scholarly journals RNA editing differently affects protein-coding genes in D. melanogaster and H. sapiens

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Luigi Grassi ◽  
Guido Leoni ◽  
Anna Tramontano
Keyword(s):  
Rna Editing ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid

mBio ◽  
2015 ◽  
Vol 6 (6) ◽  
Author(s):  
Vojtěch David ◽  
Pavel Flegontov ◽  
Evgeny Gerasimov ◽  
Goro Tanifuji ◽  
Hassan Hashimi ◽  
...  
Keyword(s):  
Rna Editing ◽  
Deep Sequencing ◽  
Gene Loss ◽  
Mitochondrial Rna ◽  
Evolutionary Perspective ◽  
Rna Seq ◽  
Protein Coding ◽  
Mitochondrial Ribosomes ◽  
Protein Coding Genes ◽  
Mitochondrial Transcripts

ABSTRACT Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts. IMPORTANCE Uridine insertion/deletion-type RNA editing, which occurs in the mitochondrion of kinetoplastid protists, has been well-studied in the model parasite genera Trypanosoma, Leishmania, and Crithidia. Perkinsela provides a unique opportunity to broaden our knowledge of RNA editing machinery from an evolutionary perspective, as it represents the earliest kinetoplastid branch and is an obligatory endosymbiont with extensive reductive trends. Interestingly, up to 50% of mitochondrial transcripts in Perkinsela contain errors. Our study was complemented by use of newly developed software designed for accurate mapping of extensively edited RNA-seq reads obtained by deep sequencing.

scholarly journals Complete chloroplast genome of Stephania tetrandra (Menispermaceae) from Zhejiang Province: insights into molecular structures, comparative genome analysis, mutational hotspots and phylogenetic relationships

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shujie Dong ◽  
Zhiqi Ying ◽  
Shuisheng Yu ◽  
Qirui Wang ◽  
Guanghui Liao ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Rna Editing ◽  
Geographical Origin ◽  
Single Copy ◽  
Zhejiang Province ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Mutational Hotspots ◽  
Cp Genome

Abstract Background The Stephania tetrandra S. Moore (S. tetrandra) is a medicinal plant belonging to the family Menispermaceae that has high medicinal value and is well worth doing further exploration. The wild resources of S. tetrandra were widely distributed in tropical and subtropical regions of China, generating potential genetic diversity and unique population structures. The geographical origin of S. tetrandra is an important factor influencing its quality and price in the market. In addition, the species relationship within Stephania genus still remains uncertain due to high morphological similarity and low support values of molecular analysis approach. The complete chloroplast (cp) genome data has become a promising strategy to determine geographical origin and understand species evolution for closely related plant species. Herein, we sequenced the complete cp genome of S. tetrandra from Zhejiang Province and conducted a comparative analysis within Stephania plants to reveal the structural variations, informative markers and phylogenetic relationship of Stephania species. Results The cp genome of S. tetrandra voucher ZJ was 157,725 bp, consisting of a large single copy region (89,468 bp), a small single copy region (19,685 bp) and a pair of inverted repeat regions (24,286 bp each). A total of 134 genes were identified in the cp genome of S. tetrandra, including 87 protein-coding genes, 8 rRNA genes, 37 tRNA genes and 2 pseudogene copies (ycf1 and rps19). The gene order and GC content were highly consistent in the Stephania species according to the comparative analysis results, with the highest RSCU value in arginine (1.79) and lowest RSCU value in serine of S. tetrandra, respectively. A total of 90 SSRs have been identified in the cp genome of S. tetrandra, where repeats that consisting of A or T bases were much higher than that of G or C bases. In addition, 92 potential RNA editing sites were identified in 25 protein-coding genes, with the most predicted RNA editing sites in ndhB gene. The variations on length and expansion extent to the junction of ycf1 gene were observed between S. tetrandra vouchers from different regions, indicating potential markers for further geographical origin discrimination. Moreover, the values of transition to transversion ratio (Ts/Tv) in the Stephania species were significantly higher than 1 using Pericampylus glaucus as reference. Comparative analysis of the Stephania cp genomes revealed 5 highly variable regions, including 3 intergenic regions (trnH-psbA, trnD-trnY, trnP) and two protein coding genes (rps16 and ndhA). The identified mutational hotspots of Stephania plants exhibited multiple SNP sites and Gaps, as well as different Ka/Ks ratio values. In addition, five pairs of specific primers targeting the divergence regions were accordingly designed, which could be utilized as potential molecular markers for species identification, population genetic and phylogenetic analysis in Stephania species. Phylogenetic tree analysis based on the conserved chloroplast protein coding genes indicated a sister relationship between S. tetrandra and the monophyletic group of S. japonica and S. kwangsiensis with high support values, suggesting a close genetic relationship within Stephania plants. However, two S. tetrandra vouches from different regions failed to cluster into one clade, confirming the occurrences of genetic diversities and requiring further investigation for geographical tracing strategy. Conclusions Overall, we provided comprehensive and detailed information on the complete chloroplast genome and identified nucleotide diversity hotspots of Stephania species. The obtained genetic resource of S. tetrandra from Zhejiang Province would facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of Stephania plants.

