De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing View Full Text


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Article Info

DATE

2021-11-26

AUTHORS

L. Sahoo, S. P. Das, A. Bit, S. Patnaik, M. Mohanty, G. Das, P. Das

ABSTRACT

Labeo rohita, one of the Indian major carps, is the most popular culture species in Indian subcontinent due to its consumer preference and delicacy. A selective breeding program for harvest body weight has resulted in an average genetic gain of 17% per generation. Transcriptome resource for this species is scanty. Here, we have characterized the liver and muscle transcriptomes of rohu using Roche 454 GS-FLX next generation sequencing platform. In total, 1.2 million reads were generated, de novo assembly and clustering resulted in 4171 transcripts. Out of these, 4171 had significant blast hit against NCBI nr database, and 2130 transcripts were successfully annotated. In total, 289 SSRs were identified with an identification rate of 5.8%, and dinucleotide repeat motifs were observed to be the most abundant SSRs. Further, 2231 putative SNPs were identified with high confidence. Validation of eight putative SNPs using Sanger sequencing resulted in 100% true SNPs. Significant allelic imbalance of M1, M4 and M5 loci between growth selected and control individual were observed. Furthermore, 13 transcription factors were identified in the present study belonging to six different transcription factor families. The present study demonstrated the utility of RNAseq to develop genomics resources in non-model fish species, and the marker resources developed would support the genetic improvement program of this species. More... »

PAGES

59-66

References to SciGraph publications

  • 2003-12. The power and promise of population genomics: from genotyping to genome typing in NATURE REVIEWS GENETICS
  • 2013-03-15. Deep sequencing for de novo construction of a marine fish (Sparus aurata)transcriptome database with a large coverage of protein-coding transcripts in BMC GENOMICS
  • 2018-04-25. The identification of growth, immune related genes and marker discovery through transcriptome in the yellow drum (Nibea albiflora) in GENES & GENOMICS
  • 2011-10-23. Effects of the total replacement of fish-based diet with plant-based diet on the hepatic transcriptome of two European sea bass (Dicentrarchus labrax) half-sibfamilies showing different growth rates with the plant-based diet in BMC GENOMICS
  • 2014-06-30. A linkage map of transcribed single nucleotide polymorphisms in rohu (Labeo rohita) and QTL associated with resistance to Aeromonas hydrophila in BMC GENOMICS
  • 2010-10-13. Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches in BMC GENOMICS
  • 2009-05-12. Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx in BMC GENOMICS
  • 2001-04-30. AP-1 – Introductory remarks in ONCOGENE
  • 2009-05-19. Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis in BMC GENOMICS
  • 2013-12-03. Combining next-generation sequencing and online databases for microsatellite development in non-model organisms in SCIENTIFIC REPORTS
  • 2018-01-08. De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species in BMC GENOMICS
  • 2010-03-16. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery in BMC GENOMICS
  • 2009-01. RNA-Seq: a revolutionary tool for transcriptomics in NATURE REVIEWS GENETICS
  • 2009-11-24. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek) in BMC PLANT BIOLOGY
  • 2018-01-02. Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile in BMC GENOMICS
  • 2015-06-14. Preliminary genetic linkage map of Indian major carp, Labeo rohita (Hamilton 1822) based on microsatellite markers in JOURNAL OF GENETICS
  • 2011-09-09. Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.) in THEORETICAL AND APPLIED GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s10709-021-00141-7

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    31 schema:description Labeo rohita, one of the Indian major carps, is the most popular culture species in Indian subcontinent due to its consumer preference and delicacy. A selective breeding program for harvest body weight has resulted in an average genetic gain of 17% per generation. Transcriptome resource for this species is scanty. Here, we have characterized the liver and muscle transcriptomes of rohu using Roche 454 GS-FLX next generation sequencing platform. In total, 1.2 million reads were generated, de novo assembly and clustering resulted in 4171 transcripts. Out of these, 4171 had significant blast hit against NCBI nr database, and 2130 transcripts were successfully annotated. In total, 289 SSRs were identified with an identification rate of 5.8%, and dinucleotide repeat motifs were observed to be the most abundant SSRs. Further, 2231 putative SNPs were identified with high confidence. Validation of eight putative SNPs using Sanger sequencing resulted in 100% true SNPs. Significant allelic imbalance of M1, M4 and M5 loci between growth selected and control individual were observed. Furthermore, 13 transcription factors were identified in the present study belonging to six different transcription factor families. The present study demonstrated the utility of RNAseq to develop genomics resources in non-model fish species, and the marker resources developed would support the genetic improvement program of this species.
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    39 Labeo
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    41 M1
    42 M4
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    47 Sanger sequencing
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    57 clustering
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    60 culture species
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    64 different transcription factor families
    65 dinucleotide repeat motifs
    66 discovery
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    77 growth
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