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



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.



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 after hybridization. The combined minimum difference at 19.5 % among homologous chromosomes in 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.
FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.|College of Life Sciences, Fujian Normal University, Fuzhou, 350108, China.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Jisen
J
Zhang
Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, 17360 Coit Road, Dallas, TX, 75252, USA.
Anupma
A
Sharma
FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.|Texas A&M AgriLife Research, Department of Plant Pathology & Microbiology, Texas A&M University System, 17360 Coit Road, Dallas, TX, 75252, USA.
Qingyi
Q
Yu
FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.|Department of Agronomy, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA.
Jianping
J
Wang
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.|College of Horticulture, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China.
Leiting
L
Li
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.|College of Plant Science, Jilin University, Changchun, Jilin, 130062, China.
Lin
L
Zhu
FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China.
Xingtan
X
Zhang
College of Life Sciences, Fujian Normal University, Fuzhou, 350108, China.
Youqiang
Y
Chen
FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian Province, China. rming@life.uiuc.edu.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. rming@life.uiuc.edu.
Ray
R
Ming
D001482:Base Composition; D019295:Computational Biology / Q000379:methods; D004251:DNA Transposable Elements; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D023061:Gene Order; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D006239:Haplotypes; D058977:Molecular Sequence Annotation; D016254:Mutagenesis, Insertional; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011123:Polyploidy; D031786:Saccharum / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
D004251:DNA Transposable Elements; D010940:Plant Proteins
Genome evolution; Haplotypes; Homologous genes; Polyploidy; Saccharum