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Title: Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum

Abstract

Here, sugarcane is a major sugar and biofuel crop, but genomic research and molecular breeding have lagged behind other major crops due to the complexity of auto-allopolyploid genomes. Sugarcane cultivars are frequently aneuploid with chromosome number ranging from 100 to 130, consisting of 70-80 % S. officinarum, 10-20 % S. spontaneum, and 10 % recombinants between these two species. Analysis of a genomic region in the progenitor autoploid genomes of sugarcane hybrid cultivars will reveal the nature and divergence of homologous chromosomes. As a result, to investigate the origin and evolution of haplotypes in the Bru1 genomic regions in sugarcane cultivars, we identified two BAC clones from S. spontaneum and four from S. officinarum and compared to seven haplotype sequences from sugarcane hybrid R570. The results clarified the origin of seven homologous haplotypes in R570, four haplotypes originated from S. officinarum, two from S. spontaneum and one recombinant.. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence ranged from 18.2 % to 60.5 % with an average of 33. 7 %. Gene content and gene structure were relatively well conserved among the homologous haplotypes. Exon splitting occurred in haplotypes of the hybrid genome but not in its progenitormore » genomes. Tajima's D analysis revealed that S. spontaneum hapotypes in the Bru1 genomic regions were under strong directional selection. Numerous inversions, deletions, insertions and translocations were found between haplotypes within each genome. In conclusion, this is the first comparison among haplotypes of a modern sugarcane hybrid and its two progenitors. Tajima's D results emphasized the crucial role of this fungal disease resistance gene for enhancing the fitness of this species and indicating that the brown rust resistance gene in R570 is from S. spontaneum. Species-specific InDel, sequences similarity and phylogenetic analysis of homologous genes can be used for identifying the origin of S. spontaneum and S. officinarum haplotype in Saccharum hybrids. Comparison of exon splitting among the homologous haplotypes suggested that the genome rearrangements in Saccharum hybrids S. officinarum would be sufficient for proper genome assembly of this autopolyploid genome. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence may allow sequencing and assembling the autopolyploid Saccharum genomes and the auto-allopolyploid hybrid genomes using whole genome shotgun sequencing.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9]
+ Show Author Affiliations
  1. Fujian Agriculture and Forestry Univ., Fuzhou, Fujian Province (China). FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Inst. of Science and Technology; Fujian Normal Univ., Fuzhou (China). College of Life Sciences; Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Plant Biology
  2. Texas A&M Univ. System, Dallas, TX (United States). Texas A&M AgriLife Research, Dept. of Plant Pathology & Microbiology
  3. Fujian Agriculture and Forestry Univ., Fuzhou, Fujian Province (China). FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Inst. of Science and Technology; Texas A&M Univ. System, Dallas, TX (United States). Texas A&M AgriLife Research, Dept. of Plant Pathology & Microbiology
  4. Fujian Agriculture and Forestry Univ., Fuzhou, Fujian Province (China). FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Inst. of Science and Technology; Univ. of Florida, Gainesville, FL (United States). Dept. of Agronomy
  5. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Plant Biology; Nanjing Agricultural Univ., Nanjing (China). College of Horticulture
  6. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Plant Biology; Jilin Univ., Changchun, Jilin (China). College of Plant Science
  7. Fujian Agriculture and Forestry Univ., Fuzhou, Fujian Province (China). FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Inst. of Science and Technology
  8. Fujian Normal Univ., Fuzhou (China). College of Life Sciences
  9. Fujian Agriculture and Forestry Univ., Fuzhou, Fujian Province (China). FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Inst. of Science and Technology;Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Plant Biology
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1287172
Grant/Contract Number:  
SC0010686
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; genome evolution; haplotypes; homologous genes; polyploidy; Saccharum; rust resistance gene; sugarcane cultivar; tragopogon-miscellus; genome complexity; whole-genome; cd-hit; sequence; evolution; maize; annotation

