scholarly journals Novel Structural Variation and Evolutionary Characteristics of Chloroplast tRNA in Gossypium Plants

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 822
Author(s):  
Ting-Ting Zhang ◽  
Yang Yang ◽  
Xiao-Yu Song ◽  
Xin-Yu Gao ◽  
Xian-Liang Zhang ◽  
...  
Keyword(s):  
Structural Variation ◽  
Transfer Rnas ◽  
Synonymous Mutations ◽  
Coding Regions ◽  
Oil Crops ◽  
Rates Of Evolution ◽  
Chloroplast Genomes ◽  
Cotton Species ◽  
Unequal Rates ◽  
Evolutionary Variation

Cotton is one of the most important fiber and oil crops in the world. Chloroplast genomes harbor their own genetic materials and are considered to be highly conserved. Transfer RNAs (tRNAs) act as “bridges” in protein synthesis by carrying amino acids. Currently, the variation and evolutionary characteristics of tRNAs in the cotton chloroplast genome are poorly understood. Here, we analyzed the structural variation and evolution of chloroplast tRNA (cp tRNA) based on eight diploid and two allotetraploid cotton species. We also investigated the nucleotide evolution of chloroplast genomes in cotton species. We found that cp tRNAs in cotton encoded 36 or 37 tRNAs, and 28 or 29 anti-codon types with lengths ranging from 60 to 93 nucleotides. Cotton chloroplast tRNA sequences possessed specific conservation and, in particular, the Ψ-loop contained the conserved U-U-C-X3-U. The cp tRNAs of Gossypium L. contained introns, and cp tRNAIle contained the anti-codon (C-A-U), which was generally the anti-codon of tRNAMet. The transition and transversion analyses showed that cp tRNAs in cotton species were iso-acceptor specific and had undergone unequal rates of evolution. The intergenic region was more variable than coding regions, and non-synonymous mutations have been fixed in cotton cp genomes. On the other hand, phylogeny analyses indicated that cp tRNAs of cotton were derived from several inferred ancestors with greater gene duplications. This study provides new insights into the structural variation and evolution of chloroplast tRNAs in cotton plants. Our findings could contribute to understanding the detailed characteristics and evolutionary variation of the tRNA family.

scholarly journals Parsing the synonymous mutations in the maize genome: isoaccepting mutations are more advantageous in regions with codon co-occurrence bias

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Duan Chu ◽  
Lai Wei
Keyword(s):  
Amino Acids ◽  
Natural Selection ◽  
Codon Bias ◽  
Synonymous Codon ◽  
Translation Efficiency ◽  
Maize Genome ◽  
Rna Seq ◽  
Synonymous Mutations ◽  
Coding Regions ◽  
The Relationship

Abstract Background Synonymous mutations do not change amino acids but do sometimes change the tRNAs (anticodons) that decode a particular codon. An isoaccepting codon is a synonymous codon that shares the same tRNA. If a mutated codon could base pair with the same anticodon as the original, the mutation is termed an isoaccepting mutation. An interesting but less-studied type of codon bias is codon co-occurrence bias. There is a trend to cluster the isoaccepting codons in the genome. The proposed advantage of codon co-occurrence bias is that the tRNA released from the ribosome E site could be quickly recharged and subsequently decode the following isoaccepting codons. This advantage would enhance translation efficiency. In plant species, whether there are signals of positive selection on isoaccepting mutations in the codon co-occurred regions has not been studied. Results We termed polymorphic mutations in coding regions using publicly available RNA-seq data in maize (Zea mays). Next, we classified all synonymous mutations into three categories according to the context, i.e., the relationship between the focal codon and the previous codon, as follows: isoaccepting, nonisoaccepting and nonsynonymous. We observed higher fractions of isoaccepting mutations in the isoaccepting context. If we looked at the minor allele frequency (MAF) spectrum, the isoaccepting mutations have a higher MAF in the isoaccepting context than that in other regions, and accordingly, the nonisoaccepting mutations have a higher MAF in the nonisoaccepting context. Conclusion Our results indicate that in regions with codon co-occurrence bias, natural selection maintains this pattern by suppressing the nonisoaccepting mutations. However, if the consecutive codons are nonisoaccepting, mutations tend to switch these codons to become isoaccepting. Our study demonstrates that the codon co-occurrence bias in the maize genome is selectively maintained by natural selection and that the advantage of this trend could potentially be the rapid recharging and reuse of tRNAs to increase translation efficiency.

