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

Zhang, Jisen; Sharma, Anupma; Yu, Qingyi; Wang, Jianping; Li, Leiting; Zhu, Lin; Zhang, Xingtan; Chen, Youqiang; Ming, Ray

doi:10.1186/s12864-016-2817-9

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

Journal Article · Fri Jun 10 00:00:00 EDT 2016 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-016-2817-9· OSTI ID:1287172

Zhang, Jisen ^[1]; Sharma, Anupma ^[2]; Yu, Qingyi ^[3]; Wang, Jianping ^[4]; Li, Leiting ^[5]; Zhu, Lin ^[6]; Zhang, Xingtan ^[7]; Chen, Youqiang ^[8]; Ming, Ray ^[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; Fujian Normal Univ., Fuzhou (China). College of Life Sciences; Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Plant Biology
Texas A&M Univ. System, Dallas, TX (United States). Texas A&M AgriLife Research, Dept. of Plant Pathology & Microbiology
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
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
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Plant Biology; Nanjing Agricultural Univ., Nanjing (China). College of Horticulture
Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept. of Plant Biology; Jilin Univ., Changchun, Jilin (China). College of Plant Science
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
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

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.

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Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0010686

OSTI ID:: 1287172

Journal Information:: BMC Genomics, Vol. 17, Issue 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 5 works

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Linked Research (24)

Figures / Tables (13)

Table 1(p. 5)

Table 2(p. 6)

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Table 3 (continued)(p. 9)

Fig. 1(p. 10)

Table 4(p. 10)

Table 5(p. 11)

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Additional file 10: Table S6. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d4.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 6: Figure S4. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d7.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 11: Figure S5. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d11.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 1: Table S1. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d2.v1 The current record is supplemented by this dataset	dataset	June 2016
Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum [Supplemental Data] Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 8: Table S4. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d5.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 3: Figure S1. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d8 The current record is supplemented by this text	text	January 2016
Additional file 6: Figure S4. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d7 The current record is supplemented by this text	text	January 2016
Additional file 2: Table S2. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d9 The current record is supplemented by this text	text	January 2016
Additional file 3: Figure S1. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d8.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 9: Table S5. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d10.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 10: Table S6. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d4 The current record is supplemented by this text	text	January 2016
Additional file 5: Figure S3. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d3 The current record is supplemented by this text	text	January 2016
Additional file 4: Figure S2. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d6 The current record is supplemented by this text	text	January 2016
Additional file 8: Table S4. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d5 The current record is supplemented by this text	text	January 2016
Additional file 1: Table S1. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d2 The current record is supplemented by this text	text	January 2016
Additional file 7: Table S3. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d1 The current record is supplemented by this text	text	January 2016
Additional file 5: Figure S3. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d3.v1 The current record is supplemented by this figure	figure	June 2016
Additional file 4: Figure S2. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d6.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 9: Table S5. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d10 The current record is supplemented by this text	text	January 2016
Additional file 11: Figure S5. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d11 The current record is supplemented by this text	text	January 2016
Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum [Supplemental Data] Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262 The current record is supplemented by this figure	figure	June 2016
Additional file 7: Table S3. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d1.v1 The current record is supplemented by this dataset	dataset	June 2016
Additional file 2: Table S2. of Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum Zhang, Jisen; Sharma, Anupma; Yu, Qingyi https://doi.org/10.6084/m9.figshare.c.3607262_d9.v1 The current record is supplemented by this dataset	dataset	June 2016