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Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species

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Abstract

Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.

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Availability of data and material

All sequencing data is available in the NCBI BioProject database under the accession number PRJNA693418 or as supplemental files to this manuscript.

References

  • Abdelrahman H, Elhady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H et al (2017) Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 18:1–23

    Article  Google Scholar 

  • Alcivar-warren AS, Al-tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Kahlil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, Steen H, Van Der Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y (2017) Aquaculture genomics genetics and breeding in the United States : current status challenges and priorities for future. BMC Genomics. https://doi.org/10.1186/s12864-017-3557-1

  • Allen PJ, Steeby JA (2011) Aquaculture: challenges and promise nature education knowledge 3:12

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ao J, Mu Y, Xiang LX, Fan D, Feng M, Zhang S, Shi Q, Zhu LY, Li T, Ding Y, Nie L, Li Q, Dong WR, Jiang L, Sun B, Zhang X, Li M, Zhang HQ, Xie S, Zhu Y, Jiang X, Wang X, Mu P, Chen W, Yue Z, Wang Z, Wang J, Shao JZ, Chen X (2015) Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation. PLoS Genet 11:e1005118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy‐Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA (2013) From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. Curr Protoc Bioinform 43(1)

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beaumont MA (2005) Adaptation and speciation: what can Fst tell us? Trends Ecol Evol 20:435–440

    Article  PubMed  Google Scholar 

  • Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 2:573–580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brooker AL, Cook D, Bentzen P, Wright JM, Doyle RW (1994) Organization of microsatellites differs between mammals and cold-water teleost fishes. Can J Fish Aquat Sci 51:1959–1966

    Article  Google Scholar 

  • Carruthers M, Yurchenko A, Augley J, Adams C, Herzyk P, Elmer K (2018) Correction to: De novo transcriptome assembly annotation and comparison of four ecological and evolutionary model salmonid fish species. BMC Genomics 19:32

    Article  PubMed  PubMed Central  Google Scholar 

  • Cenadelli S, Maran V, Bongioni G, Fusetti L, Parma P, Aleandri R (2007) Identification of nuclear SNPs in gilthead seabream. J Fish Biol 70:399–405

    Article  Google Scholar 

  • Choi M, Scholl UI, Ji W, Liu T, Tikhonova IR, Zumbo P, Nayir A, Bakkaloglu A, Ozen S, Sanjad S, Nelson-Williams C, Farhi A, Mane S, Lifton RP (2009) Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci USA 106:19096–19101. https://doi.org/10.1073/pnas0910672106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F (2009) Biopython : freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422–1423

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conesa A, García-gómez GS, JM, Terol J, Talón M, Genómica D, Valenciano I, Agrarias DI, De Valencia UP, (2005) Blast2GO: a universal tool for annotation visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Cosart T, Beja-Pereira A, Chen S, Ng SB, Shendure J, Luikart G (2011) Exome-wide DNA capture and next generation sequencing in domestic and wild species. BMC Genomics 12:347

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cowley PD, Childs A, Bennett RH (2013) The trouble with estuarine fisheries in temperate South Africa illustrated by a case study on the Sundays Estuary. Afr J Mar Sci 35:117–128

    Article  Google Scholar 

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Danzmann RG, Kocmarek AL, Norman JD, Rexroad CE, Palti Y (2016) Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients. BMC Genomics 17:1–18

    Article  CAS  Google Scholar 

  • Dickmeis T, Müller F (2004) The identification and functional characterisation of conserved regulatory elements in developmental genes. Brief Fun Geno Prot 3(4):332–350

    Article  Google Scholar 

  • Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC (2012) Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst Biol 61:717–726

    Article  PubMed  Google Scholar 

  • Fairfield H, Gilbert GJ, Barter M (2011) Mutation discovery in mice by whole exome sequencing. Genome Biol 12:R86

  • Ferreira DG, Galindo BA, Alves AN, Almeida FS, Ruas CF, Sofia SH (2013) Development and characterization of 14 microsatellite loci in the Neotropical fish Geophagus brasiliensis (Perciformes Cichlidae). J Fish Biol 83:1430–1438

    Article  CAS  PubMed  Google Scholar 

  • Foll M, Gaggiotti O (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180:977–993

    Article  PubMed  PubMed Central  Google Scholar 

  • Garfield DA, Wray GA (2010) The evolution of gene regulatory interactions. Bioscience 60:15–23

    Article  Google Scholar 

  • Gemayel R, Vinces MD, Legendre M, Verstrepen KJ (2010) Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 44:445–477

    Article  CAS  PubMed  Google Scholar 

  • Giani AM, Gallo GR, Gianfranceschi L, Formenti G (2020) Long walk to genomics: History and current approaches to genome sequencing and assembly. Comp Struct Biotech J 18:9–19

