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Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus.

Ma PF, Zhang YX, Guo ZH, Li DZ - Sci Rep (2015)

Bottom Line: Here we sequenced 6 plastid genomes of bamboos, three of which are neotropical woody species and three are herbaceous ones.Our study provided evidence of the mitochondrial-to-plastid DNA transfer in the monocots, demonstrating again that this rare event does occur in other angiosperm lineages.However, the mechanism underlying the transfer remains obscure, and more studies in other plants may elucidate it in the future.

View Article: PubMed Central - PubMed

Affiliation: 1] Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China [2] Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.

ABSTRACT
In flowering plants, three genomes (nuclear, mitochondrial, and plastid) coexist and intracellular horizontal transfer of DNA is prevalent, especially from the plastid to the mitochondrion genome. However, the plastid genomes are generally conserved in evolution and have long been considered immune to foreign DNA. Recently, the opposite direction of DNA transfer from the mitochondrial to the plastid genome has been reported in two eudicot lineages. Here we sequenced 6 plastid genomes of bamboos, three of which are neotropical woody species and three are herbaceous ones. Several unusual features were found, including the duplication of trnT-GGU and loss of one copy of rps19 due to contraction of inverted repeats (IRs). The most intriguing was the ~2.7 kb insertion in the plastid IR regions in the three herbaceous bamboos. Furthermore, the insertion was documented to be horizontally transferred from the mitochondrial to the plastid genome. Our study provided evidence of the mitochondrial-to-plastid DNA transfer in the monocots, demonstrating again that this rare event does occur in other angiosperm lineages. However, the mechanism underlying the transfer remains obscure, and more studies in other plants may elucidate it in the future.

No MeSH data available.


Related in: MedlinePlus

Variability in the trnI-CAU-trnL-CAA intergenic spacer in the plastid genomes of Bambusoideae with the size indicated in parentheses.The insertion without plastid DNA homology in the plastid genomes of Pariana is shown in blue and the other plastid DNA sequences are shown in green. Sequence deletions larger than 25 bp relative to other species are indicated by black lines.
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f1: Variability in the trnI-CAU-trnL-CAA intergenic spacer in the plastid genomes of Bambusoideae with the size indicated in parentheses.The insertion without plastid DNA homology in the plastid genomes of Pariana is shown in blue and the other plastid DNA sequences are shown in green. Sequence deletions larger than 25 bp relative to other species are indicated by black lines.

Mentions: The trnI-CAU-trnL-CAA intergenic spacer located in the IR regions is very similar in size among the 30 sequenced plastid genomes of bamboos, ranging narrowly from 2471 to 2525 bp. The remnants of the pseudogenized ycf2 gene that is encoded in most other angiosperms could be identified in this intergenic spacer in grasses26. However, sequencing of the six bamboo plastid genomes here revealed extensive variation of this intergenic spacer in length: Pariana had the longest (3811 bp) and O. glauca the shortest (950 bp) (Fig. 1). By contrast, the size of other intergenic spacers of these bamboos in the IR regions remained fairly constant as in other bamboos. In O. glauca, the trnI-CAU-trnL-CAA intergenic spacer was much reduced to 950 bp because of a large deletion of 1542 bp between nucleotide positions 234 to 1775 when using C. circinata as a reference. This spacer also experienced sequence deletion at nearly the same position as in O. glauca (positions 421 to 1799 in C. circinata) in all three species of Pariana (Fig. 1), and the size of the deletion was estimated to be 1379 bp. However, the 1379-bp deletion in Pariana was accompanied by a 2706-bp insertion with the total size of the trnI-CAU-trnL-CAA intergenic spacer expanding to 3811 bp (Fig. 1). In addition, the sequences of insertion differed by only one nucleotide site (A to C substitution) among the three sequenced species of Pariana. Although the similarity of sequences surrounding the insertion in the trnI-CAU-trnL-CAA intergenic spacer was very high (>98%) between Pariana and the other sequenced bamboos, the sequence of insertion did not show similarity to any other sequences in the bamboo plastid genomes, suggesting that it perhaps originated from foreign DNA.


