica. Molecular Ecology, 4(4):493-498.
Rousset F. 2008. GENEPOP'007:a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Notes, 8(1):103-106.
Sambrook J, Russell D W. 2001. Molecular Cloning. 3rd edn. Cold Spring Harbor Laboratory Press, New York. p.543-554.
Song N, Gao T X, Sun X F, Liu B Z. 2010. Study on species validation for Synechogobius hasta. Acta Zootaxonomica Sinica, 35(2):352-359. (in Chinese with English abstract)
Song N, Zhang X M, Sun X F, Yanagimoto T, Gao T X. 2010a. Population genetic structure and larval dispersal potential of spottedtail goby Synechogobius ommaturus in the North-west Pacific. Journal of Fish Biology, 77(2):388-402.
Song N, Zhang X M, Gao T X. 2010b. Genetic diversity and population structure of spottedtail goby (Synechogobius ommaturus) based on AFLP analysis. Biochemical Systematics and Ecology, 38(6):1 089-1 095.
Song N, Song L, Gao T X, Sun X F. 2011. Comparative analysis of genetic diversity of Synechogobius ommaturus based on the mitochondrial DNA control region. Journal of Fisheries of China, 35(3):321-326. (in Chinese with English abstract)
Song N, Li P F, Zhang X M, Gao T X. 2018. Changing phylogeographic pattern of Fenneropenaeus chinensis in the Yellow Sea and Bohai Sea inferred from microsatellite DNA:implications for genetic management. Fisheries Research, 200:11-16.
Tóth G, Gáspári Z, Jurka J. 2000. Microsatellites in different eukaryotic genomes:survey and analysis. Genome Research, 10(7):967-981.
Takezaki N, Nei M. 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics, 144(1):389-399.
Uller T, Sagvik J, Olsson M. 2006. Crosses between frog populations reveal genetic divergence in larval life history at short geographical distance. Biological Journal of the Linnean Society, 89(1):189-195.
Wang H, Zhang B W, Shi W B, Luo X, Zhou L Z, Han D M, Chang Q. 2012. Structural characteristics of di-nucleotide/tetra-nucleotide repeat microsatellite DNA in Pachyhynobius shangchengensis genomes and its effect on isolation. Biodiversity Science, 20(1):51-58. (in Chinese with English abstract)
Wang J L, Zhu M X, Xu M H, Chen S L, Zhang F Q. 2017. Analysis on SSR in Sinoswertia tetraptera base on RADseq. Bulletin of Botanical Research, 37(3):447-452, 460.(in Chinese with English abstract)
Wang S, Zhang L L, Matz M. 2009. Microsatellite characterization and marker development from public EST and WGS databases in the reef-building coral Acropora millepora (Cnidaria, Anthozoa, Scleractinia). Journal of Heredity, 100(3):329-337.
Winkelmann I, Campos P F, Strugnell J, Cherel Y, Smith P J, Kubodera T, Allcock L, Kampmann M L, Schroeder H, Guerra A, Norman M, Finn J, Ingrao D, Clarke M, Gilbert M T. 2013. Mitochondrial genome diversity and population structure of the giant squid Architeuthis:genetics sheds new light on one of the most enigmatic marine species. Proceedings of the Royal Society B-Biological Sciences, 280(1759):20130273.
Yang B, Lin L, Li C H, Xu S N, Liu Y, Xiao Y Y, Chen Z Z. 2015. Development and evaluation of microsatellite markers in Parargyrops edita. South China Fisheries Science, 11(4):116-120. (in Chinese with English abstract)
Zane L, Bargelloni L, Patarnello T. 2002. Strategies for microsatellite isolation:a review. Molecular Ecology, 11(1):1-16.
Zerbino D R, Birney E. 2008. Velvet:algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 2018, 18(5):821-829.
Zhang D X, Hewitt G M. 2003. Nuclear DNA analyses in genetic studies of populations:practice, problems and prospects. Molecular Ecology, 12(3):563-584.
Zhang G, Fang X D, Guo X M, Li L, Luo R B, Xu F, Yang P C, Zhang L L, Wang X T, Qi H G, Xiong Z Q, Que H Y, Xie Y L, Holland P W H, Paps J, Zhu Y B, Wu F C, Chen Y X, Wang J F, Peng C F, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang Z Y, Zhu Q H, Feng Y, Mount A, Hedgecock D, Xu Z, Liu Y J, Domazet-Lošo T, Du Y S, Sun X Q, Zhang S D, Liu B H, Cheng P Z, Jiang X T, Li J, Fan D D, Wang W, Fu W J, Wang T, Wang B, Zhang J B, Peng Z Y, Li Y X, Li N, Wang J P, Chen M, He Y, Tan F J, Song X R, Zheng Q, Huang R M, Yang H L, Du X D, Chen L, Yang M, Gaffney P M, Wang S, Luo L H, She Z C, Ming Y, Huang W, Zhang S, Huang B Y, Zhang Y, Qu T, Ni P X, Miao G Y, Wang J Y, Wang Q, Steinberg C E W, Wang H Y, Li N, Qian L M, Zhang G J, Li Y R, Yang H M, Liu X, Wang J, Yin Y, Wang J. 2012. The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 490(7418):49-54.
Zhao S L, Wu H L. 2008. Gobiidae:Acanthogobius. In:Wu H L, Zhong J S eds. Fauna Sinica, Ostichthyes, Perciformes(V), Gobioidei. Science Press, Beijing. p.211-215. (in Chinese)
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