A Small Multifunctional Pentatricopeptide Repeat Protein in the Chloroplast of Chlamydomonas reinhardtii

Jalal, Abdullah; Schwarz, Christian; Schmitz‐Linneweber, Christian; Vallon, Olivier; Nickelsen, Jörg; Bohne, Alexandra‐Viola

doi:10.1016/j.molp.2014.11.019

Cited by 19 publications

(18 citation statements)

References 81 publications

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“…Previous research reported that genes belong to subunits of cytochrome were under positive selection in some species 47 , 48 , we therefore inferred that petL for cytochrome b6/f complex subunit proteins may have a high evolution rate in the cp genome of F. luojishanense . The gene rpoC2 was associated with PPR7 protein, we thus speculated it may have coevolved with nuclear genes 49 . The ycf1 and ycf2 are two of the largest genes encoding for a putative membrane protein 50 , 51 and in two Fagopyrum cp genomes these two genes may have rapidly evolved 3 .…”

Section: Discussionmentioning

confidence: 98%

Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships

Wang

Zhou

Bai

et al. 2018

Sci Rep

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Fagopyrum dibotrys, belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values. Here, the complete chloroplast (cp) genome sequence of F. dibotrys is reported. The cp genome size is 159,919 bp with a typical quadripartite structure and consisting of a pair of inverted repeat regions (30,738 bp) separated by large single copy region (85,134 bp) and small single copy region (13,309 bp). Sequencing analyses indicated that the cp genome encodes 131 genes, including 80 protein-coding genes, 28 tRNA genes and 4 rRNA genes. The genome structure, gene order and codon usage are typical of angiosperm cp genomes. We also identified 48 simple sequence repeats (SSR) loci, fewer of them are distributed in the protein-coding sequences compared to the noncoding regions. Comparison of F. dibotrys cp genome to other Polygonaceae cp genomes indicated the inverted repeats (IRs) and coding regions were more conserved than single copy and noncoding regions, and several variation hotspots were detected. Coding gene sequence divergence analyses indicated that five genes (ndhK, petL rpoC2, ycf1, ycf2) were subject to positive selection. Phylogenetic analysis among 42 species based on cp genomes and 50 protein-coding genes indicated a close relationship between F. dibotrys and F. tataricum. In summary, the complete cp genome sequence of F. dibotrys reported in this study will provide useful plastid genomic resources for population genetics and pave the way for resolving phylogenetic relationships of order Caryophyllales.

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Section: Discussionmentioning

confidence: 98%

Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships

Wang

Zhou

Bai

et al. 2018

Sci Rep

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“…Interestingly, the cemA gene is related to the PPR7 protein. We speculated that cemA may have coevolved with nuclear genes (Jalal et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

et al. 2016

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Dipteronia (order Sapindales) is an endangered genus endemic to China and has two living species, D.sinensis and D. dyeriana. The plants are closely related to the genus Acer, which is also classified in the order Sapindales. Evolutionary studies on Dipteronia have been hindered by the paucity of information on their genomes and plastids. Here, we used next generation sequencing to characterize the transcriptomes and complete chloroplast genomes of both Dipteronia species. A comparison of the transcriptomes of both species identified a total of 7814 orthologs. Estimation of selection pressures using Ka/Ks ratios showed that only 30 of 5435 orthologous pairs had a ratio significantly >1, i.e., showing positive selection. However, 4041 orthologs had a Ka/Ks < 0.5 (p < 0.05), suggesting that most genes had likely undergone purifying selection. Based on orthologous unigenes, 314 single copy nuclear genes (SCNGs) were identified. Through a combination of de novo and reference guided assembly, plastid genomes were obtained; that of D. sinensis was 157,080 bp and that of D. dyeriana was 157,071 bp. Both plastid genomes encoded 87 protein coding genes, 40 tRNAs, and 8 rRNAs; no significant differences were detected in the size, gene content, and organization of the two plastomes. We used the whole chloroplast genomes to determine the phylogeny of D. sinensis and D. dyeriana and confirmed that the two species were highly divergent. Overall, our study provides comprehensive transcriptomic and chloroplast genomic resources, which will be valuable for future evolutionary studies of Dipteronia.

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“…For example, the nucleus-encoded NAC2 protein is an RNA binding protein with tetratricopeptide-like repeats that stabilizes psbD RNA (Boudreau et al, 2000). Such RNA binding proteins exhibit sequence specificity for a given chloroplast RNA and are encoded by large gene families in land plants that have not yet expanded in algae (Jalal et al, 2015).…”

Section: Chloroplast Biogenesis and Photosynthesismentioning

confidence: 99%

A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism

2019

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The unicellular alga Chlamydomonas reinhardtii is a classical reference organism for studying photosynthesis, chloroplast biology, cell cycle control, and cilia structure and function. It is also an emerging model for studying sensory cilia, the production of high-value bioproducts, and in situ structural determination. Much of the early appeal of Chlamydomonas was rooted in its promise as a genetic system, but like other classic model organisms, this rise to prominence predated the discovery of the structure of DNA, whole-genome sequences, and molecular techniques for gene manipulation. The haploid genome of C. reinhardtii facilitates genetic analyses and offers many of the advantages of microbial systems applied to a photosynthetic organism. C. reinhardtii has contributed to our understanding of chloroplast-based photosynthesis and cilia biology. Despite pervasive transgene silencing, technological advances have allowed researchers to address outstanding lines of inquiry in algal research. The most thoroughly studied unicellular alga, C. reinhardtii, is the current standard for algal research, and although genome editing is still far from efficient and routine, it nevertheless serves as a template for other algae. We present a historical retrospective of the rise of C. reinhardtii to illuminate its past and present. We also present resources for current and future scientists who may wish to expand their studies to the realm of microalgae. WHY ALGAE (IN GENERAL) AND CHLAMYDOMONAS (SPECIFICALLY)? Algae represent a very large and diverse polyphyletic group of photosynthetic eukaryotes (Blaby-Haas and Merchant, 2019). They occupy all possible ecological niches on the planet, and therefore constitute a potential reservoir of untapped functional capabilities for adaptation to the environment. Algae are primary producers that contribute ;50% of total carbon fixation worldwide (Field et al., 1998), which makes their study fundamental to our understanding of global primary production and carbon flux. They also offer a low-cost option for the large-scale production of high-value molecules, since algae only require water, salts, air, and light. Unicellular algae such as the ciliated green alga Chlamydomonas reinhardtii offer high signal-to-noise during experiments due to the ease of growth in controlled medium and environments (temperature and light regimes) and the homogenous nature of the cultures, and they grow much more rapidly than classic plant models. With its haploid genome, C. reinhardtii is well suited for classical genetics, as loss-of-function mutations are immediately expressed and more likely lead to observable phenotypes compared with diploid organisms. C. reinhardtii not only responds to light, but it also anticipates environmental transitions like dawn and dusk under the supervision of a circadian system, which coordinates cell division, photosynthesis, and cilia biogenesis, representing three fundamental research topics (Noordally and Millar, 2015). Other topics of research using C. reinhardtii include t...

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A Small Multifunctional Pentatricopeptide Repeat Protein in the Chloroplast of Chlamydomonas reinhardtii

Cited by 19 publications

References 81 publications

Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships

Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships

Comparative Transcriptome and Chloroplast Genome Analyses of Two Related Dipteronia Species

A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism

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