חיפוש מתקדם
  • David N. Kuhn
    • USDA-ARS-SHRS
  • Michael Campbell
    • Cold Spring Harbor Laboratory
  • Ian Bally
    • Queensland Department of Agriculture and Fisheries
  • Natalie Dillon
    • Queensland Department of Agriculture and Fisheries
  • David Innes
    • Queensland Department of Agriculture and Fisheries
  • Jordon Rahaman
    • Florida International University
  • Amy Groh
    • USDA-ARS
  • Barbara Freeman
    • USDA-ARS-SHRS
  • Maria A. Islas-Osuna
    • Lab. de Biologia y Genetica Molecular (CIAD, A.C.)

The mango (Mangifera indica L.) cultivar 'Tommy Atkins' is the most commonly available market mango in the United States, the world’s largest importer of mango. Although 'Tommy Atkins' is a highly heterozygous cultivar, most available mango cultivars are also highly heterozygous, so 'Tommy Atkins' was chosen due to its commercial importance to the US market. Two different technologies were used for sequencing the mango genome, ~100x Illumina paired end coupled with 10X Genomics. Assembly of the data by NRGene resulted in 571 super-scaffolds and ~80% coverage of the haploid mango genome (~490Mb). The assembly was improved using two previously published genetic maps encompassing ~5,000 SNP markers and a recombination block map (NRGene) to allow correct ordering of scaffolds within a pseudomolecule and merging of unincorporated scaffolds into pseudomolecules. The final assembly was 20 pseudomolecules corresponding to the 20 chromosomes in the haploid genome. Pseudomolecules ranged in size from 11-22 Mb. A mango specific repeat library was created for masking and annotation was done with MakerP resulting in the identification of ~27,000 genes.

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תנאי שימוש
Sequencing, Assembly and Annotation of the Mango Cultivar ′Tommy Atkins′
  • David N. Kuhn
    • USDA-ARS-SHRS
  • Michael Campbell
    • Cold Spring Harbor Laboratory
  • Ian Bally
    • Queensland Department of Agriculture and Fisheries
  • Natalie Dillon
    • Queensland Department of Agriculture and Fisheries
  • David Innes
    • Queensland Department of Agriculture and Fisheries
  • Jordon Rahaman
    • Florida International University
  • Amy Groh
    • USDA-ARS
  • Barbara Freeman
    • USDA-ARS-SHRS
  • Maria A. Islas-Osuna
    • Lab. de Biologia y Genetica Molecular (CIAD, A.C.)
Sequencing, Assembly and Annotation of the Mango Cultivar ′Tommy Atkins′

The mango (Mangifera indica L.) cultivar 'Tommy Atkins' is the most commonly available market mango in the United States, the world’s largest importer of mango. Although 'Tommy Atkins' is a highly heterozygous cultivar, most available mango cultivars are also highly heterozygous, so 'Tommy Atkins' was chosen due to its commercial importance to the US market. Two different technologies were used for sequencing the mango genome, ~100x Illumina paired end coupled with 10X Genomics. Assembly of the data by NRGene resulted in 571 super-scaffolds and ~80% coverage of the haploid mango genome (~490Mb). The assembly was improved using two previously published genetic maps encompassing ~5,000 SNP markers and a recombination block map (NRGene) to allow correct ordering of scaffolds within a pseudomolecule and merging of unincorporated scaffolds into pseudomolecules. The final assembly was 20 pseudomolecules corresponding to the 20 chromosomes in the haploid genome. Pseudomolecules ranged in size from 11-22 Mb. A mango specific repeat library was created for masking and annotation was done with MakerP resulting in the identification of ~27,000 genes.

Scientific Publication
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