Li Wanlong, Zhang Peng, Fellers John P, Friebe Bernd, Gill Bikram S
Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS 66506, USA.
Plant J. 2004 Nov;40(4):500-11. doi: 10.1111/j.1365-313X.2004.02228.x.
We investigated the composition and the basis of genome expansion in the core Triticeae genome using Aegilops tauschii, the D-genome donor of bread wheat. We sequenced an unfiltered genomic shotgun (trs) and a methylation-filtration (tmf) library of A. tauschii, and analyzed wheat expressed sequence tags (ESTs) to estimate the expression of genes and transposable elements (TEs). The sampled D-genome sequences consisted of 91.6% repetitive elements, 2.5% known genes, and 5.9% low-copy sequences of unknown function. TEs constituted 68.2% of the D-genome compared with 50% in maize and 14% in rice. The DNA transposons constituted 13% of the D-genome compared with 2% in maize. TEs were methylated unevenly within and among elements and families, and most were transcribed which contributed to genome expansion in the core Triticeae genome. The copy number of a majority of repeat families increased gradually following polyploidization. Certain TE families occupied discrete chromosome territories. Nested insertions and illegitimate recombination occurred extensively between the TE families, and a majority of the TEs contained internal deletions. The GC content varied significantly among the three sequence sets examined ranging from 42% in tmf to 46% in trs and 52% in the EST. Based on enrichment of genic sequences, methylation-filtration offers one option, although not as efficient as in maize, for isolating gene-rich regions from the large genome of wheat.
我们利用普通小麦的D基因组供体节节麦，对小麦族核心基因组的组成及基因组扩张的基础进行了研究。我们对节节麦的一个未过滤基因组鸟枪法文库（trs）和一个甲基化过滤文库（tmf）进行了测序，并分析了小麦表达序列标签（EST），以评估基因和转座元件（TE）的表达情况。所采样的D基因组序列由91.6%的重复元件、2.5%的已知基因和5.9%功能未知的低拷贝序列组成。与玉米的50%和水稻的14%相比，TE在D基因组中占68.2%。DNA转座子在D基因组中占13%，而在玉米中占2%。TE在元件内部和元件家族之间的甲基化是不均匀的，并且大多数是转录的，这促进了小麦族核心基因组的扩张。大多数重复家族的拷贝数在多倍体化后逐渐增加。某些TE家族占据离散的染色体区域。TE家族之间广泛发生嵌套插入和异常重组，并且大多数TE含有内部缺失。在所检测的三个序列组中，GC含量差异显著，从tmf中的42%到trs中的46%，再到EST中的52%。基于基因序列的富集，甲基化过滤为从小麦大基因组中分离富含基因的区域提供了一种选择，尽管不如在玉米中有效。