Evidence for horizontal transfer of mitochondrial DNA to the plastid genome in a bamboo genus.

Ma PF, Zhang YX, Guo ZH, Li DZ - Sci Rep (2015)

Variability in the trnI-CAU-trnL-CAA intergenic spacer in the plastid genomes of Bambusoideae with the size indicated in parentheses.The insertion without plastid DNA homology in the plastid genomes of Pariana is shown in blue and the other plastid DNA sequences are shown in green. Sequence deletions larger than 25 bp relative to other species are indicated by black lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4477325&req=5

f1: Variability in the trnI-CAU-trnL-CAA intergenic spacer in the plastid genomes of Bambusoideae with the size indicated in parentheses.The insertion without plastid DNA homology in the plastid genomes of Pariana is shown in blue and the other plastid DNA sequences are shown in green. Sequence deletions larger than 25 bp relative to other species are indicated by black lines.
Mentions: The trnI-CAU-trnL-CAA intergenic spacer located in the IR regions is very similar in size among the 30 sequenced plastid genomes of bamboos, ranging narrowly from 2471 to 2525 bp. The remnants of the pseudogenized ycf2 gene that is encoded in most other angiosperms could be identified in this intergenic spacer in grasses26. However, sequencing of the six bamboo plastid genomes here revealed extensive variation of this intergenic spacer in length: Pariana had the longest (3811 bp) and O. glauca the shortest (950 bp) (Fig. 1). By contrast, the size of other intergenic spacers of these bamboos in the IR regions remained fairly constant as in other bamboos. In O. glauca, the trnI-CAU-trnL-CAA intergenic spacer was much reduced to 950 bp because of a large deletion of 1542 bp between nucleotide positions 234 to 1775 when using C. circinata as a reference. This spacer also experienced sequence deletion at nearly the same position as in O. glauca (positions 421 to 1799 in C. circinata) in all three species of Pariana (Fig. 1), and the size of the deletion was estimated to be 1379 bp. However, the 1379-bp deletion in Pariana was accompanied by a 2706-bp insertion with the total size of the trnI-CAU-trnL-CAA intergenic spacer expanding to 3811 bp (Fig. 1). In addition, the sequences of insertion differed by only one nucleotide site (A to C substitution) among the three sequenced species of Pariana. Although the similarity of sequences surrounding the insertion in the trnI-CAU-trnL-CAA intergenic spacer was very high (>98%) between Pariana and the other sequenced bamboos, the sequence of insertion did not show similarity to any other sequences in the bamboo plastid genomes, suggesting that it perhaps originated from foreign DNA.

Bottom Line: Here we sequenced 6 plastid genomes of bamboos, three of which are neotropical woody species and three are herbaceous ones.Our study provided evidence of the mitochondrial-to-plastid DNA transfer in the monocots, demonstrating again that this rare event does occur in other angiosperm lineages.However, the mechanism underlying the transfer remains obscure, and more studies in other plants may elucidate it in the future.

View Article: PubMed Central - PubMed

Affiliation: 1] Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China [2] Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.

ABSTRACT
In flowering plants, three genomes (nuclear, mitochondrial, and plastid) coexist and intracellular horizontal transfer of DNA is prevalent, especially from the plastid to the mitochondrion genome. However, the plastid genomes are generally conserved in evolution and have long been considered immune to foreign DNA. Recently, the opposite direction of DNA transfer from the mitochondrial to the plastid genome has been reported in two eudicot lineages. Here we sequenced 6 plastid genomes of bamboos, three of which are neotropical woody species and three are herbaceous ones. Several unusual features were found, including the duplication of trnT-GGU and loss of one copy of rps19 due to contraction of inverted repeats (IRs). The most intriguing was the ~2.7 kb insertion in the plastid IR regions in the three herbaceous bamboos. Furthermore, the insertion was documented to be horizontally transferred from the mitochondrial to the plastid genome. Our study provided evidence of the mitochondrial-to-plastid DNA transfer in the monocots, demonstrating again that this rare event does occur in other angiosperm lineages. However, the mechanism underlying the transfer remains obscure, and more studies in other plants may elucidate it in the future.

No MeSH data available.


Related in: MedlinePlus