    Article  CAS  Google Scholar 

  • Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C (2009) Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 27:182–189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gotea V, Gartner JJ, Qutob N, Elnitski L, Samuels Y (2015) The functional relevance of somatic synonymous mutations in melanoma and other cancers. Pigment Cell Melanoma Res 28:673–684

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Griffiths MH, Hecht T (1995) Age and growth of South African dusky kob Argyrosomus japonicus (Sciaenidae) based on otoliths. S Afr J Mar Sci 16:119–128

    Article  Google Scholar 

  • Gui J (2018) Aquaculture of the large yellow croaker aquaculture of the large yellow croaker Aquaculture in China 297–308. https://doi.org/10.1002/9781119120759ch3

  • Guo Y, Long J, He J, Li CI, Cai Q, Shu XO, Zheng W, Li C (2012) Exome sequencing generates high quality data in non-target regions. BMC Genomics. https://doi.org/10.1186/1471-2164-13-194

  • Harney E, Dubief B, Boudry P, Basuyaux O, Schilhabel MB, Huchette S, Paillard C, Nunes FLD (2016) De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome. Mar Genomics 28:11–16

    Article  PubMed  Google Scholar 

  • Henzy J, Gifford R, Kenaley C, Johnson W (2017) An intact retroviral gene conserved in spiny-rayed fishes for over 100 Mya. Mol Biol Evol 34:634–639

    Article  CAS  PubMed Central  Google Scholar 

  • Henkel CV, Dirks RP, Jansen HJ, Forlenza M, Wiegertjes GF, Howe k, Guido EEJM van den Thillart, Spaink HP (2012) Comparison of the exomes of common carp (Cyprinus carpio) and zebrafish (Danio rerio). Zebrafish 9:59–67

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Howe K, Clark M, Torroja C, Torrance J, Berthelot C, Muffato M, Collins J, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett J, Koch R (2013) The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498–503

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hunt R, Sauna ZE, Ambudkar SV, Gottesman MM, Kimchi-Sarfaty C (2009) Silent (Synonymous) SNPs: should we care about them? Single Nucleotide Polymorphisms 22-39. https://doi.org/10.1007/978-1-60327-411-1_2

  • Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, SaM M et al (2020) Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 21:389–409

    Article  CAS  PubMed  Google Scholar 

  • Hutchings K, Lamberth SJ (2003) Likely impacts of an eastward expansion of the inshore gill-net fishery in the Western Cape South Africa: implications for management. Mar Freshw Res 54:39–56

    Article  Google Scholar 

  • Jansen A, Gemayel R, Verstrepen KJ (2012) Unstable microsatellite repeats facilitate rapid evolution of coding and regulatory sequences. Genome Dyn 7:108–125

    Article  CAS  PubMed  Google Scholar 

  • Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Shugart LT, YY, Price AL, De Bakker PIW, Purcell SM, Sunyaev SR (2012) Exome sequencing and the genetic basis of complex traits. Nat Genet 44:623–630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee TI, Young RA (2000) Transcription of Eukaryotic Protein-Coding Genes. Annu Rev Genet 34(1):77–137

    Article  CAS  PubMed  Google Scholar 

  • Li C, Hofreiter M, Straube N, Corrigan S, Naylor GJP (2013) Capturing protein-coding genes across highly divergent species. Biotechniques 54:321–326

    Article  CAS  PubMed  Google Scholar 

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li Z, Chen F, Huang C, Zheng W, Yu C, Cheng H, Zhou R (2017) Genome-wide mapping and characterization of microsatellites in the swamp eel genome. Sci Rep 7

  • Lin G, Thevasagayam NM, Wan ZY, Ye BQ, Yue GH (2019) Transcriptome analysis identified genes for growth and omega-3/-6 ratio in saline tilapia. Front Genet 10

  • Manzini MC, Tambunan DE, Hill RS, Yu TW, Maynard TM, Heinzen EL, Shianna KV, Stevens CR, Partlow JN, Barry BJ, Rodriguez J, Gupta VA, Al-Qudah AK, Eyaid W, Friedman M, JM, Salih MA, Clark R, Moroni I, Mora M, Beggs AH, Gabriel SB, Walsh CA (2012) Exome sequencing and functional validation in zebrafish identify GTDC2 mutations as a cause of Walker-Warburg syndrome. Am J Hum Genet 91:541–547 https://doi.org/10.1016/jajhg201207009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McClure MC, Bickhart D, Null D, Vanraden P, Xu L, Wiggans G, Liu G, Schroeder S, Glasscock J, Armstrong J, Cole JB, Van Tassell CP, Sonstegard TS (2014) Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1 HH2 and HH3 reveal a putative causative mutation in SMC2 for HH3. PLoS One 9:e92769

