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LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice.

Wang H, Xu Z, Yu H - BMC Genomics (2008)

Bottom Line: From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years.In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago.At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: T-life Research Center, Department of Physics, Fudan University, Shanghai 200433, PR China. wangh8@fudan.edu.cn

ABSTRACT

Background: Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history.

Results: The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago.

Conclusion: A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome.

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The distribution of inter-subspecies distance in large-scale samplings. (a) dinter of 3,102 pairs of LTR-related intergenic sequences. (b) dinter of the intron regions of 5,502 cDNA verified genes. Comparing to LTR-related loci, the average substitution rate in genic regions is 5–6 times slower. (c) dinter of the intron regions of 19,775 BGF predicted gene models. (d) Mismatch densities of 400,000 random samplings in the comparative map. The result gives that 15.3–18.7% of genomic sequences belong to Group-B.
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Figure 3: The distribution of inter-subspecies distance in large-scale samplings. (a) dinter of 3,102 pairs of LTR-related intergenic sequences. (b) dinter of the intron regions of 5,502 cDNA verified genes. Comparing to LTR-related loci, the average substitution rate in genic regions is 5–6 times slower. (c) dinter of the intron regions of 19,775 BGF predicted gene models. (d) Mismatch densities of 400,000 random samplings in the comparative map. The result gives that 15.3–18.7% of genomic sequences belong to Group-B.

Mentions: Large-scale sampling further confirmed that the same bimodal pattern of dinter existed in the entire genome, including non-LTR-related regions. dinter is now defined as the distance between any pair of alleles and no longer restricted in shared LTR elements. Firstly, we investigated the 3,102 intergenic LTR regions (see section "Overview of LTR retrotransposons identified by LTR_INSERT"). Comparing to the shared full-length elements, the sample capacity increased 30 folds. The distribution and percentage of group-B elements (Figure 3(a), Table 2) are clearly consistent with Figure 2(b): a peak is located at 0.015–0.018 and the two distributions separate at 0.005–0.006. Next we calculated pairwise distance of intron regions of 5,502 pairs of cDNA verified genes and 19,775 pairs of BGF annotated gene models respectively (see Methods) and found the bimodal pattern as well (Figure 3(b) and 3(c)): the peak of distribution A is located at 0.003–0.004 and two distributions separate at 0.001–0.0015. The investigation of coding regions gave similar results ([see Additional file 4]).


LTR retrotransposons reveal recent extensive inter-subspecies nonreciprocal recombination in Asian cultivated rice.

Wang H, Xu Z, Yu H - BMC Genomics (2008)

The distribution of inter-subspecies distance in large-scale samplings. (a) dinter of 3,102 pairs of LTR-related intergenic sequences. (b) dinter of the intron regions of 5,502 cDNA verified genes. Comparing to LTR-related loci, the average substitution rate in genic regions is 5–6 times slower. (c) dinter of the intron regions of 19,775 BGF predicted gene models. (d) Mismatch densities of 400,000 random samplings in the comparative map. The result gives that 15.3–18.7% of genomic sequences belong to Group-B.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2612701&req=5

Figure 3: The distribution of inter-subspecies distance in large-scale samplings. (a) dinter of 3,102 pairs of LTR-related intergenic sequences. (b) dinter of the intron regions of 5,502 cDNA verified genes. Comparing to LTR-related loci, the average substitution rate in genic regions is 5–6 times slower. (c) dinter of the intron regions of 19,775 BGF predicted gene models. (d) Mismatch densities of 400,000 random samplings in the comparative map. The result gives that 15.3–18.7% of genomic sequences belong to Group-B.
Mentions: Large-scale sampling further confirmed that the same bimodal pattern of dinter existed in the entire genome, including non-LTR-related regions. dinter is now defined as the distance between any pair of alleles and no longer restricted in shared LTR elements. Firstly, we investigated the 3,102 intergenic LTR regions (see section "Overview of LTR retrotransposons identified by LTR_INSERT"). Comparing to the shared full-length elements, the sample capacity increased 30 folds. The distribution and percentage of group-B elements (Figure 3(a), Table 2) are clearly consistent with Figure 2(b): a peak is located at 0.015–0.018 and the two distributions separate at 0.005–0.006. Next we calculated pairwise distance of intron regions of 5,502 pairs of cDNA verified genes and 19,775 pairs of BGF annotated gene models respectively (see Methods) and found the bimodal pattern as well (Figure 3(b) and 3(c)): the peak of distribution A is located at 0.003–0.004 and two distributions separate at 0.001–0.0015. The investigation of coding regions gave similar results ([see Additional file 4]).

Bottom Line: From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years.In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago.At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: T-life Research Center, Department of Physics, Fudan University, Shanghai 200433, PR China. wangh8@fudan.edu.cn

ABSTRACT

Background: Long Terminal Repeats retrotransposons (LTR elements) are ubiquitous Eukaryotic transposable elements (TEs). They are considered to be one of the major forces underlying plant genome evolution. Because of relatively high evolutionary speed, active transposition of LTR elements in the host genomes provides rich information on their short-term history. As more and more genomes, especially those of closely related organisms, have been sequenced, it is possible to perform global comparative study of their LTR retrotransposons to reveal events in the history.

Results: The present research is designed to investigate important evolutionary events in the origin of Asian cultivated rice through the comparison of LTR elements. We have developed LTR_INSERT, a new method for LTR elements discovery in two closely related genomes. Our method has a distinctive feature that it is capable of judging whether an insertion occurs prior or posterior to the divergence of genomes. LTR_INSERT identifies 993 full-length LTR elements, annotates 15916 copies related with them, and discovers at least 16 novel LTR families in the whole-genome comparative map of two cultivated rice subspecies. From the full-length LTR elements, we estimate that a significant proportion of the rice genome has experienced inter-subspecies nonreciprocal recombination (ISNR) in as recent as 53,000 years. Large-scale samplings further support that more than 15% of the rice genome has been involved in such recombination. In addition, LTR elements confirm that the genome of O. sativa ssp. indica and that of japonica diverged about 600,000 years ago.

Conclusion: A new LTR retrotransposon identification method integrating both comparative genomics and ab initio algorithm is introduced and applied to Asian cultivated rice genomes. At whole-genome level, this work confirms that recent ISNR is an important factor that molds modern cultivated rice genome.

Show MeSH
Related in: MedlinePlus