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Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean
Zhixi Tian,Meixia Zhao,Maoyun She,Jianchang Du,Steven B. Cannon,Xin Liu,Xun Xu,Xinpeng Qi,Man-Wah Li,Hon-Ming Lam,Jianxin Ma
Plant Cell
Abstract
Preferential accumulation of transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), in recombination-suppressed pericentromeric regions seems to be a general pattern of TE distribution in flowering plants. However, whether such a pattern was formed primarily by preferential TE insertions into pericentromeric regions or by selection against TE insertions into euchromatin remains obscure. We recently investigated TE insertions in 31 resequenced wild and cultivated soybean (Glycine max) genomes and detected 34,154 unique nonreference TE insertions mappable to the reference genome. Our data revealed consistent distribution patterns of the nonreference LTR-RT insertions and those present in the reference genome, whereas the distribution patterns of the nonreference DNA TE insertions and the accumulated ones were significantly different. The densities of the nonreference LTR-RT insertions were found to negatively correlate with the rates of local genetic recombination, but no significant correlation between the densities of nonreference DNA TE insertions and the rates of local genetic recombination was detected. These observations suggest that distinct insertional preferences were primary factors that resulted in different levels of effectiveness of purifying selection, perhaps as an effect of local genomic features, such as recombination rates and gene densities that reshaped the distribution patterns of LTR-RTs and DNA TEs in soybean.
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论文编号: |
DOI:10.1105/tpc.112.103630 |
论文题目: |
Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean |
英文论文题目: |
Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean |
第一作者: |
Zhixi Tian,Meixia Zhao,Maoyun She,Jianchang Du,Steven B. Cannon,Xin Liu,Xun Xu,Xinpeng Qi,Man-Wah Li,Hon-Ming Lam,Jianxin Ma |
英文第一作者: |
Zhixi Tian,Meixia Zhao,Maoyun She,Jianchang Du,Steven B. Cannon,Xin Liu,Xun Xu,Xinpeng Qi,Man-Wah Li,Hon-Ming Lam,Jianxin Ma |
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2012-11-22 |
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摘要: |
Preferential accumulation of transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), in recombination-suppressed pericentromeric regions seems to be a general pattern of TE distribution in flowering plants. However, whether such a pattern was formed primarily by preferential TE insertions into pericentromeric regions or by selection against TE insertions into euchromatin remains obscure. We recently investigated TE insertions in 31 resequenced wild and cultivated soybean (Glycine max) genomes and detected 34,154 unique nonreference TE insertions mappable to the reference genome. Our data revealed consistent distribution patterns of the nonreference LTR-RT insertions and those present in the reference genome, whereas the distribution patterns of the nonreference DNA TE insertions and the accumulated ones were significantly different. The densities of the nonreference LTR-RT insertions were found to negatively correlate with the rates of local genetic recombination, but no significant correlation between the densities of nonreference DNA TE insertions and the rates of local genetic recombination was detected. These observations suggest that distinct insertional preferences were primary factors that resulted in different levels of effectiveness of purifying selection, perhaps as an effect of local genomic features, such as recombination rates and gene densities that reshaped the distribution patterns of LTR-RTs and DNA TEs in soybean. |
英文摘要: |
Preferential accumulation of transposable elements (TEs), particularly long terminal repeat retrotransposons (LTR-RTs), in recombination-suppressed pericentromeric regions seems to be a general pattern of TE distribution in flowering plants. However, whether such a pattern was formed primarily by preferential TE insertions into pericentromeric regions or by selection against TE insertions into euchromatin remains obscure. We recently investigated TE insertions in 31 resequenced wild and cultivated soybean (Glycine max) genomes and detected 34,154 unique nonreference TE insertions mappable to the reference genome. Our data revealed consistent distribution patterns of the nonreference LTR-RT insertions and those present in the reference genome, whereas the distribution patterns of the nonreference DNA TE insertions and the accumulated ones were significantly different. The densities of the nonreference LTR-RT insertions were found to negatively correlate with the rates of local genetic recombination, but no significant correlation between the densities of nonreference DNA TE insertions and the rates of local genetic recombination was detected. These observations suggest that distinct insertional preferences were primary factors that resulted in different levels of effectiveness of purifying selection, perhaps as an effect of local genomic features, such as recombination rates and gene densities that reshaped the distribution patterns of LTR-RTs and DNA TEs in soybean. |
刊物名称: |
Plant Cell |
英文刊物名称: |
Plant Cell |
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其它备注: |
Zhixi Tian,Meixia Zhao,Maoyun She,Jianchang Du,Steven B. Cannon,Xin Liu,Xun Xu,Xinpeng Qi,Man-Wah Li,Hon-Ming Lam,Jianxin Ma. Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean. Plant Cell DOI:10.1105/tpc.112.103630 |
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