A novel chloroplast gene reported for flagellate plants

Song, Michael; Kuo, Li‐Yaung; Huiet, Layne; Pryer, Kathleen M.; Rothfels, Carl J.; Li, Fay‐Wei

doi:10.1002/ajb2.1010

Cited by 11 publications

(14 citation statements)

References 31 publications

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“…For Callistopteris apiifolia and Dipteris conjugata , we were unable to assemble the plastomes into complete circles, but instead obtained 12 and four large contigs, respectively. All the plastid genes known in ferns (including the ycf94 that was recently discovered by Song et al., ) were found in these three plastomes, except that three tRNA genes, trnK‐UUU , trnT‐UGU , and trnS‐CGA are missing, a feature also shared with other non‐Osmundales leptosporangiate plastomes (Appendix S2). In the Hymenophyllales plastomes, trnL‐CAA appears to be a pseudogene, given that the sequences are highly variable, include many indels (data not shown), and do not have proper predicted tRNA folding according to ARAGORN.…”

Section: Resultsmentioning

confidence: 84%

Order‐level fern plastome phylogenomics: new insights from Hymenophyllales

Kuo

Mā

et al. 2018

American J of Botany

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Section: Resultsmentioning

confidence: 84%

Order‐level fern plastome phylogenomics: new insights from Hymenophyllales

Kuo

Mā

et al. 2018

American J of Botany

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“…S13, Supplementary Material online), but we could not identify any candidate homologs outside of this group even when using HHpred or when considering its position relative to other genes as a clue. Following the convention for naming conserved pt genes of unknown function (Hallick and Bairoch 1994) and considering ycf94 being the most recently described gene in this category (Song et al. 2018), we designate the respective ORF as ycf95 .…”

Section: Resultsmentioning

confidence: 99%

Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts

Ševčíková

Yurchenko

Fawley

et al. 2019

Genome Biology and Evolution

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Eustigmatophytes, a class of stramenopile algae (ochrophytes), include not only the extensively studied biotechnologically important genus Nannochloropsis but also a rapidly expanding diversity of lineages with much less well characterized biology. Recent discoveries have led to exciting additions to our knowledge about eustigmatophytes. Some proved to harbor bacterial endosymbionts representing a novel genus, Candidatus Phycorickettsia, and an operon of unclear function (ebo) obtained by horizontal gene transfer from the endosymbiont lineage was found in the plastid genomes of still other eustigmatophytes. To shed more light on the latter event, as well as to generally improve our understanding of the eustigmatophyte evolutionary history, we sequenced plastid genomes of seven phylogenetically diverse representatives (including new isolates representing undescribed taxa). A phylogenomic analysis of plastid genome-encoded proteins resolved the phylogenetic relationships among the main eustigmatophyte lineages and provided a framework for the interpretation of plastid gene gains and losses in the group. The ebo operon gain was inferred to have probably occurred within the order Eustigmatales, after the divergence of the two basalmost lineages (a newly discovered hitherto undescribed strain and the Pseudellipsoidion group). When looking for nuclear genes potentially compensating for plastid gene losses, we noticed a gene for a plastid-targeted acyl carrier protein that was apparently acquired by horizontal gene transfer from Phycorickettsia. The presence of this gene in all eustigmatophytes studied, including representatives of both principal clades (Eustigmatales and Goniochloridales), is a genetic footprint indicating that the eustigmatophyte–Phycorickettsia partnership started no later than in the last eustigmatophyte common ancestor.

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“…Raw Illumina RNA reads for the A. shastense and A. aleuticum plastomes were obtained from Song et al (2018) and the 1000 plant transcriptome project (Carpenter et al, 2019), respectively. The raw reads were uploaded from the NCBI Sequence Read Archive to the Minnesota Supercomputing Institute’s High Performance Computing cluster (MSI HPC) using the sratoolkit programs prefetch and fastq‐dump (Leionen et al, 2011).…”

Section: Methodsmentioning

confidence: 99%

Variation in frequency of plastid RNA editing within Adiantum implies rapid evolution in fern plastomes

Fauskee

Sigel

Pryer

et al. 2021

American J of Botany

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Recent studies of plant RNA editing have demonstrated that the number of editing sites can vary widely among large taxonomic groups (orders, families). Yet, very little is known about intrageneric variation in frequency of plant RNA editing, and no study has been conducted in ferns. METHODS:We determined plastid RNA-editing counts for two species of Adiantum (Pteridaceae), A. shastense and A. aleuticum, by implementing a pipeline that integrated read-mapping and SNP-calling software to identify RNA-editing sites. We then compared the edits found in A. aleuticum and A. shastense with previously published edits from A. capillus-veneris by generating alignments for each plastid gene. RESULTS:We found direct evidence for 505 plastid RNA-editing sites in A. aleuticum and 509 in A. shastense, compared with 350 sites in A. capillus-veneris. We observed striking variation in the number and location of the RNA-editing sites among the three species, with reverse (U-to-C) editing sites showing a higher degree of conservation than forward (C-to-U) sites. Additionally, sites involving start and stop codons were highly conserved.CONCLUSIONS: Variation in the frequency of RNA editing within Adiantum implies that RNAediting sites can be rapidly gained or lost throughout evolution. However, varying degrees of conservation between both C-to-U and U-to-C sites and sites in start or stop codons, versus other codons, hints at the likely independent origin of both types of edits and a potential selective advantage conferred by RNA editing.

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A novel chloroplast gene reported for flagellate plants

Cited by 11 publications

References 31 publications

Order‐level fern plastome phylogenomics: new insights from Hymenophyllales

Order‐level fern plastome phylogenomics: new insights from Hymenophyllales

Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts

Variation in frequency of plastid RNA editing within Adiantum implies rapid evolution in fern plastomes

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