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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

Sequencing depth of the insertion (shown in blue) and its surrounding regions (shown in green) in the plastid genome of P. campestris.The position 82,279 is the start site of the inverted repeat regions.
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f2: Sequencing depth of the insertion (shown in blue) and its surrounding regions (shown in green) in the plastid genome of P. campestris.The position 82,279 is the start site of the inverted repeat regions.

Mentions: Given that the plastid genomes are highly conserved in bamboos232425, the large insertion being of mitochondrial DNA origin is unexpected. It is needed to confirm that the insertion was not a product of misassembly. As we used total genomic DNA of Pariana for Illumina sequencing, the reads were a mixture of DNA sequences from plastid, mitochondrial, and nuclear genomes. However, the plastid genome is usually the smallest one among these three genomes in angiosperms and the assembled plastid DNA sequences can be easily distinguished from mitochondrial and nuclear DNA sequences by sequencing depth. As shown in Fig. 2, the inserted region in P. campestris had an average sequencing depth of 56.9×, which was very similar to the surrounding regions with an average sequencing depth of 61.8× and 58.8× before and after the insertion, respectively. Although different sequencing depths of 29.8× and 28.7× were revealed for the inserted regions in Pariana sp. and P. radiciflora, respectively, the constant sequencing depth in the surrounding regions was also observed in these two bamboos (Supplementary Fig. 1). On the other hand, we mapped the Illumina reads of P. campestris to three randomly selected intronless genes from the F. rimosivaginus mitochondrial genome27, ccmFN, matR and rrn26, and obtained much lower sequencing depth of 5.6×, 7.1× and 11.9×, respectively. The sequencing depth for the three genes was also low in the other two Pariana species, ranging from 3.5× to 6.8×. These results indicated that the inserted regions had similar sequencing depth to the surrounding plastid regions, rather than the mitochondrial genome, even in considering that reads originating from the mitochondrial genome may have added a similar sequencing depth as inferred from the three mitochondrial genes to the inserted regions due to sequence similarity. The nuclear genome is much larger than mitochondrial genome and the sequencing depth would be even lower. In all, the analysis of sequencing depth demonstrated that the insertion in the plastid genomes of Pariana was unlikely due to misassembly.


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)

Sequencing depth of the insertion (shown in blue) and its surrounding regions (shown in green) in the plastid genome of P. campestris.The position 82,279 is the start site of the inverted repeat regions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Sequencing depth of the insertion (shown in blue) and its surrounding regions (shown in green) in the plastid genome of P. campestris.The position 82,279 is the start site of the inverted repeat regions.
Mentions: Given that the plastid genomes are highly conserved in bamboos232425, the large insertion being of mitochondrial DNA origin is unexpected. It is needed to confirm that the insertion was not a product of misassembly. As we used total genomic DNA of Pariana for Illumina sequencing, the reads were a mixture of DNA sequences from plastid, mitochondrial, and nuclear genomes. However, the plastid genome is usually the smallest one among these three genomes in angiosperms and the assembled plastid DNA sequences can be easily distinguished from mitochondrial and nuclear DNA sequences by sequencing depth. As shown in Fig. 2, the inserted region in P. campestris had an average sequencing depth of 56.9×, which was very similar to the surrounding regions with an average sequencing depth of 61.8× and 58.8× before and after the insertion, respectively. Although different sequencing depths of 29.8× and 28.7× were revealed for the inserted regions in Pariana sp. and P. radiciflora, respectively, the constant sequencing depth in the surrounding regions was also observed in these two bamboos (Supplementary Fig. 1). On the other hand, we mapped the Illumina reads of P. campestris to three randomly selected intronless genes from the F. rimosivaginus mitochondrial genome27, ccmFN, matR and rrn26, and obtained much lower sequencing depth of 5.6×, 7.1× and 11.9×, respectively. The sequencing depth for the three genes was also low in the other two Pariana species, ranging from 3.5× to 6.8×. These results indicated that the inserted regions had similar sequencing depth to the surrounding plastid regions, rather than the mitochondrial genome, even in considering that reads originating from the mitochondrial genome may have added a similar sequencing depth as inferred from the three mitochondrial genes to the inserted regions due to sequence similarity. The nuclear genome is much larger than mitochondrial genome and the sequencing depth would be even lower. In all, the analysis of sequencing depth demonstrated that the insertion in the plastid genomes of Pariana was unlikely due to misassembly.

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