Transposable elements(TEs),particularly,long terminal repeat retrotransposons(LTR-RTs),are the most abun-dant DNA components in all plant species that have been investigated,and are largely responsible for plant genom...Transposable elements(TEs),particularly,long terminal repeat retrotransposons(LTR-RTs),are the most abun-dant DNA components in all plant species that have been investigated,and are largely responsible for plant genome size variation.Although plant genomes have experi-enced periodic proliferation and/or recent burst of LTR-retrotransposons,the majority of LTR-RTs are inactivated by DNA methylation and small RNA-mediated silencing mechanisms,and/or were deleted/truncated by unequal homologous recombination and illegitimate recombina-tion,as suppression mechanisms that counteract genome expansion caused by LTR-RT amplifi cation.LTR-RT DNA is generally enriched in pericentromeric regions of the host genomes,which appears to be the outcomes of pref-erential insertions of LTR-RTs in these regions and low effectiveness of selection that purges LTR-RT DNA from these regions relative to chromosomal arms.Potential functions of various TEs in their host genomes remain blurry;nevertheless,LTR-RTs have been recognized to play important roles in maintaining chromatin structures and centromere functions and regulation of gene expres-sions in their host genomes.展开更多
Long terminal repeat retrotransposons(LTR-RTs) are a predominant group of plant transposable elements(TEs) that are an important component of plant genomes. A large number of LTR-RTs have been annotated in the genomes...Long terminal repeat retrotransposons(LTR-RTs) are a predominant group of plant transposable elements(TEs) that are an important component of plant genomes. A large number of LTR-RTs have been annotated in the genomes of the agronomically important oil and vegetable crops of the genus Brassica. Herein, full-length LTR-RTs in the genomes of Brassica and other closely related species were systematically analyzed. The full-length LTR-RT content varied greatly(from 0.43% to 23.4%) between different species, with Gypsy-like LTR-RTs constituting a primary group across these genomes. More importantly, many annotated LTR-RTs(from 10.03% to 33.25% of all detected LTR-RTs) were found to be enriched in localized hotspot regions. Furthermore, all of the analyzed species showed evidence of having experienced at least one round of a LTR-RT burst, with Raphanus sativus experiencing three or more. Moreover, these relatively ancient LTR-RT amplifications exhibited a clear expansion at specific time points. To gain a further understanding of this timing, Brassica rapa, B. oleracea, and R. sativus were examined for the presence of syntenic regions, but none were present. These findings indicate that these LTR-RT burst events were not inherited from a common ancestor,but instead were species-specific bursts that occurred after the divergence of Brassica species. This study further exemplifies the complexities of TE amplifications during the evolution of plant genomes and suggests that these LTR-RT bursts play an important role in genome expansion and divergence in Brassica species.展开更多
文摘Transposable elements(TEs),particularly,long terminal repeat retrotransposons(LTR-RTs),are the most abun-dant DNA components in all plant species that have been investigated,and are largely responsible for plant genome size variation.Although plant genomes have experi-enced periodic proliferation and/or recent burst of LTR-retrotransposons,the majority of LTR-RTs are inactivated by DNA methylation and small RNA-mediated silencing mechanisms,and/or were deleted/truncated by unequal homologous recombination and illegitimate recombina-tion,as suppression mechanisms that counteract genome expansion caused by LTR-RT amplifi cation.LTR-RT DNA is generally enriched in pericentromeric regions of the host genomes,which appears to be the outcomes of pref-erential insertions of LTR-RTs in these regions and low effectiveness of selection that purges LTR-RT DNA from these regions relative to chromosomal arms.Potential functions of various TEs in their host genomes remain blurry;nevertheless,LTR-RTs have been recognized to play important roles in maintaining chromatin structures and centromere functions and regulation of gene expres-sions in their host genomes.
基金supported by the National Natural Science Foundation of China (NSFC grants 31722048 and 31630068)the National Program on Key Research Project (2016YFD0100307)+2 种基金the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciencesthe Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, ChinaProspect of Shandong Seed Project, China (Shandong Gov. [2015] Reference No. 212)
文摘Long terminal repeat retrotransposons(LTR-RTs) are a predominant group of plant transposable elements(TEs) that are an important component of plant genomes. A large number of LTR-RTs have been annotated in the genomes of the agronomically important oil and vegetable crops of the genus Brassica. Herein, full-length LTR-RTs in the genomes of Brassica and other closely related species were systematically analyzed. The full-length LTR-RT content varied greatly(from 0.43% to 23.4%) between different species, with Gypsy-like LTR-RTs constituting a primary group across these genomes. More importantly, many annotated LTR-RTs(from 10.03% to 33.25% of all detected LTR-RTs) were found to be enriched in localized hotspot regions. Furthermore, all of the analyzed species showed evidence of having experienced at least one round of a LTR-RT burst, with Raphanus sativus experiencing three or more. Moreover, these relatively ancient LTR-RT amplifications exhibited a clear expansion at specific time points. To gain a further understanding of this timing, Brassica rapa, B. oleracea, and R. sativus were examined for the presence of syntenic regions, but none were present. These findings indicate that these LTR-RT burst events were not inherited from a common ancestor,but instead were species-specific bursts that occurred after the divergence of Brassica species. This study further exemplifies the complexities of TE amplifications during the evolution of plant genomes and suggests that these LTR-RT bursts play an important role in genome expansion and divergence in Brassica species.
