Comparative Analysis of RNA Genes

2007 ◽  
pp. 465-473 ◽  
Author(s):  
Hélène Touzet
Keyword(s):  
Comparative Analysis ◽  
Rna Genes

scholarly journals Comparative analysis of the complete mitochondrial genomes of four cordyceps fungi

2021 ◽  
Author(s):  
can zhong ◽  
jian jin ◽  
rongrong zhou ◽  
hao liu ◽  
jing xie ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Ribosomal Rna ◽  
Evolutionary Biology ◽  
Purifying Selection ◽  
Circular Dna ◽  
Close Relationship ◽  
Conserved Genes ◽  
Rna Genes ◽  
Entire Mitochondrial Genome ◽  
Complete Mitochondrial Genomes

Cordyceps is a large group of entomogenous, medicinally important fungi. In this study, we sequenced, assembled, and annotated the entire mitochondrial genome of O. xuefengensis, in addition to comparing it against three other complete cordyceps mitogenomes that were previously published. Comparative analysis indicated that the four complete mitogenomes are all composed of circular DNA molecules, although their sizes significantly differ due to high variability in intron and intergenic region sizes in the O. sinensis and O. xuefengensis mitogenomes. All mitogenomes contain 14 conserved genes and two ribosomal RNA genes, but varying numbers of tRNA introns. The Ka/Ks ratios for all 14 PCGs and rps3 were all less than 1, indicating that these genes have been subject to purifying selection. Phylogenetic analysis was conducted using concatenated amino acid and nucleotide sequences of the 14 PCGs and rps3 using two different methods (Maximum Likelihood and Bayesian analysis), revealing highly supported relationships between O. xuefengensis and other Ophiocordyceps species, in addition to a close relationship with O. sinensis. Further, the analyses indicated that cox1 and rps3 play important roles in population differentiation. These mitogenomes will allow further study of the population genetics, taxonomy, and evolutionary biology of medicinally important cordyceps species.

scholarly journals The complete chloroplast genomes of seventeen Aegilops tauschii: genome comparative analysis and phylogenetic inference

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8678 ◽  
Author(s):  
Qing Su ◽  
Luxian Liu ◽  
Mengyu Zhao ◽  
Cancan Zhang ◽  
Dale Zhang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Bread Wheat ◽  
Yellow River ◽  
Genomic Structure ◽  
Aegilops Tauschii ◽  
Western China ◽  
Chloroplast Genomes ◽  
River Region ◽  
Cp Genome ◽  
Rna Genes

The D genome progenitor of bread wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14), which is naturally distributed in Central Eurasia, ranging from northern Syria and Turkey to western China, is considered a potential genetic resource for improving bread wheat. In this study, the chloroplast (cp) genomes of 17 Ae. tauschii accessions were reconstructed. The cp genome sizes ranged from 135,551 bp to 136,009 bp and contained a typical quadripartite structure of angiosperms. Within these genomes, we identified a total of 124 functional genes, including 82 protein-coding genes, 34 transfer RNA genes and eight ribosomal RNA genes, with 17 duplicated genes in the IRs. Although the comparative analysis revealed that the genomic structure (gene order, gene number and IR/SC boundary regions) is conserved, a few variant loci were detected, predominantly in the non-coding regions (intergenic spacer regions). The phylogenetic relationships determined based on the complete genome sequences were consistent with the hypothesis that Ae. tauschii populations in the Yellow River region of China originated in South Asia not Xinjiang province or Iran, which could contribute to more effective utilization of wild germplasm resources. Furthermore, we confirmed that Ae. tauschii was derived from monophyletic speciation rather than hybrid speciation at the cp genome level. We also identified four variable genomic regions, rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20, showing high levels of nucleotide polymorphisms, which may accordingly prove useful as cpDNA markers in studying the intraspecific genetic structure and diversity of Ae. tauschii.

scholarly journals Comparative analysis of the complete chloroplast genome sequences in psammophyticHaloxylonspecies (Amaranthaceae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2699 ◽  
Author(s):  
Wenpan Dong ◽  
Chao Xu ◽  
Delu Li ◽  
Xiaobai Jin ◽  
Ruili Li ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Higher Plants ◽  
Single Copy ◽  
Comparative Genomic ◽  
Complete Chloroplast Genome ◽  
Phylogenetic Evolution ◽  
Cp Genome ◽  
Nucleotide Repeats ◽  
Rna Genes ◽  
Small Single Copy

