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Sharko FS, Petrova KO, Patrushev MV, Fedosov DY, Toshchakov SV. Chloroplast Genome Variation and Phylogenetic Relationships of Autochthonous Varieties of Vitis vinifera from the Don Valley. Int J Mol Sci 2024; 25:9928. [PMID: 39337416 PMCID: PMC11432254 DOI: 10.3390/ijms25189928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 09/10/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
The autochthonous grape varieties of the Don Valley, situated in southern Russia, constitute a distinctive element of regional cultural heritage. These varieties have been adapted over centuries to the region's specific local climatic and soil conditions. For the most part, these varieties are not imported from other countries. They are closely related to varieties found in Crimea and the North Caucasus. In this study, we obtained the first complete, unfragmented sequences of the chloroplast genomes of eight autochthonous varieties from the Don Valley and one from Crimea. We also performed a comparative analysis of their genomic features. The size of Vitis vinifera chloroplast genome sequences varied from 160,925 to 160,991 bp, depending on the cultivar, with a uniform GC ratio of 37.38%. Each genome consists of four subregions: a single copy region (LSC) ranging from 89,158 to 89,336 bp, a small single copy region (SSC) ranging from 19,070 to 19,073 bp, and a pair of inverted repeat regions (IRa and IRb) in the range of 26,292 to 26,353 bp. The chloroplast genomes of the studied V. vinifera varieties contained 130 genes, including 85 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The sequence divergence analysis has enabled the identification of four highly variable regions, which may be utilized as potential markers for phylogenetic analysis. The analysis revealed the presence of 58 to 61 SSRs and multiple long repeated sequences in the chloroplast genomes of these varieties. The phylogenetic analyses of the sequences obtained and complete chloroplast genomes available from public databases indicated that the majority of autochthonous V. vinifera varieties do not have a direct origin from any European variety.
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Affiliation(s)
- F S Sharko
- National Research Center "Kurchatov Institute", Academician Kurchatov pl., 1, Moscow 123182, Russia
| | - K O Petrova
- National Research Center "Kurchatov Institute", Academician Kurchatov pl., 1, Moscow 123182, Russia
| | - M V Patrushev
- National Research Center "Kurchatov Institute", Academician Kurchatov pl., 1, Moscow 123182, Russia
| | - D Y Fedosov
- National Research Center "Kurchatov Institute", Academician Kurchatov pl., 1, Moscow 123182, Russia
| | - S V Toshchakov
- National Research Center "Kurchatov Institute", Academician Kurchatov pl., 1, Moscow 123182, Russia
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Gao Y, Chen Z, Li X, Malik K, Li C. Comparative Analyses of Complete Chloroplast Genomes of Microula sikkimensis and Related Species of Boraginaceae. Genes (Basel) 2024; 15:226. [PMID: 38397215 PMCID: PMC10887780 DOI: 10.3390/genes15020226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The present study provides a detailed analysis of the chloroplast genome of Microula sikkimensis. The genome consisted of a total of 149,428 bp and four distinct regions, including a large single-copy region (81,329 bp), a small single-copy region (17,261 bp), and an inverted repeat region (25,419 bp). The genome contained 112 genes, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, and some exhibited duplication in the inverted repeat region. The chloroplast genome displayed different GC content across regions, with the inverted repeat region exhibiting the highest. Codon usage analysis and the identification of simple sequence repeats (SSRs) offer valuable genetic markers. Comparative analysis with other Boraginaceae species highlighted conservation and diversity in coding and noncoding regions. Phylogenetic analysis placed M. sikkimensis within the Boraginaceae family, revealing its distinct relationship with specific species.
