Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes(plastomes)of flowering plants in diverse habitats,yet our knowledge of the evolution of plastid posttranscriptional modif...Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes(plastomes)of flowering plants in diverse habitats,yet our knowledge of the evolution of plastid posttranscriptional modifications is limited.In this study,we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium,a genus with diverse trophic lifestyles.Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives.This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex,but independent pseudogenization of ndh genes has also occurred in the epiphyte C.mannii,which was reported to use strong crassulacean acid metabolism photosynthesis.RNA editing sites are abundant but variable in number among Cymbidium plastomes.The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial,mycoheterotrophic,and C.mannii plastomes.The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed,leading to nonrandom loss of ancestral edited sites via reduced editing efficiency.This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus.We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium.展开更多
RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C...RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position, ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed.展开更多
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(grant no.XDB31010000)by the Large-scale Scientific Facilities of the Chinese Academy of Sciences(grant no.2017-LSF-GBOWS-02)+1 种基金by an open research project for“Cross-Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciencesby the CAS Pioneer Hundred Talents Program(to A.Z.).
文摘Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes(plastomes)of flowering plants in diverse habitats,yet our knowledge of the evolution of plastid posttranscriptional modifications is limited.In this study,we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium,a genus with diverse trophic lifestyles.Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives.This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex,but independent pseudogenization of ndh genes has also occurred in the epiphyte C.mannii,which was reported to use strong crassulacean acid metabolism photosynthesis.RNA editing sites are abundant but variable in number among Cymbidium plastomes.The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial,mycoheterotrophic,and C.mannii plastomes.The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed,leading to nonrandom loss of ancestral edited sites via reduced editing efficiency.This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus.We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium.
基金supported by the Fundamental Research Fund for the Central Universities (Grant No. GK200902028)
文摘RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position, ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed.
