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<p><i>Neolissochilus pnar</i>, identified as the world’s largest cave fish, belongs to the family Cyprinidae and is endemic to one of India’s biodiversity hotspots, specifically in the limestones caves of Meghalaya, India. This species is notably different from its closely related counterpart, <i>Neolissochilus hexastichus</i>, primarily in its lack of pigmentation and the absence or reduction of eyes. While juvenile <i>N. pnar</i> may have small or reduced eyes, adults exhibit a absence of external ocular features. Thus, genome sequence resources of this species would be an effective tool for bioprospecting and mining of novel genes responsible for the important traits. In this study, genome sequencing was done through long reads technology (PacBio) and high quality draft genome assembly, of 1.56 Gb in size with 1,423 contigs, N<sub>50</sub> of 18.990 Mb was generated, which showed 99% (BUSCO) genome completenes. The genome assembly contains 44.30% repetitive elements, 1,416,376 SSRs, and 37,559 functionally annotated genes. Single-copy orthologs (SOGs) analysis indicated <i>N. pnar</i> to be in the same cluster with other cave dwelling Cyprinids used in the sudy.The extensive genomic information generated in present study would be a useful resource for understanding evolutionaly significance and genes governing the traits including the body colour and eye development in Mahseer species.</p>

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Genome sequencing and assembly of Neolissochilus pnar, the largest cavefish species of Mahseer

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月17日

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  • Vindhya Mohindra,
  • Labrechai Mog Chowdhury,
  • Dran Khlur Baiaineh Mukhim,
  • Kangkan Sarma,
  • Deisakee Pyrbot Warbah,
  • Dandadhar Sarma,
  • Joykrushna Jena

摘要

Neolissochilus pnar, identified as the world’s largest cave fish, belongs to the family Cyprinidae and is endemic to one of India’s biodiversity hotspots, specifically in the limestones caves of Meghalaya, India. This species is notably different from its closely related counterpart, Neolissochilus hexastichus, primarily in its lack of pigmentation and the absence or reduction of eyes. While juvenile N. pnar may have small or reduced eyes, adults exhibit a absence of external ocular features. Thus, genome sequence resources of this species would be an effective tool for bioprospecting and mining of novel genes responsible for the important traits. In this study, genome sequencing was done through long reads technology (PacBio) and high quality draft genome assembly, of 1.56 Gb in size with 1,423 contigs, N50 of 18.990 Mb was generated, which showed 99% (BUSCO) genome completenes. The genome assembly contains 44.30% repetitive elements, 1,416,376 SSRs, and 37,559 functionally annotated genes. Single-copy orthologs (SOGs) analysis indicated N. pnar to be in the same cluster with other cave dwelling Cyprinids used in the sudy.The extensive genomic information generated in present study would be a useful resource for understanding evolutionaly significance and genes governing the traits including the body colour and eye development in Mahseer species.