Singh Nagendra K, Raghuvanshi Saurabh, Srivastava Subodh K, Gaur Anupama, Pal Ajit K, Dalal Vivek, Singh Archana, Ghazi Irfan A, Bhargav Ashutosh, Yadav Mahavir, Dixit Anupam, Batra Kamlesh, Gaikwad Kishor, Sharma Tilak R, Mohanty Amitabh, Bharti Arvind K, Kapur Anita, Gupta Vikrant, Kumar Dibyendu, Vij Shubha, Vydianathan Ravi, Khurana Parul, Sharma Sulabha, McCombie W Richard, Messing Joachim, Wing Rod, Sasaki Takuji, Khurana Paramjit, Mohapatra Trilochan, Khurana Jitendra P, Tyagi Akhilesh K
Indian Initiative for Rice Genome Sequencing, National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, 110012, New Delhi, India.
Funct Integr Genomics. 2004 May;4(2):102-17. doi: 10.1007/s10142-004-0109-y. Epub 2004 Apr 14.
The DNA sequence of 106 BAC/PAC clones in the minimum tiling path (MTP) of the long arm of rice chromosome 11, between map positions 57.3 and 116.2 cM, has been assembled to phase 2 or PLN level. This region has been sequenced to 10x redundancy by the Indian Initiative for Rice Genome Sequencing (IIRGS) and is now publicly available in GenBank. The region, excluding overlaps, has been predicted to contain 2,932 genes using different software. A gene-by-gene BLASTN search of the NCBI wheat EST database of over 420,000 cDNA sequences revealed that 1,143 of the predicted rice genes (38.9%) have significant homology to wheat ESTs (bit score >/= 100). Further BLASTN search of these 1,143 rice genes with the GrainGenes database of sequence contigs containing bin-mapped wheat ESTs allowed 113 of the genes to be placed in bins located on wheat chromosomes of different homoeologous groups. The largest number of genes, about one-third, mapped to the homoeologous group 4 chromosomes of wheat, suggesting a common evolutionary origin. The remaining genes were located on wheat chromosomes of different groups with significantly higher numbers for groups 3 and 5. Location of bin-mapped wheat contigs to chromosomes of all the seven homoeologous groups can be ascribed to movement of genes (transpositions) or chromosome segments (translocations) within rice or the hexaploid wheat genomes. Alternatively, it could be due to ancient duplications in the common ancestral genome of wheat and rice followed by selective elimination of genes in the wheat and rice genomes. While there exists definite conservation of gene sequences and the ancestral chromosomal identity between rice and wheat, there is no obvious conservation of the gene order at this level of resolution. Lack of extensive colinearity between rice and wheat genomes suggests that there have been many insertions, deletions, duplications and translocations that make the synteny comparisons much more complicated than earlier thought. However, enhanced resolution of comparative sequence analysis may reveal smaller conserved regions of colinearity, which will facilitate selection of markers for saturation mapping and sequencing of the gene-rich regions of the wheat genome.
水稻第11号染色体长臂最小拼接路径（MTP）上，位于图谱位置57.3和116.2厘摩之间的106个细菌人工染色体/噬菌体P1人工染色体（BAC/PAC）克隆的DNA序列已组装到2期或PLN水平。印度水稻基因组测序计划（IIRGS）已对该区域进行了10倍冗余度测序，目前可在GenBank上公开获取。使用不同软件预测该区域（不包括重叠部分）含有2932个基因。对NCBI中超过420,000个cDNA序列的小麦EST数据库进行逐个基因的BLASTN搜索发现，预测的水稻基因中有1143个（38.9%）与小麦EST具有显著同源性（比特得分≥100）。使用包含定位到染色体区间的小麦EST的GrainGenes数据库对这1143个水稻基因进一步进行BLASTN搜索，使得其中113个基因能够定位到位于不同同源群小麦染色体上的区间。数量最多的基因，约三分之一，定位到小麦的同源群4染色体上，这表明它们有共同的进化起源。其余基因位于不同组的小麦染色体上，其中第3组和第5组的数量明显更多。定位到所有七个同源群染色体上的区间定位的小麦重叠群，可能归因于水稻或六倍体小麦基因组内基因的移动（转座）或染色体片段的移动（易位）。或者，这可能是由于小麦和水稻共同祖先基因组中的古老重复，随后小麦和水稻基因组中的基因被选择性消除。虽然水稻和小麦之间存在明确的基因序列保守性和祖先染色体一致性，但在这种分辨率水平上没有明显的基因顺序保守性。水稻和小麦基因组之间缺乏广泛的共线性，这表明存在许多插入、缺失、重复和易位，使得同线性比较比早期想象的要复杂得多。然而，比较序列分析分辨率的提高可能会揭示较小的共线性保守区域，这将有助于选择标记，用于小麦基因组富含基因区域的饱和作图和测序。
