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This article in TPG

  1. Vol. 9 No. 3
    unlockOPEN ACCESS
     
    Received: Mar 02, 2016
    Accepted: July 10, 2016
    Published: October 6, 2016


    * Corresponding author(s): linkui@bnu.edu.cn
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doi:10.3835/plantgenome2015.10.0099

Hierarchical Map of Orthologous Genomic Regions Reconstructed from Two Closely Related Genomes: Cucumber Case Study

  1. Huifen Caoa,
  2. Erli Panga and
  3. Kui Lin *a
  1. a MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal Univ., Beijing 100875, China
Core Ideas:
  • A strategy for reconstructing a hierarchical map of orthologous genomic regions from two genomes.
  • Both large- and small-scale genomic changes could be more accurately detected from this map.
  • Many large-scale genomic changes are inferred between two cucumber subspecies diverged shortly.

Abstract

Accurate identification of orthologous genomic regions (OGRs) between two closely related genomes is crucial for the reliable detection of genomic changes, which range from small-scale changes (e.g., single nucleotide or small nucleotides) to large-scale structural changes. Although diverse OGRs inferred at different levels have been successfully applied to address various biological questions, a limited number of studies have simultaneously integrated OGRs from different levels. Here, we report on a new approach to construct a hierarchical map of OGRs. Using different types of genomic markers, this approach was applied to two very closely related cucumber genomes [Cucumis sativus L. var. sativus and C. sativus L. var. hardwickii (Royle) Alef.]. We identified two different levels of OGRs using Mugsy (denoted as dnaOGRs) and i-ADHoRe (denoted as proOGRs). Using information regarding the anchored chromosomes of the two genomes, a third level of OGRs (denoted chrOGRs) could be built at the chromosomal level. Together, these OGRs could be organized into a hierarchical map that represented the parent–child relationships (chrOGR:proOGRs:dnaOGRs) between the two genomes. For this case study, the map consisted of seven chrOGRs, 540 proOGRs, and 22,321 dnaOGRs. Based on this map, we designed different methods to detect both small-scale and large-scale genomic changes. Surprisingly, many genomic changes were detected at each OGR level despite the very short divergence time between the two subspecies. Together, our results show that a hierarchical map of OGRs and their related genomic changes are useful resources for elucidating the diversity and evolution of cucumber genomes and phenotypes.

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