Mutations in Mitochondrial DNA Is An Adverse Factor for Survival in Patients with Acute Myeloid Leukemia.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1523-1523
Author(s):  
Trine Silkjaer ◽  
Anni Aggerholm ◽  
Charlotte Guldborg Nyvold ◽  
Peter Hokland ◽  
Jan Maxwell Norgaard
Keyword(s):  
Overall Survival ◽  
Acute Myeloid Leukemia ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Myeloid Leukemia ◽  
Base Pairs ◽  
Synonymous Mutations ◽  
Coding Regions ◽  
Entire Mitochondrial Genome ◽  
Acute Myeloid

Abstract BACKGROUND: In acute myeloid leukemia (AML), cytogenetic and molecular genetic abnormalities are known to play an essential role in the pathogenesis and are now accepted to be of paramount prognostic significance. However, mitochondrial dysfunction is also emerging as a major factor of importance in cancer. The mitochondrion has its own double-stranded circular 16.569 base pairs DNA (mtDNA) encoding 13 genes involved in oxidative phosphorylation and the respiratory chain, 2 rRNAs, and 22 tRNAs. As such, they are important in apoptosis and might, thus, be crucial in response to chemotherapy and to disease progression. The purpose of this study was to determine if mtDNA mutations are of importance to outcome of chemotherapy and to long-term survival in AML. METHODS: The whole mitochondrial genome was sequenced using a resequencing system based on 46 PCR amplicons (MitoSEQr, Applied Biosystems, Foster City, CA) performed on a Genetic Analyzer 3130 (Applied Biosystems). Diagnostic bone marrow from 20 patients with AML, treated with curative intent, was analyzed. To avoid problems with misinterpretation of heteroplasmy due to admixture of other non-malignant cells, all patient samples selected had more than 80 percent blasts according to immunophenotyping. Data were analyzed using SeqScape v.2.5, Applied Biosystems and statistically analysis in Stata 10. RESULTS: We sequenced the entire mitochondrial genome in 20 patients with AML with 99.5% base pairs sequenced (in 20 patients 329.734 base pairs were successfully sequenced out of 331.380 possible), and compared our findings with clinical data and survival data. In both coding and non-coding regions, a total number of 432 mutations (substitutions, insertions, and deletions) (range 8–44, median 15.5) were found. Mutations were scattered throughout the entire mitochondrial genome, and observed in all genes as well as in non-coding regions. Though, most were known polymorphisms in the Mitomap database (www.mitomap.org), eleven of the non-synonymous mutations were novel in the Mitomap database. All patients had non-synonymous mutations, resulting in amino acid changes (range 2–10, median 3.5), with a total number of 90 non-synonymous mutations. Two of the known non-synonymous mutations were present in all patients (A8860G, A15326G). While most changes were homoplasmic changes, heteroplasmic ones were observed in 12 of 20 patients (range 1-2). Notably, by dividing the patients by the median of the total number of mutations, patients with less than 16 mutations have a 5 years survival of 50% as compared to 10% for patients with 16 mutations or more. This revealed a significant (p=0.04) impact on overall survival of total number of mutations in both coding and non-coding regions (Fig.). Importantly, regression analysis revealed that the number of mutations was independent of age. The non-synonymous mutations show a trend towards a difference in overall survival (p=0.07). CONCLUSION: This is, to our knowledge, the first demonstration of a prognostic impact on survival in AML patients of mutations in the mitochondrial DNA. Further studies on more patients are, however, clearly warranted to discern by which mechanisms mitochondrial DNA mutations are impacting prognosis in AML. Disclosure: No relevant conflict of interest to declare. Figure Figure

Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae)

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 634-641 ◽  
Author(s):  
T HM Mes ◽  
P Kuperus ◽  
J Kirschner ◽  
J Stepanek ◽  
P Oosterveld ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Hot Spot ◽  
Phylogenetic Signal ◽  
Direct Repeats ◽  
Nucleotide Substitutions ◽  
Replication Slippage ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Structural Mutations

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.Key words: Taraxacum, indel, non-coding chloroplast DNA, hairpin, evolution.

scholarly journals Assembly and comparative analysis of chloroplast genome of wheat K-CMS line and maintainer line