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Affiliation(s)
- Yunqing Gao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730000, China; (Y.G.); (K.M.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Tech Innovation Centre of Western China Grassland Industry, Lanzhou University, Lanzhou 730000, China
- Centre for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
| | - Zhenjiang Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730000, China; (Y.G.); (K.M.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Xiuzhang Li
- Qinghai Academy of Animal and Veterinary Science, Qinghai University, Xining 810016, China;
| | - Kamran Malik
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730000, China; (Y.G.); (K.M.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Tech Innovation Centre of Western China Grassland Industry, Lanzhou University, Lanzhou 730000, China
- Centre for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
| | - Chunjie Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730000, China; (Y.G.); (K.M.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730000, China
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730000, China
- Gansu Tech Innovation Centre of Western China Grassland Industry, Lanzhou University, Lanzhou 730000, China
- Centre for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
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Yang J, Chu Q, Meng G, Kong W. The complete chloroplast genome sequences of three Broussonetia species and comparative analysis within the Moraceae. PeerJ 2022; 10:e14293. [PMID: 36340196 PMCID: PMC9632464 DOI: 10.7717/peerj.14293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/03/2022] [Indexed: 01/22/2023] Open
Abstract
Background Species of Broussonetia (family Moraceae) are commonly used to make textiles and high-grade paper. The distribution of Broussonetia papyrifera L. is considered to be related to the spread and location of humans. The complete chloroplast (cp) genomes of B. papyrifera, Broussonetia kazinoki Sieb., and Broussonetia kaempferi Sieb. were analyzed to better understand the status and evolutionary biology of the genus Broussonetia. Methods The cp genomes were assembled and characterized using SOAPdenovo2 and DOGMA. Phylogenetic and molecular dating analysis were performed using the concatenated nucleotide sequences of 35 species in the Moraceae family and were based on 66 protein-coding genes (PCGs). An analysis of the sequence divergence (pi) of each PCG among the 35 cp genomes was conducted using DnaSP v6. Codon usage indices were calculated using the CodonW program. Results All three cp genomes had the typical land plant quadripartite structure, ranging in size from 160,239 bp to 160,841 bp. The ribosomal protein L22 gene (RPL22) was either incomplete or missing in all three Broussonetia species. Phylogenetic analysis revealed two clades. Clade 1 included Morus and Artocarpus, whereas clade 2 included the other seven genera. Malaisia scandens Lour. was clustered within the genus Broussonetia. The differentiation of Broussonetia was estimated to have taken place 26 million years ago. The PCGs' pi values ranged from 0.0005 to 0.0419, indicating small differences within the Moraceae family. The distribution of most of the genes in the effective number of codons plot (ENc-plot) fell on or near the trend line; the slopes of the trend line of neutrality plots were within the range of 0.0363-0.171. These results will facilitate the identification, taxonomy, and utilization of the Broussonetia species and further the evolutionary studies of the Moraceae family.
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Affiliation(s)
- Jinhong Yang
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, China
| | - Qu Chu
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, China
| | - Gang Meng
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, China
| | - Weiqing Kong
- Shaanxi Key Laboratory of Sericulture, Ankang University, Ankang, China
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Xiao G, Zhou J, Huo Z, Wu T, Li Y, Li Y, Wang Y, Wang M. The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice. Int J Mol Sci 2022; 23:12860. [PMID: 36361651 PMCID: PMC9656316 DOI: 10.3390/ijms232112860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 10/29/2023] Open
Abstract
The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops.
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Affiliation(s)
- Guilian Xiao
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Junzhi Zhou
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Zhiheng Huo
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Tong Wu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yingchun Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yajing Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
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Tian G, Xiao G, Wu T, Zhou J, Xu W, Wang Y, Xia G, Wang M. Alteration of synonymous codon usage bias accompanies polyploidization in wheat. Front Genet 2022; 13:979902. [PMID: 36313462 PMCID: PMC9614214 DOI: 10.3389/fgene.2022.979902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
The diploidization of polyploid genomes is accompanied by genomic variation, including synonymous nucleotide substitutions that may lead to synonymous codon usage bias (SCUB). SCUB can mirror the evolutionary specialization of plants, but its effect on the formation of polyploidies is not well documented. We explored this issue here with hexaploid wheat and its progenitors. Synonymous codons (SCs) ending in either cytosine (NNC) or guanidine (NNG) were more frequent than those ending in either adenosine (NNA) or thymine (NNT), and the preference for NNC/G codons followed the increase in genome ploidy. The ratios between NNC/G and NNA/T codons gradually decreased in genes with more introns, and the difference in these ratios between wheat and its progenitors diminished with increasing ploidy. SCUB frequencies were heterogeneous among exons, and the bias preferred to NNA/T in more internal exons, especially for genes with more exons; while the preference did not appear to associate with ploidy. The SCUB alteration of the progenitors was different during the formation of hexaploid wheat, so that SCUB was the homogeneous among A, B and D subgenomes. DNA methylation-mediated conversion from cytosine to thymine weakened following the increase of genome ploidy, coinciding with the stronger bias for NNC/G SCs in the genome as a function of ploidy, suggesting that SCUB contribute to the epigenetic variation in hexaploid wheat. The patterns in SCUB mirrored the formation of hexaploid wheat, which provides new insight into genome shock-induced genetic variation during polyploidization. SCs representing non-neutral synonymous mutations can be used for genetic dissection and improvement of agricultural traits of wheat and other polyploidies.