Citation Formats

Zhang, Jisen, Sharma, Anupma, Yu, Qingyi, Wang, Jianping, Li, Leiting, Zhu, Lin, Zhang, Xingtan, Chen, Youqiang, and Ming, Ray. Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. United States: N. p., 2016. Web. doi:10.1186/s12864-016-2817-9.
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Zhang, Jisen, Sharma, Anupma, Yu, Qingyi, Wang, Jianping, Li, Leiting, Zhu, Lin, Zhang, Xingtan, Chen, Youqiang, & Ming, Ray. Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. United States. https://doi.org/10.1186/s12864-016-2817-9
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Zhang, Jisen, Sharma, Anupma, Yu, Qingyi, Wang, Jianping, Li, Leiting, Zhu, Lin, Zhang, Xingtan, Chen, Youqiang, and Ming, Ray. Fri . "Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum". United States. https://doi.org/10.1186/s12864-016-2817-9. https://www.osti.gov/servlets/purl/1287172.
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@article{osti_1287172,
title = {Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum},
author = {Zhang, Jisen and Sharma, Anupma and Yu, Qingyi and Wang, Jianping and Li, Leiting and Zhu, Lin and Zhang, Xingtan and Chen, Youqiang and Ming, Ray},
abstractNote = {Here, sugarcane is a major sugar and biofuel crop, but genomic research and molecular breeding have lagged behind other major crops due to the complexity of auto-allopolyploid genomes. Sugarcane cultivars are frequently aneuploid with chromosome number ranging from 100 to 130, consisting of 70-80 % S. officinarum, 10-20 % S. spontaneum, and 10 % recombinants between these two species. Analysis of a genomic region in the progenitor autoploid genomes of sugarcane hybrid cultivars will reveal the nature and divergence of homologous chromosomes. As a result, to investigate the origin and evolution of haplotypes in the Bru1 genomic regions in sugarcane cultivars, we identified two BAC clones from S. spontaneum and four from S. officinarum and compared to seven haplotype sequences from sugarcane hybrid R570. The results clarified the origin of seven homologous haplotypes in R570, four haplotypes originated from S. officinarum, two from S. spontaneum and one recombinant.. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence ranged from 18.2 % to 60.5 % with an average of 33. 7 %. Gene content and gene structure were relatively well conserved among the homologous haplotypes. Exon splitting occurred in haplotypes of the hybrid genome but not in its progenitor genomes. Tajima's D analysis revealed that S. spontaneum hapotypes in the Bru1 genomic regions were under strong directional selection. Numerous inversions, deletions, insertions and translocations were found between haplotypes within each genome. In conclusion, this is the first comparison among haplotypes of a modern sugarcane hybrid and its two progenitors. Tajima's D results emphasized the crucial role of this fungal disease resistance gene for enhancing the fitness of this species and indicating that the brown rust resistance gene in R570 is from S. spontaneum. Species-specific InDel, sequences similarity and phylogenetic analysis of homologous genes can be used for identifying the origin of S. spontaneum and S. officinarum haplotype in Saccharum hybrids. Comparison of exon splitting among the homologous haplotypes suggested that the genome rearrangements in Saccharum hybrids S. officinarum would be sufficient for proper genome assembly of this autopolyploid genome. Retrotransposon insertions and sequences variations among the homologous haplotypes sequence divergence may allow sequencing and assembling the autopolyploid Saccharum genomes and the auto-allopolyploid hybrid genomes using whole genome shotgun sequencing.},
doi = {10.1186/s12864-016-2817-9},
journal = {BMC Genomics},
number = 1,
volume = 17,
place = {United States},
year = {Fri Jun 10 00:00:00 EDT 2016},
month = {Fri Jun 10 00:00:00 EDT 2016}
}
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Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1186/s12864-016-2817-9
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Figures / Tables:

Table 1 Table 1: Summary of the sequence length, GC content, transposable element content, and gene number
All figures and tables (13 total)
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    Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype
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