Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

Rui Jiang Wang, Chiao Lei Cheng, Ching-Chun Chang, Chun Lin Wu, Tian Mu Su, Shu Miaw Chaw

Research output: Contribution to journalArticle

150 Citations (Scopus)

Abstract

Background. Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a trnH-rps19 gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots. Results. The organizations of genes flanking IR-LSC junctions in angiosperms can be classified into three types. Generally each IR of monocots contains a trnH-rps19 gene cluster near the IR-LSC junctions, which differs from those in non-monocot angiosperms. Moreover, IRs expanded more progressively in monocots than in non-monocot angiosperms. IR-LSC junctions commonly occurred at polyA tract or A-rich regions in angiosperms. Our RT-PCR assays indicate that in monocot IRA the trnH-rps19 gene cluster is regulated by two opposing promoters, S10A and psbA. Conclusion. Two hypotheses are proposed to account for the evolution of IR expansions in monocots. Based on our observations, the inclusion of a trnH-rps19 cluster in majority of monocot IRs could be reasonably explained by the hypothesis that a DSB event first occurred at IRB and led to the expansion of IRs to trnH, followed by a successive DSB event within IR A and lead to the expansion of IRs to rps19 or to rpl22 so far. This implies that the duplication of trnH-rps19 gene cluster was prior to the diversification of extant monocot lineages. The duplicated trnH genes in the IRB of most monocots and non-monocot angiosperms have distinct fates, which are likely regulated by different expression levels of S10A and S10B promoters. Further study is needed to unravel the evolutionary significance of IR expansion in more recently diverged monocots.

Original languageEnglish
Article number36
JournalBMC Evolutionary Biology
Volume8
Issue number1
DOIs
Publication statusPublished - 2008 May 20

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Liliopsida
chloroplast
angiosperm
genome
gene
Angiospermae
multigene family
chloroplast genome
promoter regions
contraction
divergence
genes
assay
reverse transcriptase polymerase chain reaction

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics

Cite this

Wang, Rui Jiang ; Cheng, Chiao Lei ; Chang, Ching-Chun ; Wu, Chun Lin ; Su, Tian Mu ; Chaw, Shu Miaw. / Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. In: BMC Evolutionary Biology. 2008 ; Vol. 8, No. 1.
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abstract = "Background. Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a trnH-rps19 gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots. Results. The organizations of genes flanking IR-LSC junctions in angiosperms can be classified into three types. Generally each IR of monocots contains a trnH-rps19 gene cluster near the IR-LSC junctions, which differs from those in non-monocot angiosperms. Moreover, IRs expanded more progressively in monocots than in non-monocot angiosperms. IR-LSC junctions commonly occurred at polyA tract or A-rich regions in angiosperms. Our RT-PCR assays indicate that in monocot IRA the trnH-rps19 gene cluster is regulated by two opposing promoters, S10A and psbA. Conclusion. Two hypotheses are proposed to account for the evolution of IR expansions in monocots. Based on our observations, the inclusion of a trnH-rps19 cluster in majority of monocot IRs could be reasonably explained by the hypothesis that a DSB event first occurred at IRB and led to the expansion of IRs to trnH, followed by a successive DSB event within IR A and lead to the expansion of IRs to rps19 or to rpl22 so far. This implies that the duplication of trnH-rps19 gene cluster was prior to the diversification of extant monocot lineages. The duplicated trnH genes in the IRB of most monocots and non-monocot angiosperms have distinct fates, which are likely regulated by different expression levels of S10A and S10B promoters. Further study is needed to unravel the evolutionary significance of IR expansion in more recently diverged monocots.",
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Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. / Wang, Rui Jiang; Cheng, Chiao Lei; Chang, Ching-Chun; Wu, Chun Lin; Su, Tian Mu; Chaw, Shu Miaw.

In: BMC Evolutionary Biology, Vol. 8, No. 1, 36, 20.05.2008.

Research output: Contribution to journalArticle

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T1 - Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

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AU - Cheng, Chiao Lei

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AU - Chaw, Shu Miaw

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N2 - Background. Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a trnH-rps19 gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots. Results. The organizations of genes flanking IR-LSC junctions in angiosperms can be classified into three types. Generally each IR of monocots contains a trnH-rps19 gene cluster near the IR-LSC junctions, which differs from those in non-monocot angiosperms. Moreover, IRs expanded more progressively in monocots than in non-monocot angiosperms. IR-LSC junctions commonly occurred at polyA tract or A-rich regions in angiosperms. Our RT-PCR assays indicate that in monocot IRA the trnH-rps19 gene cluster is regulated by two opposing promoters, S10A and psbA. Conclusion. Two hypotheses are proposed to account for the evolution of IR expansions in monocots. Based on our observations, the inclusion of a trnH-rps19 cluster in majority of monocot IRs could be reasonably explained by the hypothesis that a DSB event first occurred at IRB and led to the expansion of IRs to trnH, followed by a successive DSB event within IR A and lead to the expansion of IRs to rps19 or to rpl22 so far. This implies that the duplication of trnH-rps19 gene cluster was prior to the diversification of extant monocot lineages. The duplicated trnH genes in the IRB of most monocots and non-monocot angiosperms have distinct fates, which are likely regulated by different expression levels of S10A and S10B promoters. Further study is needed to unravel the evolutionary significance of IR expansion in more recently diverged monocots.

AB - Background. Various expansions or contractions of inverted repeats (IRs) in chloroplast genomes led to fluxes in the IR-LSC (large single copy) junctions. Previous studies revealed that some monocot IRs contain a trnH-rps19 gene cluster, and it has been speculated that this may be an evidence of a duplication event prior to the divergence of monocot lineages. Therefore, we compared the organizations of genes flanking two IR-LSC junctions in 123 angiosperm representatives to uncover the evolutionary dynamics of IR-LSC junctions in basal angiosperms and monocots. Results. The organizations of genes flanking IR-LSC junctions in angiosperms can be classified into three types. Generally each IR of monocots contains a trnH-rps19 gene cluster near the IR-LSC junctions, which differs from those in non-monocot angiosperms. Moreover, IRs expanded more progressively in monocots than in non-monocot angiosperms. IR-LSC junctions commonly occurred at polyA tract or A-rich regions in angiosperms. Our RT-PCR assays indicate that in monocot IRA the trnH-rps19 gene cluster is regulated by two opposing promoters, S10A and psbA. Conclusion. Two hypotheses are proposed to account for the evolution of IR expansions in monocots. Based on our observations, the inclusion of a trnH-rps19 cluster in majority of monocot IRs could be reasonably explained by the hypothesis that a DSB event first occurred at IRB and led to the expansion of IRs to trnH, followed by a successive DSB event within IR A and lead to the expansion of IRs to rps19 or to rpl22 so far. This implies that the duplication of trnH-rps19 gene cluster was prior to the diversification of extant monocot lineages. The duplicated trnH genes in the IRB of most monocots and non-monocot angiosperms have distinct fates, which are likely regulated by different expression levels of S10A and S10B promoters. Further study is needed to unravel the evolutionary significance of IR expansion in more recently diverged monocots.

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