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Affiliation(s)
- Geng Tian
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Guilian Xiao
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Tong Wu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Junzhi Zhou
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Wenjing Xu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, China
- *Correspondence: Mengcheng Wang,
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Wang L, Zhang S, Fang J, Jin X, Mamut R, Li P. The Chloroplast Genome of the Lichen Photobiont Trebouxiophyceae sp. DW1 and Its Phylogenetic Implications. Genes (Basel) 2022; 13:genes13101840. [PMID: 36292725 PMCID: PMC9601494 DOI: 10.3390/genes13101840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Lichens are symbiotic associations of algae and fungi. The genetic mechanism of the symbiosis of lichens and the influence of symbiosis on the size and composition of the genomes of symbiotic algae have always been intriguing scientific questions explored by lichenologists. However, there were limited data on lichen genomes. Therefore, we isolated and purified a lichen symbiotic alga to obtain a single strain (Trebouxiophyceae sp. DW1), and then obtained its chloroplast genome information by next-generation sequencing (NGS). The chloroplast genome is 129,447 bp in length, and the GC content is 35.2%. Repetitive sequences with the length of 30–35 bp account for 1.27% of the total chloroplast genome. The simple sequence repeats are all mononucleotide repeats. Codon usage analysis showed that the genome tended to use codon ending in A/U. By comparing the length of different regions of Trebouxiophyceae genomes, we found that the changes in the length of exons, introns, and intergenic sequences affect the size of genomes. Trebouxiophyceae had an unstable chloroplast genome structure, with IRs repeatedly losing during evolution. Phylogenetic analysis showed that Trebouxiophyceae is paraphyletic, and Trebouxiophyceae sp. DW1 is sister to the clade of Koliella longiseta and Pabia signiensis.
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Affiliation(s)
- Lidan Wang
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
| | - Shenglu Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jinjin Fang
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
| | - Xinjie Jin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Reyim Mamut
- College of Life Sciences and Technology, Xinjiang University, Urumchi 830046, China
- Correspondence: (R.M.); (P.L.)
| | - Pan Li
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Correspondence: (R.M.); (P.L.)
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Zhao Y, Qu D, Ma Y. Characterization of the Chloroplast Genome of Argyranthemum frutescens and a Comparison with Other Species in Anthemideae. Genes (Basel) 2022; 13:genes13101720. [PMID: 36292605 PMCID: PMC9602088 DOI: 10.3390/genes13101720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Argyranthemum frutescens, which belongs to the Anthemideae (Asteraceae), is widely cultivated as an ornamental plant. In this study, the complete chloroplast genome of A. frutescens was obtained based on the sequences generated by Illumina HiSeq. The chloroplast genome of A. frutescens was 149,626 base pairs (bp) in length, containing a pair of inverted repeats (IR, 24,510 bp) regions separated by a small single-copy (SSC, 18,352 bp) sequence and a large single-copy (LSC, 82,254 bp) sequence. The genome contained 132 genes, consisting of 85 coding DNA sequences, 37 tRNA genes, and 8 rRNA genes, with nineteen genes duplicated in the IR region. A comparison chloroplast genome analysis among ten species from the tribe of Anthemideae revealed that the chloroplast genome size varied, but the genome structure, gene content, and oligonucleotide repeats were highly conserved. Highly divergent regions, e.g., ycf1, trnK-psbK, petN-psbM intronic, were detected. Phylogenetic analysis supported Argyranthemum as a separate genus. The findings of this study will be helpful in the exploration of the phylogenetic relationships of the tribe of Anthemideae and contribute to the breeding improvement of A. frutescens.
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Dong S, Ying Z, Yu S, Wang Q, Liao G, Ge Y, Cheng R. 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; 22:880. [PMID: 34872502 PMCID: PMC8647421 DOI: 10.1186/s12864-021-08193-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 11/16/2021] [Indexed: 01/14/2023] Open
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.
