AUTHOR=Sharma Anupma , Song Jinjin , Lin Qingfan , Singh Ratnesh , Ramos Ninfa , Wang Kai , Zhang Jisen , Ming Ray , Yu Qingyi 

TITLE=Comparative Analysis of Homologous Sequences of Saccharum officinarum and Saccharum spontaneum Reveals Independent Polyploidization Events

JOURNAL=Frontiers in Plant Science

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.01414

DOI=10.3389/fpls.2018.01414

ISSN=1664-462X

ABSTRACT=<p>Sugarcane (<italic>Saccharum</italic> spp. hybrids) is an economically important crop widely grown in tropical and subtropical regions for sugar and ethanol production. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between <italic>S. officinarum</italic> and <italic>S. spontaneum</italic> with 80–90% of the genome from <italic>S. officinarum</italic> and 10–20% of the genome from <italic>S. spontaneum</italic>. We constructed bacterial artificial chromosome (BAC) libraries of <italic>S. officinarum</italic> variety LA Purple (2n = 8x = 80) and <italic>S. spontaneum</italic> haploid clone AP85-441 (2n = 4x = 32), and selected and sequenced 97 BAC clones from the two <italic>Saccharum</italic> BAC libraries. A total of 5,847,280 bp sequence from <italic>S. officinarum</italic> and 5,011,570 bp from <italic>S. spontaneum</italic> were assembled and 749 gene models were annotated in these BACs. A relatively higher gene density and lower repeat content were observed in <italic>S. spontaneum</italic> BACs than in <italic>S. officinarum</italic> BACs. Comparative analysis of syntenic regions revealed a high degree of collinearity in genic regions between <italic>Saccharum</italic> and <italic>Sorghum bicolor</italic> and between <italic>S. officinarum</italic> and <italic>S. spontaneum</italic>. In the syntenic regions, <italic>S. spontaneum</italic> showed expansion relative to <italic>S. officinarum</italic>, and both <italic>S. officinarum</italic> and <italic>S. spontaneum</italic> showed expansion relative to sorghum. Among the 75 full-length LTR retrotransposons identified in the <italic>Saccharum</italic> BACs, none of them are older than 2.6 mys and no full-length LTR elements are shared between <italic>S. officinarum</italic> and <italic>S. spontaneum</italic>. In addition, divergence time estimated using a LTR junction marker and a syntenic gene shared by 3 <italic>S. officinarum</italic> and 1 <italic>S. spontaneum</italic> BACs revealed that the <italic>S. spontaneum</italic> intergenic region was distant to those from the 3 homologous regions in <italic>S. officinarum</italic>. Our results suggested that <italic>S. officinarum</italic> and <italic>S. spontaneum</italic> experienced at least two rounds of independent polyploidization in each lineage after their divergence from a common ancestor.</p>