2020 ◽  
Author(s):  
Yucui Han ◽  
Yujie Gao ◽  
Xiaoguang Zhai ◽  
Hao Zhou ◽  
Qin Ding ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Chloroplast Genome ◽  
Triticum Aestivum L ◽  
Practical Significance ◽  
Rrna Genes ◽  
Trna Genes ◽  
Maintainer Line ◽  
Synonymous Mutations ◽  
Chloroplast Genomes ◽  
Cms Line

Abstract The sterile line is vital for the heterosis utilization of wheat (Triticum aestivum L.), and the cytoplasmic male sterility (CMS) line has more practical significance in the utilization of heterosis. To reveal the sterile mechanism of wheat K-CMS line K519A from the perspective of the chloroplast genome, the chloroplast genomes of the K519A and its same nuclear genotype maintainer line 519B were sequenced using second-generation high-throughput technology and assembled. Then the chloroplast genomic contents, SSR sequences, long repeat fragments, and qPCR were analyzed. The results showed that the total length of K519A and 519B were 136,996 bp and 136,235 bp, respectively. Both chloroplast genomes encode 126 genes, including 89 protein-coding genes, 8 rRNA genes, and 39 tRNA genes. There were 186 and 188 SSRs in K519A and 519B, respectively. And a developed SSR maker, which from atpF, can be used to distinguish the cytoplasmic type of Aegilops kotschyi and Triticum aestivum, respectively. There were 50 and 52 long repeat fragments, which come from the gene sequences, in K519A and 519B, respectively. A total of 107 mutations between K519A and 519B, which from 45 genes, were identified, of which, 16 genes (matK, rps16, rpoB, rpoC2, atpI, ndhK, atpB, rbcL, psbB, psbH, rpl14, ndhH, ndhF, rpl32, ccsA, ndhA) contained non-synonymous mutations. Further, the qPCR analysis was performed, and the gene expression levels of selected six genes for K519A compared to 519B were mostly downregulated at the binucleate and trinucleate stages of pollen development, thus, these non-synonymous mutant genes might affect the fertility of K519A.

scholarly journals Mutational Analysis of cis-Acting RNA Signals in Segment 7 of Influenza A Virus

2008 ◽  
Vol 82 (23) ◽  
pp. 11869-11879 ◽  
Author(s):  
Edward C. Hutchinson ◽  
Martin D. Curran ◽  
Eliot K. Read ◽  
Julia R. Gog ◽  
Paul Digard
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
Mdck Cells ◽  
Wild Type Virus ◽  
Wild Type ◽  
Genome Packaging ◽  
Virus Growth ◽  
Virus Particles ◽  
Synonymous Mutations ◽  
Coding Regions

ABSTRACT The genomic viral RNA (vRNA) segments of influenza A virus contain specific packaging signals at their termini that overlap the coding regions. To further characterize cis-acting signals in segment 7, we introduced synonymous mutations into the terminal coding regions. Mutation of codons that are normally highly conserved reduced virus growth in embryonated eggs and MDCK cells between 10- and 1,000-fold compared to that of the wild-type virus, whereas similar alterations to nonconserved codons had little effect. In all cases, the growth-impaired viruses showed defects in virion assembly and genome packaging. In eggs, nearly normal numbers of virus particles that in aggregate contained apparently equimolar quantities of the eight segments were formed, but with about fourfold less overall vRNA content than wild-type virions, suggesting that, on average, fewer than eight segments per particle were packaged. Concomitantly, the particle/PFU and segment/PFU ratios of the mutant viruses showed relative increases of up to 300-fold, with the behavior of the most defective viruses approaching that predicted for random segment packaging. Fluorescent staining of infected cells for the nucleoprotein and specific vRNAs confirmed that most mutant virus particles did not contain a full genome complement. The specific infectivity of the mutant viruses produced by MDCK cells was also reduced, but in this system, the mutations also dramatically reduced virion production. Overall, we conclude that segment 7 plays a key role in the influenza A virus genome packaging process, since mutation of as few as 4 nucleotides can dramatically inhibit infectious virus production through disruption of vRNA packaging.

scholarly journals Seven Complete Chloroplast Genomes from Symplocos: Genome Organization and Comparative Analysis

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 608
Author(s):  
Sang-Chul Kim ◽  
Jei-Wan Lee ◽  
Byoung-Ki Choi
Keyword(s):  
Chloroplast Genome ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Ion Torrent Sequencing ◽  
Species Specific ◽  
Taxonomic Characterization