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Affiliation(s)
- Shujie Dong
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Zhiqi Ying
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Shuisheng Yu
- The Administration Bureau of Zhejiang Jiulongshan National Nature Reserve, Suichang, Zhejiang Province, People's Republic of China
| | - Qirui Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Guanghui Liao
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China
| | - Yuqing Ge
- The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, Zhejiang Province, People's Republic of China.
| | - Rubin Cheng
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, Zhejiang Province, People's Republic of China.
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Xu W, Li Y, Li Y, Liu C, Wang Y, Xia G, Wang M. Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat. Front Genet 2021; 12:682324. [PMID: 34178040 PMCID: PMC8226224 DOI: 10.3389/fgene.2021.682324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/07/2021] [Indexed: 11/24/2022] Open
Abstract
Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nucleotide substitution causes synonymous codon usage bias (SCUB), an indicator of genomic mutation and natural selection. However, how asymmetric somatic hybridization affects SCUB has not been addressed. Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Asymmetric somatic hybridization affected SCUB and promoted the bias to A- and T-ending synonymous codon (SCs). SCUB frequencies in chromosomes introgressed with exogenous fragments were comparable to those in chromosomes without exogenous fragments, showing that exogenous fragments had no local chromosomal effect. Asymmetric somatic hybridization affected SCUB frequencies in indel-flanking sequences more strongly than in non-flanking sequences, and this stronger effect was present in both chromosomes with and without exogenous fragments. DNA methylation-driven SCUB shift was more pronounced than other SC pairs. SCUB shift was similar among seven groups of allelic chromosomes as well as three sub-genomes. Our work demonstrates that the SCUB shift induced by asymmetric somatic hybridization is attributed to the whole genomic shock, and DNA methylation is a putative force of SCUB shift during asymmetric somatic hybridization. Asymmetric somatic hybridization provides an available method for deepening the nature of SCUB shift and genetic variation induced by genomic shock.
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Affiliation(s)
- Wenjing Xu
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yingchun Li
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yajing Li
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Chun Liu
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
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Liu S, Feng S, Huang Y, An W, Yang Z, Xie C, Zheng X. Characterization of the Complete Chloroplast Genome of Buddleja Lindleyana. J AOAC Int 2021; 105:202-210. [PMID: 33944934 DOI: 10.1093/jaoacint/qsab066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/25/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Buddleja lindleyana Fort., which belongs to the Loganiaceae with a distribution throughout the tropics, is widely used as an ornamental plant in China. Buddleja contains several morphologically similar species, which need to be identified by molecular identification. But there is little molecular research on the genus Buddleja. OBJECTIVE Using molecular biology techniques to sequence and analyze the complete chloroplast (cp) genome of B. lindleyana. METHODS According to next-generation sequencing to sequence the genome data, a series of bioinformatics software were used to assembly and analysis the molecular structure of cp genome of B. lindleyana. RESULTS The complete cp genome of B. lindleyana is a circular 154,487-bp-long molecule with a GC content of 38.1%. It has a familiar quadripartite structure, including a large single-copy region (LSC; 85,489 bp), a small single-copy region (SSC; 17,898bp) and a pair of inverted repeats (IRs; 25,550 bp). A total of 133 genes were identified in the genome, including 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 2 pseudogenes. CONCLUSIONS These results suggested that B. lindelyana cp genome could be used as a potential genomic resource to resolve the phylogenetic positions and relationships of Loganiaceae, and will offer valuable information for future research in the identification of Buddleja species and will conduce to genomic investigations of these species.