    Article  PubMed  PubMed Central  Google Scholar 

  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2009) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    Article  Google Scholar 

  • Mi H, Muruganujan A, Thomas PD (2013) PANTHER in 2013: modeling the evolution of gene function and other gene attributes in the context of phylogenetic trees. Nucleic Acids Res 41:D377–D386

    Article  CAS  PubMed  Google Scholar 

  • Nguyen LS, Wilkinson MF, Gecz J (2014) Nonsense-mediated mRNA decay: Inter-individual variability and human disease. Neurosci Biobehav Rev 46:175–186

    Article  CAS  PubMed  Google Scholar 

  • Ozsolak F, Milos PM (2011) RNA sequencing: advances challenges and opportunities. Nat Rev Genet 12:87–98

    Article  CAS  PubMed  Google Scholar 

  • Paibomesai M, Moghadam H, Ferguson M, Danzmann R (2010) Clock genes and their genomic distributions in three species of salmonid fishes: associations with genes regulating sexual maturation and cell cycling. BMC Res Notes 3:215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA (2010) Transcriptome sequencing in an ecologically important tree species: assembly annotation and marker discovery. BMC Genomics 11:180

    Article  PubMed  PubMed Central  Google Scholar 

  • Pardo BG, Fernández C, Millán A, Bouza C, Vázquez-López A (2008) Expressed sequence tags (ESTs) from immune tissues of turbot (Scophthalmus maximus) challenged with pathogens. BMC Vet Res 4:37

    Article  PubMed  PubMed Central  Google Scholar 

  • Parla JS, Iossifov I, Grabill I (2011) A comparative analysis of exome capture. Genome Biol 12:R97

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Porreca AP, Hintz WD, Coulter DP, Garvey JE (2017) Subtle physiological and morphological differences explain ecological success of sympatric congeners. Ecosphere 8

  • Rhode C, Roodt-Wilding R (2011) Bioinformatic survey of Haliotis midae microsatellites reveals a non-random distribution of repeat motifs. Biol Bull 221:147–154

    Article  CAS  PubMed  Google Scholar 

  • Richard GF, Kerrest A, Dujon B (2008) Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 72(4):686-727. https://doi.org/10.1128/MMBR.00011-08

  • Robledo D, Palaiokostas C, Bargelloni L, Martínez P, Houston R (2018) Applications of genotyping by sequencing in aquaculture breeding and genetics. Rev Aquac 10:670–682

    Article  PubMed  Google Scholar 

  • Ryan S, Willer J, Marjoram L, Bagwell J, Mankiewicz J, Leshchiner I, Goessling W, Bagnat M, Katsanis N (2013) Rapid identification of kidney cyst mutations by whole exome sequencing in zebrafish. Development 140:4445–4451

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saker ML, Griffiths DJ (2000) The effect of temperature on growth and cylindrospermopsin content of seven isolates of Cylindrospermopsis raciborskii (Nostocales Cyanophyceae) from water bodies in northern Australia. Phycologia 39:349–354

    Article  Google Scholar 

  • Salem M, Vallejo RL Leeds TD, Palti Y, Liu S, Sabbagh A, Rexroad CE, Yao J (2012) RNA-seq identifies SNP markers for growth traits in rainbow trout. PLoS One 7 

  • Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y (2013) Finding the lost treasures in exome sequencing data. Trends Genet 29:593–599

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schott RK, Panesar B, Card DC, Preston M, Castoe TA, Chang BSW (2017) Targeted capture of complete coding regions across divergent species. Genome Biol Evol 9:398–414

    CAS  PubMed  PubMed Central  Google Scholar 

  • Singh SM, Zouros E (1978) Genetic variation associated with growth rate in the american oyster (Crassostrea virginica). Evolution 32:342–353

  • Smith CT, Elfstrom CM, Seeb LW, Seeb JE (2005) Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Mol Ecol 14:4193–4203

    Article  CAS  PubMed  Google Scholar 

  • Srivastava S, Avvaru A, Sowpati D, Mishra R (2019) Patterns of microsatellite distribution across eukaryotic genomes. BMC Genomics 20

  • Stanke M, Morgenstern B (2005) AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res 33:465–467

    Article  CAS  Google Scholar 

  • Stickney HL (2002) Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res 12:1929–1934

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suzuki N, Ueda K, Sakamoto H, Sasayama Y (1999) Fish calcitonin genes: primitive bony fish genes have been conserved in some lower vertebrates. Gen Comp Endocrinol 113:369–373

