Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats.
Transposable elements in Phyllostachys pubescens (Poaceae) genome survey sequences and the full-length cDNA sequences, and their association with simple-sequence repeats.
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DOI：
10.4238/2011.december.6.3
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发表时间：
2011-12
期刊：
影响因子：
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通讯作者：
Mingbing Zhou;X. M. Liu;D. Tang
中科院分区：
文献类型：
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作者：
Mingbing Zhou;X. M. Liu;D. Tang
毛竹（Phyllostachys pubescens）是亚洲最具生态、经济和文化价值的木本竹材。目前，短毛竹的基因组数据比其他竹种都要多，包括2.12 mb的基因组调查序列（GSS）和11.4 mb的全长cDNA序列（fl -cDNA）。对这些序列的分析表明，在pubescens基因组中，转座因子（te）丰富、多样且具有多系性，其中Ty3-gypsy和Ty1-copia是两个最丰富的家族。系统发育分析表明，这两个元素可能出现在竹科其他亚科分离出来之前。我们发现一些基因内te的分布与转录谱相关，其中Mutator元件倾向于插入转录因子的转录本中。此外，我们还发现，在短毛霉基因组中，te中SSRs的丰度（4.56%）显著高于GSS（0.098%）和fl - cdna(2.60%)，并且发现TA/AT和CT/AG重复序列分别与En/Spm和Mutator元件密切相关。虽然需要大规模的基因组测序才能完全了解pubescens基因组的结构，但我们的数据提供了pubescens基因组结构和进化的一瞥。
Phyllostachys pubescens is a woody bamboo with the highest ecological, economic, and cultural values of all bamboos in Asia. There is more genomic data available for P. pubescens than for any other bamboo species, including 2.12-Mb genome survey sequences (GSS) and 11.4-Mb full-length cDNA sequences (FL-cDNAs) currently deposited in GenBank. Analysis of these sequences revealed that transposable elements (TEs) are abundant, diverse and polyphyletic in the P. pubescens genome, of which Ty3-gypsy and Ty1-copia are the two most abundant families. Phylogenic analysis showed that both elements probably arose before the Bambusoideae separated from the other Poaceae subfamilies. We found evidence that the distribution of some intragenic TEs correlated with transcript profiles, of which Mutator elements preferred to insert in the transcripts of transcription factors. Additionally, we found that the abundance of SSRs in TEs (4.56%) was significantly higher than in GSS (0.098%) and in FL-cDNAs (2.60%) in P. pubescens genome, and TA/AT and CT/AG repeats were found to be intimately associated with En/Spm and Mutator elements, respectively. Our data provide a glimpse of the structure and evolution of P. pubescens genome, although large-scale sequencing of the genome would be required to fully understand the architecture of the P. pubescens genome.