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Affiliation(s)
- Shanshan Liu
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Shiyin Feng
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405
| | - Yuying Huang
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Wenli An
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Zerui Yang
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Chunzhu Xie
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Xiasheng Zheng
- National Engineering Research Center for Modernization of Traditional Chinese Medicine, Mathematical Engineering Academy of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
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Xiong Y, Lei X, Bai S, Xiong Y, Liu W, Wu W, Yu Q, Dong Z, Yang J, Ma X. Genomic survey sequencing, development and characterization of single- and multi-locus genomic SSR markers of Elymus sibiricus L. BMC PLANT BIOLOGY 2021; 21:3. [PMID: 33407133 PMCID: PMC7789342 DOI: 10.1186/s12870-020-02770-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/02/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Siberian wildrye (Elymus sibiricus L.) attracts considerable interest for grassland establishment and pasture recovery in the Qinghai-Tibet Plateau (QTP) due to its excellence in strong stress tolerance, high nutritional value and ease to cultivate. However, the lack of genomic information of E. sibiricus hampers its genetics study and breeding process. RESULTS In this study, we performed a genome survey and developed a set of SSR markers for E. sibiricus based on Next-generation sequencing (NGS). We generated 469.17 Gb clean sequence which is 58.64× of the 6.86 Gb estimated genome size. We assembled a draft genome of 4.34 Gb which has 73.23% repetitive elements, a heterozygosity ratio of 0.01% and GC content of 45.68%. Based on the gnomic sequences we identified 67,833 SSR loci and from which four hundred were randomly selected to develop markers. Finally, 30 markers exhibited polymorphism between accessions and ten were identified as single-locus SSR. These newly developed markers along with previously reported 30 ones were applied to analyze genetic polymorphism among 27 wild E. sibiricus accessions. We found that single-locus SSRs are superior to multi-loci SSRs in effectiveness. CONCLUSIONS This study provided insights into further whole genome sequencing of E. sibiricus in strategy selection. The novel developed SSR markers will facilitate genetics study and breeding for Elymus species.
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Affiliation(s)
- Yi Xiong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiong Lei
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
- Sichuan Academy of Grassland Science, Chengdu, 611731, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, 611731, China
| | - Yanli Xiong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, 81108, China
| | - Wendan Wu
- Sichuan Pratacultural Technology Research and Extension Center, Chengdu, 610041, China
| | - Qingqing Yu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhixiao Dong
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Yang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130, China.
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Tian G, Li G, Liu Y, Liu Q, Wang Y, Xia G, Wang M. Polyploidization is accompanied by synonymous codon usage bias in the chloroplast genomes of both cotton and wheat. PLoS One 2020; 15:e0242624. [PMID: 33211753 PMCID: PMC7676672 DOI: 10.1371/journal.pone.0242624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 11/05/2020] [Indexed: 11/27/2022] Open
Abstract
Synonymous codon usage bias (SCUB) of both nuclear and organellar genes can mirror the evolutionary specialization of plants. The polyploidization process exposes the nucleus to genomic shock, a syndrome which promotes, among other genetic variants, SCUB. Its effect on organellar genes has not, however, been widely addressed. The present analysis targeted the chloroplast genomes of two leading polyploid crop species, namely cotton and bread wheat. The frequency of codons in the chloroplast genomes ending in either adenosine (NNA) or thymine (NNT) proved to be higher than those ending in either guanidine or cytosine (NNG or NNC), and this difference was conserved when comparisons were made between polyploid and diploid forms in both the cotton and wheat taxa. Preference for NNA/T codons was heterogeneous among genes with various numbers of introns and was also differential among the exons. SCUB patterns distinguished tetraploid cotton from its diploid progenitor species, as well as bread wheat from its diploid/tetraploid progenitor species, indicating that SCUB in the chloroplast genome partially mirrors the formation of polyploidies.
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Affiliation(s)
- Geng Tian
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Guoqing Li
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Yanling Liu
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Qinghua Liu
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, Shandong, China
- * E-mail:
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14
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Liu H, Lu Y, Lan B, Xu J. Codon usage by chloroplast gene is bias in Hemiptelea davidii. J Genet 2020; 99:8. [PMID: 32089527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The base composition of the chloroplast genes is of great interest because they play a highly significant role in the evolutionary development of the plants. Evaluation of the 48 chloroplast protein-coding genes of Hemiptelea davidii showed that the average GC content was about 37.32%, while at the third codon base position alone the average GC content was only 27.80%. The 48 genes were classified into five groups based on the gene function and each group displayed specific codon characteristics. Based on the relative synonymous codon usage analysis, a total of 30 high-frequency codons and 11 optimal codons were identified, most of them ended with A or T. Neutrality plot, ENC-plot and PR2-plot analyses showed that the codon usage bias of the chloroplast genes of H. davidii was greatly influenced by natural selection pressures. Meanwhile, the frequency of codon usage of chloroplast genes among different plant species displayed similarities, with some synonymous codons were preferred to be used in H. davidii. In this study, the codon usage pattern of the chloroplast protein coding genes of H. davidii provides us with a better understanding of the expression of chloroplast genes, and may advice the future molecular breeding programmes.