RNA Editing Sites Exist in Protein-coding Genes in the Chloroplast Genome of Cycas taitungensis

2011 ◽  
Vol 53 (12) ◽  
pp. 961-970 ◽  
Author(s):  
Haiyan Chen ◽  
Likun Deng ◽  
Yuan Jiang ◽  
Ping Lu ◽  
Jianing Yu
Keyword(s):  
Chloroplast Genome ◽  
Rna Editing ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals The mitochondrial genomes of bryophytes

2021 ◽  
Vol 43 (1) ◽  
Author(s):  
SHANSHAN DONG ◽  
YANG LIU
Keyword(s):  
Rna Editing ◽  
Genome Structure ◽  
Repeated Sequences ◽  
Land Plants ◽  
Trna Genes ◽  
Large Set ◽  
Gene Repertoire ◽  
Protein Coding ◽  
Gene Set ◽  
Protein Coding Genes

In contrast to the highly variable mitogenomes of vascular plants, the composition and architecture of mitogenomes within the three bryophyte lineages appear stable and invariant. Currently, complete mitogenomes are available from 113 bryophyte accessions of 71 genera and 28 orders. Liverworts and mosses hold a rich mitochondrial (mt) gene repertoire among land plants with 40–42 protein-coding genes, whereas hornworts maintain the smallest functional gene set among land plants, of only around two dozen protein-coding genes, with the majority of ribosomal genes pseudogenized and all cytochrome c maturase genes lost. The rRNA and tRNA genes are also conserved and rich in mosses and liverworts, whereas subject to patchy losses in hornworts. In contrast to the conserved gene set, intron content varies significantly with only one intron shared among the three bryophyte lineages. Bryophytes hold relatively compact mitogenomes with narrow size fluctuations. Among the three bryophyte lineages, intergenic spacers and repeat content are smallest in mosses, largest in hornworts, and intermediate in liverworts, mirroring their size differences and levels of structural dynamics among the three lineages. Mosses, with the least repeated sequences, show the most static genome structure; whereas hornworts, with a relatively large set of repeated sequences, experience 1–4 rearrangements; liverworts, with intermediate repeat levels, see only one structural variant that requires two inversions to gain collinearity with the mitogenome of other liverworts. Repeat sequences were evoked to explain the mt gene order rearrangements in hornwort and liverwort mitogenomes; with the latter also supported by sequencing read evidence, which suggests that the conserved mitogenome structure observed in bryophyte lineages might be shaped by low repeat recombination level, and/or along with the intensified nucleus’ surveillance. Mitochondrial RNA editing is abundant in hornworts, with medium frequency and high variation in liverwort species, and generally limited in mosses, reflecting the diversity of nuclear encoded PPR proteins that are functionally related to RNA editing processes.

scholarly journals Deciphering tea tree chloroplast and mitochondrial genomes of Camellia sinensis var. assamica

2019 ◽  
Author(s):  
Fen Zhang ◽  
Wei Li ◽  
Cheng-wen Gao ◽  
Li-zhi Gao
Keyword(s):  
Rna Editing ◽  
Camellia Sinensis ◽  
De Novo ◽  
Single Copy ◽  
Rrna Genes ◽  
Protein Coding ◽  
Tea Tree ◽  
Protein Coding Genes ◽  
Cp Genome ◽  
Mt Genome

ABSTRACTTea is the most popular non-alcoholic caffeine-containing and the oldest beverage in the world. Despite its enormous industrial, cultural and medicinal values, the chloroplast (cp) and mitochondrial (mt) genomes are not available for Camellia sinensis var. assamica. In this study, we de novo assembled the cp genome sequence of C. sinensis var. assamica into a circular contig of 157,100 bp in length with an overall GC content of 37.29%, comprising a large single-copy region (LSC, 86,649 bp) and a small single-copy region (SSC, 18,285 bp) separated by a pair of inverted repeats (IRs, 26,083 bp). We annotated a total of 141 cp genes, of which 87 are protein-coding genes, 46 are tRNA genes, and eight are rRNA genes. We also de novo assembled the mt genome of C. sinensis var. assamica into two complete circular scaffolds (702,253 bp and 178,082 bp) with overall GC contents of 45.63% and 45.81%, respectively. We annotated a total of 71 mt genes, including 44 protein-coding genes, 24 tRNAs, and 3 rRNAs. Comparative analysis suggests repeat-rich nature of the mt genome compared to the cp genome, for example, with the characterization of 37,878 bp and 149 bp of long repeat sequences and 665 and 214 SSRs, respectively. We also detected 478 RNA-editing sites in 42 protein-coding mt genes, which are ∼4.4-fold more than 54 RNA-editing sites detected in 21 protein-coding cp genes. The high-quality cp and mt genomes of C. sinensis var. assamica presented in this study will become an invaluable resource for a range of genetic, functional, evolutionary and comparative genomic studies in tea tree and other Camellia species of the Theaceae family.

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