The evolution of chloroplast genes and genomes in ferns

Wolf, Paul G.; Der, Joshua P.; Duffy, Aaron M.; Davidson, Jacob B.; Grusz, Amanda L.; Pryer, Kathleen M.

doi:10.1007/s11103-010-9706-4

Cited by 87 publications

(66 citation statements)

References 60 publications

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“…It has further been argued that a relaxed evolutionary pressure as a result of the parasitic lifestyle might have had effects beyond photosynthesis, but substitution rate analyses did not strongly support this assumption, either (Krause 2010). In context with reports that many genes exhibit a generally high level of substitution rates in seed plants, independent of the absence of photosynthesis (Greiner et al 2008;Guisinger et al 2008;Wolf et al 2011), one must conclude, therefore, that the informative value of such analyses with respect to the evolutionary development of parasites is rather limited.…”

Section: Nucleotide Substitution Ratesmentioning

confidence: 99%

Piecing together the puzzle of parasitic plant plastome evolution

Krause

2011

Planta

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The importance of photosynthesis as a mode of energy production has put plastid genomes of plants under a constant purifying selection. This has shaped the characteristic features of plastid genomes across the entire spectrum of photosynthetic plants and has led to a highly uniform and conserved plastid genome with respect to structure, size, gene order, intron and editing site positions and coding capacity. Parasitic species that have dropped photosynthesis as the main energy provider share striking deviations from the plastid genome norm: multiple rearrangements within the circular chromosome, pseudogenization and gene deletions, promoter losses, intron losses as well as the extensive loss of mRNA editing competence have been reported. The collective loss of larger sets of functionally related genes like those for the plastid NADH-dehydrogenase complex and concomitant losses of RNA polymerase genes together with their target promoters point to "domino effects" where an initial loss might have triggered others. An example, which will be discussed in more detail, is the concomitant loss of the intron maturase gene matK and all introns that are supposedly subject to MatK-dependent splicing in two Cuscuta species.

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Section: Nucleotide Substitution Ratesmentioning

confidence: 99%

Piecing together the puzzle of parasitic plant plastome evolution

Krause

2011

Planta

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“…These are Alsophila spinulosa (Gao et al, 2009), Adiantum capillus-veneris (Wolf et al, 2003), Cheilanthes lindheimeri, Pteridium aquilinum subsp. a quilinum (Wolf et al, 2011), Lygodium japonicum , and Marsilea crenata (Gao et al, 2013). In addition, the incomplete sequences were also used for the reconstruction of the fern trees (Wolf et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Chloroplast Genome Evolution in Early Diverged Leptosporangiate Ferns

Kim¹,

Chung²,

Kim³

2014

Molecules and Cells

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In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of co-dons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.

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“…In monilophytes, a sister group to that of seed plants, no comparative cp genome analyses have been performed in intraspecific taxa despite the availability of seven complete cp genome sequences [12]–[15]. Previous monilophyte cp genome analyses focused on higher taxonomic levels and examined gene content, gene rearrangement, nucleotide substitution, and phylogenetic relationships.…”

Section: Introductionmentioning

confidence: 99%

Chloroplast Genome Differences between Asian and American Equisetum arvense (Equisetaceae) and the Origin of the Hypervariable trnY-trnE Intergenic Spacer

Kim

2014

PLoS ONE

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Comparative analyses of complete chloroplast (cp) DNA sequences within a species may provide clues to understand the population dynamics and colonization histories of plant species. Equisetum arvense (Equisetaceae) is a widely distributed fern species in northeastern Asia, Europe, and North America. The complete cp DNA sequences from Asian and American E. arvense individuals were compared in this study. The Asian E. arvense cp genome was 583 bp shorter than that of the American E. arvense. In total, 159 indels were observed between two individuals, most of which were concentrated on the hypervariable trnY-trnE intergenic spacer (IGS) in the large single-copy (LSC) region of the cp genome. This IGS region held a series of 19 bp repeating units. The numbers of the 19 bp repeat unit were responsible for 78% of the total length difference between the two cp genomes. Furthermore, only other closely related species of Equisetum also show the hypervariable nature of the trnY-trnE IGS. By contrast, only a single indel was observed in the gene coding regions: the ycf1 gene showed 24 bp differences between the two continental individuals due to a single tandem-repeat indel. A total of 165 single-nucleotide polymorphisms (SNPs) were recorded between the two cp genomes. Of these, 52 SNPs (31.5%) were distributed in coding regions, 13 SNPs (7.9%) were in introns, and 100 SNPs (60.6%) were in intergenic spacers (IGS). The overall difference between the Asian and American E. arvense cp genomes was 0.12%. Despite the relatively high genetic diversity between Asian and American E. arvense, the two populations are recognized as a single species based on their high morphological similarity. This indicated that the two regional populations have been in morphological stasis.

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The evolution of chloroplast genes and genomes in ferns

Cited by 87 publications

References 60 publications

Piecing together the puzzle of parasitic plant plastome evolution

Piecing together the puzzle of parasitic plant plastome evolution

Chloroplast Genome Evolution in Early Diverged Leptosporangiate Ferns

Chloroplast Genome Differences between Asian and American Equisetum arvense (Equisetaceae) and the Origin of the Hypervariable trnY-trnE Intergenic Spacer

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