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Affiliation(s)
- Huabo Liu
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, People's Republic of China.
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The Complete Chloroplast Genomes of Punica granatum and a Comparison with Other Species in Lythraceae. Int J Mol Sci 2019; 20:ijms20122886. [PMID: 31200508 PMCID: PMC6627765 DOI: 10.3390/ijms20122886] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/02/2019] [Accepted: 06/02/2019] [Indexed: 02/06/2023] Open
Abstract
Pomegranates (Punica granatum L.) are one of the most popular fruit trees cultivated in arid and semi-arid tropics and subtropics. In this study, we determined and characterized three complete chloroplast (cp) genomes of P. granatum cultivars with different phenotypes using the genome skimming approach. The complete cp genomes of three pomegranate cultivars displayed the typical quadripartite structure of angiosperms, and their length ranged from 156,638 to 156,639 bp. They encoded 113 unique genes and 17 are duplicated in the inverted regions. We analyzed the sequence diversity of pomegranate cp genomes coupled with two previous reports. The results showed that the sequence diversity is extremely low and no informative sites were detected, which suggests that cp genome sequences may be not be suitable for investigating the genetic diversity of pomegranate genotypes. Further, we analyzed the codon usage pattern and identified the potential RNA editing sites. A comparative cp genome analysis with other species within Lythraceae revealed that the gene content and organization are highly conserved. Based on a site-specific model, 11 genes with positively selected sites were detected, and most of them were photosynthesis-related genes and genetic system-related genes. Together with previously released cp genomes of the order Myrtales, we determined the taxonomic position of P. granatum based on the complete chloroplast genomes. Phylogenetic analysis suggested that P. granatum form a single clade with other species from Lythraceae with a high support value. The complete cp genomes provides valuable information for understanding the phylogenetic position of P. gramatum in the order Myrtales.
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Abstract
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower sequence evolution. We also find a strong correlation between gbM and codon bias, resulting from systematic replacement of CpG bearing codons. We conclude that gbM has strong effects on codon evolution and speculate that this may influence establishment of optimal codons.
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Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
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17
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Wang M, Liu C, Xing T, Wang Y, Xia G. Asymmetric somatic hybridization induces point mutations and indels in wheat. BMC Genomics 2015; 16:807. [PMID: 26476565 PMCID: PMC4609470 DOI: 10.1186/s12864-015-1974-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 10/03/2015] [Indexed: 01/06/2023] Open
Abstract
Background Allopolyploid genome needs wide structural variation to deal with genomic shock. The introgression line, generated via asymmetric somatic hybridization, is introgressed with a minimum of exogenous chromatin, which also leads to genomic shock to induce genetic variation. However, the extent of its genomic variation and its difference from allopolyploidies remains unknown. Methods Here, we explored this issue using the bread wheat cultivar SR3, a derivative of an asymmetric somatic hybrid between the cultivar JN177 and an accession of tall wheatgrass (Thinopyrum elongatum). The ESTs (expressed sequence taqs) were large-scale sequenced using the cDNA library constructed in each of SR3 and JN177. Point mutations and indels (insertions and deletions) of SR3 were calculated, and their difference from the genetic variation of bread wheat and its ancestors were compared, with aim to analyze the extent and pattern of sequence variation induced by somatic hybridization. Results Both point mutations and indels (insertions and deletions) were frequently induced by somatic hybridization in the coding sequences. While the genomic shock caused by allopolyploidization tends to favor deletion over insertion, there was no evidence for such a preference following asymmetric somatic hybridization. The GC content of sequence adjacent to indel sites was also distinct from what has been observed in allopolyploids. Conclusions This study demonstrates that asymmetric somatic hybridization induces high frequency of genetic variation in a manner partially different from allopolipoidization. Asymmetric somatic hybridization provides appropriate material to comprehensively explore the nature of the genetic variation induced by genomic shock. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1974-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, 250100, Shandong, P. R. China.
| | - Chun Liu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, 250100, Shandong, P. R. China.
| | - Tian Xing
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, 250100, Shandong, P. R. China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, 479 Shengli North Avenue, Shijiazhuang, 050041, Hebei, China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, 250100, Shandong, P. R. China.
