Chromosome-scale assembly of the Monopterus genome

Abstract Background The teleost fish Monopterus albus is emerging as a new model for biological studies due to its natural sex transition and small genome, in addition to its enormous economic and potential medical value. However, no genomic information for the Monopterus is currently available. Findings Here, we sequenced and de novo assembled the genome of M. albus and report the de novochromosome assembly by FISH walking assisted by conserved synteny (Cafs). Using Cafs, 328 scaffolds were assembled into 12 chromosomes, which covered genomic sequences of 555 Mb, accounting for 81.3% of the sequences assembled in scaffolds (∼689 Mb). A total of 18 ,660 genes were mapped on the chromosomes and showed a nonrandom distribution along chromosomes. Conclusions We report the first reference genome of the Monopterus and provide an efficient Cafs strategy for a de novo chromosome-level assembly of the Monopterus genome, which provides a valuable resource, not only for further studies in genetics, evolution, and development, particularly sex determination, but also for breed improvement of the species.

• Publication year

  2018

• Venue

  GigaScience

• Publication date

  2018-04-24

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/gigascience/giy046PMID 29688346PMCID 5946948
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2012cited by this paper
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  2012cited by this paper
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  2011cited by this paper
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  2009cited by this paper
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  2008cited by this paper
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  2007cited by this paper
• InterPro and InterProScan

  2007cited by this paper
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  2007cited by this paper
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  2007cited by this paper
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  2005cited by this paper
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  2005cited by this paper
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  2004cited by this paper
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  2004cited by this paper
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  2004cited by this paper
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  2003cited by this paper
• The rice field eel as a model system for vertebrate sexual development

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  2002cited by this paper
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  2002cited by this paper
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  2002cited by this paper
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  2001cited by this paper
• The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains

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• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• KEGG: Kyoto Encyclopedia of Genes and Genomes

  2000cited by this paper
• Ab initio gene finding in Drosophila genomic DNA.

  2000cited by this paper
• The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

  2000cited by this paper
• KEGG: Kyoto Encyclopedia of Genes and Genomes

  1999cited by this paper
• Prediction of complete gene structures in human genomic DNA.

  1997cited by this paper
• Hermaphroditism in the Lower Vertebrates

  1947cited by this paper

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