Singh Nagendra K, Dalal Vivek, Batra Kamlesh, Singh Binay K, Chitra G, Singh Archana, Ghazi Irfan A, Yadav Mahavir, Pandit Awadhesh, Dixit Rekha, Singh Pradeep K, Singh Harvinder, Koundal Kirpa R, Gaikwad Kishor, Mohapatra Trilochan, Sharma Tilak R
Rice Genome Laboratory, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India.
Funct Integr Genomics. 2007 Jan;7(1):17-35. doi: 10.1007/s10142-006-0033-4. Epub 2006 Jul 25.
The high-quality rice genome sequence is serving as a reference for comparative genome analysis in crop plants, especially cereals. However, early comparisons with bread wheat showed complex patterns of conserved synteny (gene content) and colinearity (gene order). Here, we show the presence of ancient duplicated segments in the progenitor of wheat, which were first identified in the rice genome. We also show that single-copy (SC) rice genes, those representing unique matches with wheat expressed sequence tag (EST) unigene contigs in the whole rice genome, show more than twice the proportion of genes mapping to syntenic wheat chromosome as compared to the multicopy (MC) or duplicated rice genes. While 58.7% of the 1,244 mapped SC rice genes were located in single syntenic wheat chromosome groups, the remaining 41.3% were distributed randomly to the other six non-syntenic wheat groups. This could only be explained by a background dispersal of genes in the genome through transposition or other unknown mechanism. The breakdown of rice-wheat synteny due to such transpositions was much greater near the wheat centromeres. Furthermore, the SC rice genes revealed a conserved primordial gene order that gives clues to the origin of rice and wheat chromosomes from a common ancestor through polyploidy, aneuploidy, centromeric fusions, and translocations. Apart from the bin-mapped wheat EST contigs, we also compared 56,298 predicted rice genes with 39,813 wheat EST contigs assembled from 409,765 EST sequences and identified 7,241 SC rice gene homologs of wheat. Based on the conserved colinearity of 1,063 mapped SC rice genes across the bins of individual wheat chromosomes, we predicted the wheat bin location of 6,178 unmapped SC rice gene homologs and validated the location of 213 of these in the telomeric bins of 21 wheat chromosomes with 35.4% initial success. This opens up the possibility of directed mapping of a large number of conserved SC rice gene homologs in wheat. Overall, only 46.4% of these SC genes code for proteins with known functional domains; the remaining 53.6% have unknown function, and hence, represent an important, but yet, under explored category of genes.
高质量的水稻基因组序列正作为作物尤其是谷类作物比较基因组分析的参考。然而，早期与面包小麦的比较显示出保守的共线性（基因含量）和共线性（基因顺序）的复杂模式。在这里，我们展示了小麦祖先中存在古老的重复片段，这些片段最初是在水稻基因组中鉴定出来的。我们还表明，单拷贝（SC）水稻基因，即在整个水稻基因组中与小麦表达序列标签（EST）单基因重叠群有唯一匹配的那些基因，与多拷贝（MC）或重复的水稻基因相比，映射到共线小麦染色体上的基因比例高出两倍多。在1244个映射的SC水稻基因中，58.7%位于单个共线小麦染色体组中，其余41.3%随机分布到其他六个非共线小麦组中。这只能通过基因通过转座或其他未知机制在基因组中的背景分散来解释。由于这种转座导致的水稻 - 小麦共线性破坏在小麦着丝粒附近更为严重。此外，SC水稻基因揭示了一种保守的原始基因顺序，这为通过多倍体、非整倍体、着丝粒融合和易位从共同祖先起源的水稻和小麦染色体提供了线索。除了按染色体区域映射的小麦EST重叠群外，我们还将56298个预测的水稻基因与从409765个EST序列组装的39813个小麦EST重叠群进行了比较，并鉴定出7241个小麦的SC水稻基因同源物。基于1063个映射的SC水稻基因在各个小麦染色体区域的保守共线性，我们预测了6178个未映射的SC水稻基因同源物在小麦染色体区域的位置，并在21条小麦染色体的端粒区域验证了其中213个的位置，初始成功率为35.4%。这为在小麦中定向映射大量保守的SC水稻基因同源物开辟了可能性。总体而言，这些SC基因中只有46.4%编码具有已知功能域的蛋白质；其余53.6%功能未知，因此，代表了一类重要但尚未充分探索的基因。
