TY - JOUR
T1 - Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots
AU - Wang, Rui Jiang
AU - Cheng, Chiao Lei
AU - Chang, Ching Chun
AU - Wu, Chun Lin
AU - Su, Tian Mu
AU - Chaw, Shu Miaw
N1 - Funding Information:
This work was supported by a research grant from the Research Center for Biodiversity, Academia Sinica, to SMC, and in part by a grant from Guangzhou Forestry Administration to RJW. We thank Yin-Long Qiu for providing DNA of some basal angiosperms, and the staff of the RBG Kew DNA Bank for some plant genomic DNA materials. We gratefully acknowledge the critical reading of the manuscript by Pablo Bolanos-Villegas and Yu-Ting Lai and the valuable comments by three anonymous reviewers.
PY - 2008
Y1 - 2008
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.
UR - http://www.scopus.com/inward/record.url?scp=43549096694&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=43549096694&partnerID=8YFLogxK
U2 - 10.1186/1471-2148-8-36
DO - 10.1186/1471-2148-8-36
M3 - Article
C2 - 18237435
AN - SCOPUS:43549096694
SN - 1471-2148
VL - 8
JO - BMC Evolutionary Biology
JF - BMC Evolutionary Biology
IS - 1
M1 - 36
ER -