In the present study, chloroplast genome sequences of four species of Symplocos (S. chinensis for. pilosa, S. prunifolia, S. coreana, and S. tanakana) from South Korea were obtained by Ion Torrent sequencing and compared with the sequences of three previously reported Symplocos chloroplast genomes from different species. The length of the Symplocos chloroplast genome ranged from 156,961 to 157,365 bp. Overall, 132 genes including 87 functional genes, 37 tRNA genes, and eight rRNA genes were identified in all Symplocos chloroplast genomes. The gene order and contents were highly similar across the seven species. The coding regions were more conserved than the non-coding regions, and the large single-copy and small single-copy regions were less conserved than the inverted repeat regions. We identified five new hotspot regions (rbcL, ycf4, psaJ, rpl22, and ycf1) that can be used as barcodes or species-specific Symplocos molecular markers. These four novel chloroplast genomes provide basic information on the plastid genome of Symplocos and enable better taxonomic characterization of this genus.

scholarly journals Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Jiao Fang ◽  
Benwen Liu ◽  
Guoxiang Liu ◽  
Heroen Verbruggen ◽  
Huan Zhu
Keyword(s):  
Genetic Code ◽  
Chloroplast Genome ◽  
Genetic Information ◽  
Vascular Plants ◽  
Gc Content ◽  
Valid Species ◽  
Chloroplast Genes ◽  
Rates Of Evolution ◽  
Chloroplast Genomes ◽  
Shed Light

Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia. The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26–36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata, which does have an inverted repeat. The duplicated trnD-GTC, petD, and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.

scholarly journals Genomic Epidemiology and Evolution of Duck Hepatitis A Virus

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1592
Author(s):  
Enikő Fehér ◽  
Szilvia Jakab ◽  
Krisztina Bali ◽  
Eszter Kaszab ◽  
Borbála Nagy ◽  
...  
Keyword(s):  
Hepatitis A ◽  
Hepatitis A Virus ◽  
Evolutionary Mechanisms ◽  
Protein Coding ◽  
Genomic Epidemiology ◽  
Coding Regions ◽  
Duck Hepatitis ◽  
Rates Of Evolution ◽  
Genomic Regions ◽  
Globally Distributed

Duck hepatitis A virus (DHAV), an avian picornavirus, causes high-mortality acute disease in ducklings. Among the three serotypes, DHAV-1 is globally distributed, whereas DHAV-2 and DHAV-3 serotypes are chiefly restricted to Southeast Asia. In this study, we analyzed the genomic evolution of DHAV-1 strains using extant GenBank records and genomic sequences of 10 DHAV-1 strains originating from a large disease outbreak in 2004–2005, in Hungary. Recombination analysis revealed intragenotype recombination within DHAV-1 as well as intergenotype recombination events involving DHAV-1 and DHAV-3 strains. The intergenotype recombination occurred in the VP0 region. Diversifying selection seems to act at sites of certain genomic regions. Calculations estimated slightly lower rates of evolution of DHAV-1 (mean rates for individual protein coding regions, 5.6286 × 10−4 to 1.1147 × 10−3 substitutions per site per year) compared to other picornaviruses. The observed evolutionary mechanisms indicate that whole-genome-based analysis of DHAV strains is needed to better understand the emergence of novel strains and their geographical dispersal.

scholarly journals The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3919 ◽  
Author(s):  
Hui Cheng ◽  
Jinfeng Li ◽  
Hong Zhang ◽  
Binhua Cai ◽  
Zhihong Gao ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Genome Structure ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Complete Chloroplast Genome ◽  
Coding Regions ◽  
Chloroplast Genomes

Compared with other members of the family Rosaceae, the chloroplast genomes ofFragariaspecies exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing ofFragariaspecies is needed. In this study, we sequenced the complete chloroplast genome ofF. × ananassa‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination ofde novoassembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of theF. × ananassa‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallestFragariachloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content inFragaria, particularly among three octoploid strawberries which wereF. × ananassa‘Benihoppe’,F.chiloensis(GP33) andF.virginiana(O477). However, when the sequences of the coding and non-coding regions ofF. × ananassa‘Benihoppe’ were compared in detail with those ofF.chiloensis(GP33) andF.virginiana(O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK,trnS-trnG,atpF-atpH,trnC-petN,trnT-psbDandtrnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genusFragaria.

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