Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion

Aii, Jotaro; Kishima, Yuji; Mikami, Tetsuo; Adachi, Tomohiko

doi:10.1007/s002940050206

Cited by 23 publications

(20 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Expansion of the IR into the SSC region is much less common, and only a few angiosperm families exhibit this phenomenon, including Campanulaceae (Cosner et al 1997; Haberle et al 2008; Knox and Palmer 1999), Geraniaceae (Chumley et al 2006; Palmer et al 1987), and Polygonaceae (Aii et al 1997; Logacheva et al 2008). Earlier investigations of one or two plastid genomes of Poaceae (Hiratsuka et al 1989; Maier et al 1995; Prombona and Subramanian 1989) identified expansion of the IR into the SSC region resulting in the duplication of rps15 .…”

Section: Discussionmentioning

confidence: 99%

“…We hypothesize that rates of sequence evolution may be correlated to genomic changes in grass plastid genomes. It should be noted that after the divergence of the grasses no major genomic changes occurred aside from minor expansions of the IR region, a very common process that accounts for size variation in plastid genomes throughout angiosperms (Aii et al 1997; Goulding et al 1996; Plunkett and Downie 2000) including the monocots (Wang et al 2008). …”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

et al. 2010

View full text Add to dashboard Cite

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00239-009-9317-3) contains supplementary material, which is available to authorized users.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

et al. 2010

View full text Add to dashboard Cite

show abstract

“…However, the conventional circular map does summarize many of the heritable structural features of the genome correctly. Among plant lineages that retain both copies of the IR, the sizes and boundaries of these regions, relative to the adjacent LSC and SSC, have been modified in various groups (e.g., Goulding et al, 1996; Aii et al, 1997; Plunkett and Downie, 2000; Perry et al, 2002; Stefanović and Olmstead, 2005; Wang et al, 2008).…”

Section: Plastid Genome Structurementioning

confidence: 99%

Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae)

Davis

Soreng

2010

American J of Botany

View full text Add to dashboard Cite

Overlapping genes occur widely in microorganisms and in some plastid genomes, but unique properties are observed when such genes span the boundaries between single-copy and repeat regions. The termini of ndhH and ndhF, situated near opposite ends of the small single-copy region (SSC) in the plastid genomes of grasses (Poaceae), have migrated repeatedly into and out of the adjacent inverted-repeat regions (IR). The two genes are transcribed in the same direction, and the 5' terminus of ndhH extends into the IR in some species, while the 3' terminus of ndhF extends into the IR in others. When both genes extend into the IR, portions of the genes overlap and are encoded by the same nucleotide positions. Fine-scale mapping of the SSC-IR junctions across a sample of 92 grasses and outgroups, integrated into a phylogenetic analysis, indicates that the earliest grasses resembled the related taxa Joinvillea (Joinvilleaceae) and Ecdeiocolea (Ecdeiocoleaceae), with ca. 180 nucleotides of ndhH extending into the IR, and with ndhF confined to the SSC. This structure is maintained in early-diverging grass lineages and in most species of the BEP clade. In the PACMAD clade, ndhH lies completely or nearly completely within the SSC, and ca. 20 nucleotides of ndhF extend into the IR. The nucleotide substitution rate has increased in the PACMAD clade in the portion of ndhH that has migrated into the SSC.

show abstract

“…For example, the unusual triple-sized expansion of the Geranium IR was hypothesized as an outcome of inversion due to recombination between homologous dispersed repeats [16]. Similarly, the at least 4 kb expansion of the IR in buckwheat ( Fagopyrum esculentum ) cpDNA was also considered to be associated with an inversion [17]. …”

Section: Introductionmentioning

confidence: 99%

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

et al. 2008

View full text Add to dashboard Cite

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.

show abstract

Expansion of the IR in the chloroplast genomes of buckwheat species is due to incorporation of an SSC sequence that could be mediated by an inversion

Cited by 23 publications

References 11 publications

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

Migration of endpoints of two genes relative to boundaries between regions of the plastid genome in the grass family (Poaceae)

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

Contact Info

Product

Resources

About