TheHaloxylongenus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes ofHaloxylon ammodendron(HA) andHaloxylon persicum(HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that theHaloxyloncp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. EachHaloxyloncp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in thepetA-psbJ intergenic region andrpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies onHaloxylongenetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.

scholarly journals Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea)

Forests ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 861
Author(s):  
Huijuan Zhou ◽  
Xiaoxiao Gao ◽  
Keith Woeste ◽  
Peng Zhao ◽  
Shuoxin Zhang
Keyword(s):  
Comparative Analysis ◽  
Phylogenetic Analyses ◽  
Single Copy ◽  
Nucleotide Substitutions ◽  
Protein Coding ◽  
Variable Regions ◽  
Chloroplast Genomes ◽  
Cp Genome ◽  
Species Hybrids ◽  
Rna Genes

Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.

scholarly journals Complete chloroplast genomes of Rubus species (Rosaceae) and comparative analysis within the genus

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Jiaojun Yu ◽  
Jun Fu ◽  
Yuanping Fang ◽  
Jun Xiang ◽  
Hongjin Dong
Keyword(s):  
Comparative Analysis ◽  
Ornamental Plants ◽  
Gc Content ◽  
Central China ◽  
Dabie Mountains ◽  
Nucleotide Variability ◽  
Chloroplast Genomes ◽  
The Family ◽  
Cp Genome ◽  
Rna Genes

Abstract Background Rubus is the largest genus of the family Rosaceae and is valued as medicinal, edible, and ornamental plants. Here, we sequenced and assembled eight chloroplast (cp) genomes of Rubus from the Dabie Mountains in Central China. Fifty-one Rubus species were comparatively analyzed for the cp genomes including the eight newly discovered genomes and forty-three previously reported in GenBank database (NCBI). Results The eight newly obtained cp genomes had the same quadripartite structure as the other cp genomes in Rubus. The length of the eight plastomes ranged from 155,546 bp to 156,321 bp with similar GC content (37.0 to 37.3%). The results indicated 133–134 genes were annotated for the Rubus plastomes, which contained 88 or 89 protein coding genes (PCGs), 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Among them, 16 (or 18) of the genes were duplicated in the IR region. Structural comparative analysis results showed that the gene content and order were relatively preserved. Nucleotide variability analysis identified nine hotspot regions for genomic divergence and multiple simple sequences repeats (SSRs), which may be used as markers for genetic diversity and phylogenetic analysis. Phylogenetic relationships were highly supported within the family Rosaceae, as evidenced by sub-clade taxa cp genome sequences. Conclusion Thus, the whole plastome may be used as a super-marker in phylogenetic studies of this genus.

scholarly journals Characterization and Comparative Analysis of Complete Mitogenomes of Three Cacatua Parrots (Psittaciformes: Cacatuidae)

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 209
Author(s):  
Jung-Il Kim ◽  
Thinh Dinh Do ◽  
Yisoo Choi ◽  
Yonggu Yeo ◽  
Chang-Bae Kim
Keyword(s):  
Comparative Analysis ◽  
Ribosomal Rna ◽  
Molecular Dating ◽  
Crown Group ◽  
Protein Coding ◽  
The Family ◽  
Domain Iii ◽  
Domain I ◽  
Rna Genes ◽  
Control Regions

Cacatua alba, Cacatua galerita, and Cacatua goffiniana are parrots of the family Cacatuidae. Wild populations of these species are declining with C. alba listed by the International Union for the Conservation of Nature and Natural Resources (IUCN) as Endangered. In this study, complete mitogenomes were sequenced for a comparative analysis among the Cacatua species, and a detailed analysis of the control region. Mitogenome lengths of C. alba,C. galerita, and C. goffiniana were 18,894, 18,900, and 19,084 bp, respectively. They included 13 protein coding genes, two ribosomal RNA genes, 24 transfer RNA genes, three degenerated genes, and two control regions. Ten conserved motifs were found in three domains within each of the two control regions. For an evolution of duplicated control regions of Cacatua, domain I and the 3′ end of domain III experienced an independent evolution, while domain II and most of the regions of domain III was subjected to a concerted evolution. Based on a phylogenetic analysis of 37 mitochondrial genes, the genus Cacatua formed a well-supported, monophyletic, crown group within the Cacatuidae. Molecular dating results showed that Cacatua diverged from other genera of Cacatuinae in the middle of Miocene.

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