    Article  CAS  PubMed  Google Scholar 

  • Tan H, Xu Z, Jin P (2012) Role of noncoding RNAs in trinucleotide repeat neurodegenerative disorders. Exp Neurol 235:469–475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Toth G (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–98

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vallender EJ (2011) Expanding whole exome resequencing into non- human primates. Genome Biol 12:R87

    Article  PubMed  PubMed Central  Google Scholar 

  • Vera M, Alvarez-Dios JA, Millán A, Pardo BG, Bouza C (2011) Validation of single nucleotide polymorphism (SNP) markers from an immune expressed sequence tag (EST) turbot Scophthalmus maximus database. Aquaculture 313:31–41

    Article  CAS  Google Scholar 

  • Vera M, Alvarez-Dios J-A, Fernandez C, Bouza C, Vilas R, Martinez P (2013) Development and validation of single nucleotide polymorphisms (SNPs) markers from two transcriptome 454-runs of turbot (Scophthalmus maximus) Using High-Throughput Genotyping. Int J Mol Sci 14:5694–5711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Warr A, Robert C, Hume D, Archibald A, Deeb N, Watson M (2015) Exome sequencing: current and future perspectives. Genes|Genomes|Genetics 5:1543–1550

  • Xu P, Zhang X, Wang X, Li J, Liu G, Kuang Y, Xu J, Zheng X, Ren L, Wang G, Zhang Y, Huo L, Zhao Z, Cao D, Lu C, Li C, Zhou Y, Liu Z, Fan Z, Shan G, Li X, Wu S, Song L, Hou G, Jiang Y, Jeney Z, Yu D, Wang L, Shao C, Song L, Sun J, Ji P, Wang J, Li Q, Xu L, Sun F, Feng J, Wang C, Wang S, Wang B, Li Y, Zhu Y, Xue W, Zhao L, Wang J, Gu Y, Lv W, Wu K, Xiao J, Wu J, Zhang Z, Yu J, Sun X (2014) Genome sequence and genetic diversity of the common carp Cyprinus carpio Nat Publ Group 46 

  • Yang C, Zhu X, Sun X (2008) Development of microsatellite markers and their utilization in genetic diversity analysis of cultivated and wild populations of the mud carp (Cirrhina molitorella). J Genet Genomics 35:201–206

    Article  CAS  PubMed  Google Scholar 

  • Yasuike M, Iwasaki Y, Nishiki I, Nakamura Y, Matsuura A, Yoshida K, Noda T, Andoh T, Fujiwara A (2018) The yellowtail (Seriola quinqueradiata) genome and transcriptome atlas of the digestive tract. DNA Res 25(5):547–560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • You X, Shan X, Shi Q (2020) Research advances in the genomics and applications for molecular breeding of aquaculture animals. Aquaculture 735357

  • Yue GH (2014) Recent advances of genome mapping and marker-assisted selection in aquaculture. Fish Fish 15:376–396

    Article  Google Scholar 

  • Yue G, Wang L (2017) Current status of genome sequencing and its applications in aquaculture. Aquaculture 468:337–347

    Article  CAS  Google Scholar 

  • Zhang Z, Ding X, Liu J, Zhang Q, De Koning D-J (2011) Accuracy of genomic prediction using low-density marker panels. J Dairy Sci 94:3642–3650

    Article  CAS  PubMed  Google Scholar 

  • Zhu Y, Xue W, Wang J, Wan Y, Wang S, Xu P, Zhang Y, Li J, Sun X (2012) Identification of common carp (Cyprinus carpio) microRNAs and microRNA-related SNPs. BMC Genomics 13:413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu C, Pan Z, Wang H, Chang G, Wu N, Ding H (2017) De novo assembly characterization and annotation for the transcriptome of Sarcocheilichthys sinensis. PLoS One 12:e0171966

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

The authors would like to thank the various aquaculture facilities for the use of their infrastructure and access to biological materials.

Funding

The South African National Research Foundation funded this research: Grant reference number: MCR180616347589.

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  1. Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa

    T. Jackson, E. Ishengoma & C. Rhode

  2. Department of Biological Sciences, Mkwawa University College of Education, University of Dar Es Salaam, P.O. Box 2329, Dar es Salaam, Tanzania

    E. Ishengoma

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Correspondence to C. Rhode.

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The experimental protocols for the collection of biological samples and handling of live animals were approved by the Stellenbosch University, Research Ethics Committee: Animal Care and Use, protocol reference numbers: SU-ACUM14-00,007 and 6569.

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Jackson, T., Ishengoma, E. & Rhode, C. Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species. Mar Biotechnol 23, 560–575 (2021). https://doi.org/10.1007/s10126-021-10046-3

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