Limits...
Rapid degeneration of noncoding DNA regions surrounding SlAP3X/Y after recombination suppression in the dioecious plant Silene latifolia.

Ishii K, Nishiyama R, Shibata F, Kazama Y, Abe T, Kawano S - G3 (Bethesda) (2013)

Bottom Line: Using the nucleotide divergence calculated between left and right long terminal repeat sequences, insertion dates were estimated to be 0.083-1.6 million years ago, implying that all elements detected were inserted after recombination stopped.A reciprocal sequence homology search facilitated the identification of four homologous noncoding DNA regions between the X and Y chromosomes, spanning 6.7% and 10.6% of the X chromosome-derived and Y chromosome-derived sequences, respectively, investigated.Genomic Southern blotting and fluorescence in situ hybridization showed that the noncoding DNA flanking SlAP3X/Y has homology to many regions throughout the genome, regardless of whether they were homologous between the X and Y chromosomes.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Nishina Center, Wako, Saitama 351-0198, Japan.

ABSTRACT
Silene latifolia is a dioecious plant with heteromorphic XY sex chromosomes. Previous studies of sex chromosome-linked genes have suggested a gradual divergence between the X-linked and the Y-linked genes in proportion to the distance from the pseudoautosomal region. However, such a comparison has yet to be made for the noncoding regions. To better characterize the nonrecombining region of the X and Y chromosomes, we sequenced bacterial artificial chromosome clones containing the sex chromosome-linked paralogs SlAP3X and SlAP3Y, including 115 kb and 73 kb of sequences, respectively, flanking these genes. The synonymous nucleotide divergence between SlAP3X and SlAP3Y indicated that recombination stopped approximately 3.4 million years ago. Sequence homology analysis revealed the presence of six long terminal repeat retrotransposon-like elements. Using the nucleotide divergence calculated between left and right long terminal repeat sequences, insertion dates were estimated to be 0.083-1.6 million years ago, implying that all elements detected were inserted after recombination stopped. A reciprocal sequence homology search facilitated the identification of four homologous noncoding DNA regions between the X and Y chromosomes, spanning 6.7% and 10.6% of the X chromosome-derived and Y chromosome-derived sequences, respectively, investigated. Genomic Southern blotting and fluorescence in situ hybridization showed that the noncoding DNA flanking SlAP3X/Y has homology to many regions throughout the genome, regardless of whether they were homologous between the X and Y chromosomes. This finding suggests that most noncoding DNA regions rapidly lose their counterparts because of the introduction of transposable elements and indels (insertion-deletions) after recombination has stopped.

Show MeSH

Related in: MedlinePlus

Genomic Southern blot analysis of SlAP3X and SlAP3Y. (A) Schematics of genomic sequences of SlAP3X and SlAP3Y. White and black boxes indicate untranslated regions and exons, respectively. Numbers indicate intron numbers of the genes and bold lines indicate probe sequence coverage of each intron for Southern hybridization. (B) Genomic Southern blot analysis of introns of SlAP3X and SlAP3Y. Numbers above lanes indicate intron numbers of the genes corresponding to those in (A).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3852375&req=5

fig2: Genomic Southern blot analysis of SlAP3X and SlAP3Y. (A) Schematics of genomic sequences of SlAP3X and SlAP3Y. White and black boxes indicate untranslated regions and exons, respectively. Numbers indicate intron numbers of the genes and bold lines indicate probe sequence coverage of each intron for Southern hybridization. (B) Genomic Southern blot analysis of introns of SlAP3X and SlAP3Y. Numbers above lanes indicate intron numbers of the genes corresponding to those in (A).

Mentions: We conducted dot plot analyses of each pair of introns (Figure 1). All five pairs contained regions of sequence homology, which implied that the pairs were homologous before recombination suppression. However, these homologous regions did not span the full lengths of the introns but were interspersed like island chains. To investigate whether introns consisted of unique or repetitive sequences, we designed probes inside the introns and performed genomic Southern blot analyses (Figure 2). The probes designed for the introns showed three patterns: a strong smear pattern (introns 1 and 2 of SlAP3X and introns 1 and 4 of SlAP3Y); a weak smear pattern (intron 3, 4, and 5 of SlAP3X and introns 3 of SlAP3Y); and a multiple-banded pattern (introns 5 and 6 of SlAP3Y). From this, it was revealed that all introns contained repetitive sequences; the distinctness of these patterns implied that each intron contained a different type of repeat sequence.


