Variable presence of the inverted repeat and plastome stability in<i>Erodium</i>

Blazier, John C.; Jansen, Robert K.; Mower, Jeffrey P.; Govindu, Madhu; Zhang, Jin; Weng, Mao‐Lun; Ruhlman, Tracey A.

doi:10.1093/aob/mcw065

Cited by 83 publications

(110 citation statements)

References 58 publications

Supporting

Mentioning

108

Contrasting

Order By: Relevance

“…The slower rate of gene rearrangements observed for the IR-containing genomes of the Oedogoniales could possibly be explained by a stabilizing role of the IR through its participation in homologous recombination events. However, a number of studies in land plants (Jansen & Ruhlman, 2012; Blazier et al, 2016) are not consistent with the long-held hypothesis that the IR prevents gene rearrangements by limiting the frequency of recombination between single-copy regions (Palmer, 1991). A positive correlation has rather been observed between the level of gene rearrangements and the amount of dispersed repeats in land plant lineages displaying highly rearranged genomes (Weng et al, 2014; Blazier et al, 2016).…”

Section: Discussionmentioning

confidence: 92%

“…However, a number of studies in land plants (Jansen & Ruhlman, 2012; Blazier et al, 2016) are not consistent with the long-held hypothesis that the IR prevents gene rearrangements by limiting the frequency of recombination between single-copy regions (Palmer, 1991). A positive correlation has rather been observed between the level of gene rearrangements and the amount of dispersed repeats in land plant lineages displaying highly rearranged genomes (Weng et al, 2014; Blazier et al, 2016). But this correlation does not appear to hold for several green algal lineages (Turmel, Otis & Lemieux, 2015; Lemieux, Otis & Turmel, 2016), including the Oedogoniales in which the repeat-poor and gene-dense Oedogonium cpDNA differs from the repeat-rich Oedocladium cpDNA by a single reversal.…”

Section: Discussionmentioning

confidence: 92%

See 1 more Smart Citation

Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

Brouard

Turmel

Otis

et al. 2016

PeerJ

View full text Add to dashboard Cite

BackgroundThe chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA) structure, size, gene order, and intron content have been observed. The large inverted repeat (IR), an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales) but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum.MethodsThe Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed.ResultsThe 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold longer and dispersed repeats are more abundant, but a smaller fraction of the Oedocladium genome is occupied by introns. Six additional group II introns are present, five of which lack ORFs and carry highly similar sequences to that of the ORF-less IIA intron shared with Oedogonium. Secondary structure analysis of the group IIA introns disclosed marked differences in the exon-binding sites; however, each intron showed perfect or nearly perfect base pairing interactions with its target site.DiscussionOur results suggest that chloroplast genes rearrange more slowly in the Oedogoniales than in the Chaetophorales and raise questions as to what was the nature of the foreign coding sequences in the IR of the common ancestor of the Oedogoniales. They provide the first evidence for intragenomic proliferation of group IIA introns in the Viridiplantae, revealing that intron spread in the Oedocladium lineage likely occurred by retrohoming after sequence divergence of the exon-binding sites.

show abstract

Section: Discussionmentioning

confidence: 92%

Section: Discussionmentioning

confidence: 92%

Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

Brouard

Turmel

Otis

et al. 2016

PeerJ

View full text Add to dashboard Cite

show abstract

“…Larger variation in plastome size due to IR expansion and contraction has been documented in several unrelated lineages, including Geraniaceae (Chumley et al, ; Blazier et al, ; Weng et al, , 2017), Plantago (Zhu et al, ), Ericaceae (Fajardo et al, ; Martínez‐Alberola et al, ), Berberis (Ma et al, ), Annona (Blazier et al, ) and Trochodendraceae (Sun et al, ). Among these lineages, Geraniaceae has the broadest range of IR sizes including species with enormous IR expansion to ∼88 kb in Pelargonium transvaalense (Weng et al, ), significant reduction to ∼7 kb in Monsonia speciosa (Guisinger et al, ) and species lacking an IR entirely in Erodium and Monsonia (Blazier et al, ; Ruhlman et al, ). Inverted repeat loss has been documented in other angiosperm lineages such as Fabaceae (Palmer & Thompson, ; Downie & Palmer, ) and Cactaceae (Sanderson et al, ).…”