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Ressayre A, Glémin S, Montalent P, Serre-Giardi L, Dillmann C, Joets J. Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes. Genome Biol Evol 2015; 7:2913-28. [PMID: 26450849 PMCID: PMC4684703 DOI: 10.1093/gbe/evv189] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Plant genomes present a continuous range of variation in nucleotide composition (G + C content). In coding regions, G + C-poor species tend to have unimodal distributions of G + C content among genes within genomes and slight 5′–3′ gradients along genes. In contrast, G + C-rich species display bimodal distributions of G + C content among genes and steep 5′–3′ decreasing gradients along genes. The causes of these peculiar patterns are still poorly understood. Within two species (Arabidopsis thaliana and rice), each representative of one side of the continuum, we studied the consequences of intron presence on coding region and intron G + C content at different scales. By properly taking intron structure into account, we showed that, in both species, intron presence is associated with step changes in nucleotide, codon, and amino acid composition. This suggests that introns have a barrier effect structuring G + C content along genes and that previous continuous characterizations of the 5′–3′ gradients were artifactual. In external gene regions (located upstream first or downstream last introns), species-specific factors, such as GC-biased gene conversion, are shaping G + C content whereas in internal gene regions (surrounded by introns), G + C content is likely constrained to remain within a range common to both species.
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Affiliation(s)
- Adrienne Ressayre
- UMR 0320/UMR 8120 Génétique Quantitative et Evolution-Le Moulon, INRA, Gif-sur-Yvette, France
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution (ISEM), UMR 5554, Université de Montpellier, CNRS-IRD-EPHE, France Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Sweden
| | - Pierre Montalent
- UMR 0320/UMR 8120 Génétique Quantitative et Evolution-Le Moulon, INRA, Gif-sur-Yvette, France
| | - Laurana Serre-Giardi
- UMR 1345 IRHS Institut de Recherche en Horticulture et Semences, INRA, Centre de Recherche Angers-Nantes, Beaucousé, France
| | - Christine Dillmann
- UMR 0320/UMR 8120 Génétique Quantitative et Evolution-Le Moulon, Université Paris-Sud, Gif-sur-Yvette, France
| | - Johann Joets
- UMR 0320/UMR 8120 Génétique Quantitative et Evolution-Le Moulon, INRA, Gif-sur-Yvette, France
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Xu W, Xing T, Zhao M, Yin X, Xia G, Wang M. Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution. PLoS One 2015; 10:e0131508. [PMID: 26110418 PMCID: PMC4481540 DOI: 10.1371/journal.pone.0131508] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/03/2015] [Indexed: 11/21/2022] Open
Abstract
Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.
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Affiliation(s)
- Wenjing Xu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Tian Xing
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Mingming Zhao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Xunhao Yin
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100, China
- * E-mail:
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Qi Y, Xu W, Xing T, Zhao M, Li N, Yan L, Xia G, Wang M. Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity. Evol Bioinform Online 2015; 11:65-77. [PMID: 25922569 PMCID: PMC4395140 DOI: 10.4137/ebo.s22566] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/22/2015] [Accepted: 02/22/2015] [Indexed: 01/26/2023] Open
Abstract
Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation–induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.
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Affiliation(s)
- Yueying Qi
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Wenjing Xu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Tian Xing
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Mingming Zhao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Nana Li
- Shandong Center of Crop Germplasm Resources, Jinan 250100,Shandong, China
| | - Li Yan
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, Jinan 250100, Shandong, China
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Li C, Pan LL, Wang Y, Wang J, Ding ZT. Codon bias of the gene for chloroplast glycerol-3-phosphate acyltransferase in Camellia sinensis (L.) O. Kuntze. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Behura SK, Singh BK, Severson DW. Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications. Evol Appl 2013; 6:1079-89. [PMID: 24187589 PMCID: PMC3804240 DOI: 10.1111/eva.12088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 06/14/2013] [Indexed: 12/17/2022] Open
Abstract
Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vectorborne diseases such as malaria, dengue, West Nile, and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the covariance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other nonmosquito insects. By applying a maximum likelihood-based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny-dependent manner, but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame Notre Dame, IN, USA
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