Rapid degeneration of noncoding DNA regions surrounding SlAP3X/Y after recombination suppression in the dioecious plant Silene latifolia.

Ishii K, Nishiyama R, Shibata F, Kazama Y, Abe T, Kawano S - G3 (Bethesda) (2013)

Genomic Southern blot analysis of SlAP3X and SlAP3Y. (A) Schematics of genomic sequences of SlAP3X and SlAP3Y. White and black boxes indicate untranslated regions and exons, respectively. Numbers indicate intron numbers of the genes and bold lines indicate probe sequence coverage of each intron for Southern hybridization. (B) Genomic Southern blot analysis of introns of SlAP3X and SlAP3Y. Numbers above lanes indicate intron numbers of the genes corresponding to those in (A).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3852375&req=5

fig2: Genomic Southern blot analysis of SlAP3X and SlAP3Y. (A) Schematics of genomic sequences of SlAP3X and SlAP3Y. White and black boxes indicate untranslated regions and exons, respectively. Numbers indicate intron numbers of the genes and bold lines indicate probe sequence coverage of each intron for Southern hybridization. (B) Genomic Southern blot analysis of introns of SlAP3X and SlAP3Y. Numbers above lanes indicate intron numbers of the genes corresponding to those in (A).
Mentions: We conducted dot plot analyses of each pair of introns (Figure 1). All five pairs contained regions of sequence homology, which implied that the pairs were homologous before recombination suppression. However, these homologous regions did not span the full lengths of the introns but were interspersed like island chains. To investigate whether introns consisted of unique or repetitive sequences, we designed probes inside the introns and performed genomic Southern blot analyses (Figure 2). The probes designed for the introns showed three patterns: a strong smear pattern (introns 1 and 2 of SlAP3X and introns 1 and 4 of SlAP3Y); a weak smear pattern (intron 3, 4, and 5 of SlAP3X and introns 3 of SlAP3Y); and a multiple-banded pattern (introns 5 and 6 of SlAP3Y). From this, it was revealed that all introns contained repetitive sequences; the distinctness of these patterns implied that each intron contained a different type of repeat sequence.

Bottom Line: Using the nucleotide divergence calculated between left and right long terminal repeat sequences, insertion dates were estimated to be 0.083-1.6 million years ago, implying that all elements detected were inserted after recombination stopped.A reciprocal sequence homology search facilitated the identification of four homologous noncoding DNA regions between the X and Y chromosomes, spanning 6.7% and 10.6% of the X chromosome-derived and Y chromosome-derived sequences, respectively, investigated.Genomic Southern blotting and fluorescence in situ hybridization showed that the noncoding DNA flanking SlAP3X/Y has homology to many regions throughout the genome, regardless of whether they were homologous between the X and Y chromosomes.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Nishina Center, Wako, Saitama 351-0198, Japan.

ABSTRACT
Silene latifolia is a dioecious plant with heteromorphic XY sex chromosomes. Previous studies of sex chromosome-linked genes have suggested a gradual divergence between the X-linked and the Y-linked genes in proportion to the distance from the pseudoautosomal region. However, such a comparison has yet to be made for the noncoding regions. To better characterize the nonrecombining region of the X and Y chromosomes, we sequenced bacterial artificial chromosome clones containing the sex chromosome-linked paralogs SlAP3X and SlAP3Y, including 115 kb and 73 kb of sequences, respectively, flanking these genes. The synonymous nucleotide divergence between SlAP3X and SlAP3Y indicated that recombination stopped approximately 3.4 million years ago. Sequence homology analysis revealed the presence of six long terminal repeat retrotransposon-like elements. Using the nucleotide divergence calculated between left and right long terminal repeat sequences, insertion dates were estimated to be 0.083-1.6 million years ago, implying that all elements detected were inserted after recombination stopped. A reciprocal sequence homology search facilitated the identification of four homologous noncoding DNA regions between the X and Y chromosomes, spanning 6.7% and 10.6% of the X chromosome-derived and Y chromosome-derived sequences, respectively, investigated. Genomic Southern blotting and fluorescence in situ hybridization showed that the noncoding DNA flanking SlAP3X/Y has homology to many regions throughout the genome, regardless of whether they were homologous between the X and Y chromosomes. This finding suggests that most noncoding DNA regions rapidly lose their counterparts because of the introduction of transposable elements and indels (insertion-deletions) after recombination has stopped.

Show MeSH
Related in: MedlinePlus