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

Abstract

BackgroundVarious 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.ResultsThe 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.ConclusionTwo 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 IRA 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.

The Complete Plastid Genome Sequence of Iris gatesii (Section Oncocyclus), a Bearded Species from Southeastern Turkey

“…Wang et al (2008) also demonstrated a further expansion of the IR at the 39 LSC boundary to include rps19 in plastid genomes of Asparagales and commelinid (Commelinales, Zingiberales, Arecales, Dasypogonaceae, and Poales) species included in their study. They concluded that plastid genomes of the more derived monocots, including Asparagales, and members of the commelinid clade, are all likely to share an expansion of the IR to include rps19.…”

“…They further concluded that the endpoint of the IR is highly conserved because across Asparagales and commelinids only 35-99 bp were duplicated beyond rps19. The Wang et al (2008) study is based on results of Sanger sequencing at the IR-LSC boundaries to identify genes present and reverse transcriptase-polymerase chain reaction (RT-PCR) assays to verify transcription of the trnH-GUG and/or rps19 genes. The results of this study are not entirely concordant with the Wang et al study with respect to the duplication of rps19.…”

The Complete Chloroplast Genome Sequences of<em> Fritillaria ussuriensis</em> Maxim. and <em>Fritillaria cirrhosa</em> D. Don, and Comparative Analysis with Other<em> Fritillaria</em> Species

“…However, the contraction and expansion at the borders of IR regions are common evolutionary events, and are major causes of rearrangements and size variation [7,15,38]. In this study, we compared the SC/IR boundaries among six Fritillaria genomes.…”

“…The SSC region of F. ussuriensis was 423 bp shorter than that of F. cirrhosa. IR contraction and expansion are common evolutionary events and contribute to genome size variation [6,7,24]. We analyzed the border structure of the two cp genomes.…”

Analysis of the chloroplast genome and SNP detection in a salt tolerant breeding line in Korean ginseng

“…Chloroplast is a plant organelle containing its own circular DNA molecules that vary in size from 120 kb to 160 kb depending on the plant species. Chloroplast DNA (CpDNA) is largely composed of LSC, SSC, and they encode 4 rRNAs, 30 tRNAs, and 80 proteins on average, which are involved in photosynthesis or the expression of chromosomal genes (Palmer 1985;Jansen et al 2005;Wang et al 2008).…”