Section: Introductionmentioning

confidence: 99%

Passiflora plastome sequencing reveals widespread genomic rearrangements

Rabah

Shrestha

Hajrah

et al. 2018

J of Sytematics Evolution

Self Cite

View full text Add to dashboard Cite

Although past studies have included Passiflora among angiosperm lineages with highly rearranged plastid genomes (plastomes), knowledge about plastome organization in the genus is limited. So far only one draft and one complete plastome have been published. Expanded sampling of Passiflora plastomes is needed to understand the extent of the genomic rearrangement in the genus, which is also unusual in having biparental plastid inheritance and plastome‐genome incompatibility. We sequenced 15 Passiflora plastomes using either Illumina paired‐end or shotgun cloning and Sanger sequencing approaches. Assembled plastomes were annotated using Dual Organellar GenoMe Annotator (DOGMA) and tRNAscan‐SE. The Populus trichocarpa plastome was used as a reference to estimate genomic rearrangements in Passiflora by performing whole genome alignment in progressiveMauve. The phylogenetic distribution of rearrangements was plotted on the maximum likelihood tree generated from 64 plastid encoded protein genes. Inverted repeat (IR) expansion/contraction and loss of the two largest hypothetical open reading frames, ycf1 and ycf2, account for most plastome size variation, which ranges from 139 262 base pairs (bp) in P. biflora to 161 494 bp in P. pittieri. Passiflora plastomes have experienced numerous inversions, gene and intron losses along with multiple independent IR expansions and contractions resulting in a distinct organization in each of the three subgenera examined. Each Passiflora subgenus has a unique plastome structure in terms of gene content, order and size. The phylogenetic distribution of rearrangements shows that Passiflora has experienced widespread genomic changes, suggesting that such events may not be reliable phylogenetic markers.

show abstract

“…However, recent studies showed that the presence of the IR does not ensure genome stability. In the plastomes of Oleaceae (Lee et al ., ), Erodium (Blazier et al ., ), Pelargonium (Chumley et al ., ; Weng et al ., ) and Plantago (Zhu et al ., ), genomic rearrangements were observed despite the presence of the IR. In addition, no correlation between the presence or absence of the IR and genome stability was detected in Erodium (Blazier et al ., ).…”

Section: Introductionmentioning

confidence: 99%

Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes

2016

Self Cite

View full text Add to dashboard Cite

For species with minor inverted repeat (IR) boundary changes in the plastid genome (plastome), nucleotide substitution rates were previously shown to be lower in the IR than the single copy regions (SC). However, the impact of large-scale IR expansion/contraction on plastid nucleotide substitution rates among closely related species remains unclear. We included plastomes from 22 Pelargonium species, including eight newly sequenced genomes, and used both pairwise and model-based comparisons to investigate the impact of the IR on sequence evolution in plastids. Ten types of plastome organization with different inversions or IR boundary changes were identified in Pelargonium. Inclusion in the IR was not sufficient to explain the variation of nucleotide substitution rates. Instead, the rate heterogeneity in Pelargonium plastomes was a mixture of locus-specific, lineage-specific and IR-dependent effects. Our study of Pelargonium plastomes that vary in IR length and gene content demonstrates that the evolutionary consequences of retaining these repeats are more complicated than previously suggested.

show abstract

Variable presence of the inverted repeat and plastome stability inErodium

Abstract: The presence or absence of the IR does not affect plastome stability in Erodium. Rather, the overall repeat content shows a negative correlation with genome stability, a pattern in agreement with other angiosperm groups and recent findings on genome stability in bacterial endosymbionts.

Cited by 83 publications

References 58 publications

Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

Passiflora plastome sequencing reveals widespread genomic rearrangements

Expansion of inverted repeat does not decrease substitution rates in Pelargonium plastid genomes

Contact Info

Product

Resources

About