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Ling L, Zhang S, Yang T. Analysis of Codon Usage Bias in Chloroplast Genomes of Dryas octopetala var. asiatica (Rosaceae). Genes (Basel) 2024; 15:899. [PMID: 39062678 PMCID: PMC11275609 DOI: 10.3390/genes15070899] [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: 06/22/2024] [Revised: 07/04/2024] [Accepted: 07/07/2024] [Indexed: 07/28/2024] Open
Abstract
Dryas octopetala var. asiatica, a dwarf shrub belonging to the Rosaceae family and native to Asia, exhibits notable plasticity in photosynthesis in response to temperature variations. However, the codon usage patterns and factors influencing them in the chloroplast genome of this species have not yet been documented. This study sequenced and assembled the complete genome of D. octopetala var. asiatica. The annotated genes in the chloroplast genome were analyzed for codon composition through multivariate statistical methods including a neutrality plot, a parity rule 2 (PR2) bias plot, and an effective number of codons (ENC) plot using CodonW 1.4.2 software. The results indicated that the mean GC content of 53 CDSs was 38.08%, with the average GC content at the third codon base position being 27.80%, suggesting a preference for A/U(T) at the third codon position in chloroplast genes. Additionally, the chloroplast genes exhibited a weak overall codon usage bias (CUB) based on ENC values and other indicators. Correlation analysis showed a significant negative correlation between ENC value and GC2, an extremely positive correlation with GC3, but no correlation with GC1 content. These findings highlight the importance of the codon composition at the third position in influencing codon usage bias. Furthermore, our analysis indicated that the CUB of the chloroplast genome of D. octopetala var. asiatica was primarily influenced by natural selection and other factors. Finally, this study identified UCA, CCU, GCU, AAU, GAU, and GGU as the optimal codons. These results offer a foundational understanding for genetic modification and evolutionary dynamics of the chloroplast genome of D. octopetala var. asiatica.
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Affiliation(s)
| | - Shudong Zhang
- Key Laboratory for Specialty Agricultural Germplasm Resources Development and Utilization of Guizhou Province, Liupanshui Normal University, Liupanshui 553004, China; (L.L.); (T.Y.)
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Wang H, Wu Z, Li T, Zhao J. Highly active repeat-mediated recombination in the mitogenome of the aquatic grass Hygroryza aristata. BMC PLANT BIOLOGY 2024; 24:644. [PMID: 38973002 PMCID: PMC11229283 DOI: 10.1186/s12870-024-05331-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/24/2024] [Indexed: 07/09/2024]
Abstract
BACKGROUND Floating bamboo (Hygroryza aristata) is an endangered species with a narrow native distribution and is renowned for its unique aesthetic qualities, which holds significant ecological and ornamental value. However, the lack of genetic information research, with only one complete plastome available, significantly hampers conservation efforts and further research for this species. RESULTS In this research, we sequenced and assembled the organelle genomes of floating bamboo, including the mitogenome (587,847 bp) and plastome (135,675 bp). The mitogenome can recombine into various configurations, which are mediated by 25 repeat pairs (13 SRs, 6 MRs, 1 LR, and 5 CRs). LR1 and SR5 are particularly notable as they have the ability to combine with other contigs, forming complex repeat units that facilitate further homologous recombination. The rate of homologous recombination varies significantly among species, yet there is still a pronounced positive correlation observed between the length of these repeat pairs and the rate of recombination they mediate. The mitogenome integrates seven intact protein-coding genes from the chloroplast. The codon usage patterns in both organelles are similar, with a noticeable bias towards C and T on the third codon. The gene map of Poales shows the entire loss of rpl6, succinate dehydrogenase subunits (sdh3 and sdh4). Additionally, the BOP clade retained more variable genes compared to the PACMAD clade. CONCLUSIONS We provided a high-quality and well-annotated mitogenome for floating bamboo and demonstrated the presence of diverse configurations. Our study has revealed the correlation between repeat length and their corresponding recombination rate despite variations among species. Although the mitogenome can potentially exist in the form of a unicircular in vivo, this occurrence is rare and may not be stable.
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Affiliation(s)
- Huijun Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhigang Wu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Tao Li
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jindong Zhao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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Zhang X, Li P, Wang J, Fu D, Zhao B, Dong W, Liu Y. Comparative genomic and phylogenetic analyses of mitochondrial genomes of hawthorn (Crataegus spp.) in Northeast China. Int J Biol Macromol 2024; 272:132795. [PMID: 38830497 DOI: 10.1016/j.ijbiomac.2024.132795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/18/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
Hawthorn (Crataegus spp.) plants are major sources of health food and medicines. Twenty species and seven variations of Crataegus are present in China. A variety of unique Crataegus species was found in their natural distribution in northeast China. In the present study, we assembled and annotated the mitochondrial genomes of five Crataegus species from northeastern China. The sizes of the newly sequenced mitochondrial genomes ranged from 245,907 bp to 410,837 bp. A total of 45-55 genes, including 12-19 transfer RNA genes, three ribosomal RNA genes, and 29-33 protein-coding genes (PCGs) were encoded by these mitochondrial genomes. Seven divergent hotspot regions were identified by comparative analyses: atp6, nad3, ccmFN, matR, nad1, nad5, and rps1. The most conserved genes among the Crataegus species, according to the whole-genome correlation analysis, were nad1, matR, nad5, ccmFN, cox1, nad4, trnQ-TTG, trnK-TTT, trnE-TTC, and trnM-CAT. Horizontal gene transfer between organellar genomes was common in Crataegus plants. Based on the phylogenetic trees of mitochondrial PCGs, C. maximowiczii, C. maximowiczii var. ninganensis, and C. bretschneideri shared similar maternal relationships. This study improves Crataegus mitochondrial genome resources and offers important insights into the taxonomy and species identification of this genus.
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Affiliation(s)
- Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; National Field Genebank for Hawthorn, Shenyang, Liaoning 110866, China
| | - Peihao Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Jian Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Dongxu Fu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Baipeng Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; National Field Genebank for Hawthorn, Shenyang, Liaoning 110866, China
| | - Yuexue Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; National Field Genebank for Hawthorn, Shenyang, Liaoning 110866, China.
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Xu X, Huang H, Lin S, Zhou L, Yi Y, Lin E, Feng L, Zheng Y, Lin A, Yu L, Shen Y, Henry RJ, Fang J. Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species. BMC PLANT BIOLOGY 2024; 24:331. [PMID: 38664619 PMCID: PMC11044428 DOI: 10.1186/s12870-024-04995-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Jasmine (Jasminum), renowned for its ornamental value and captivating fragrance, has given rise to numerous species and accessions. However, limited knowledge exists regarding the evolutionary relationships among various Jasminum species. RESULTS In the present study, we sequenced seven distinct Jasminum species, resulting in the assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that the size of the 12 cp genomes ranged from 159 to 165 kb and encoded 134-135 genes, including 86-88 protein-coding genes, 38-40 tRNA genes, and 8 rRNA genes. J. nudiflorum exhibited a larger genome size compared to other species, mainly attributed to the elevated number of forward repeats (FRs). Despite the typically conservative nature of chloroplasts, variations in the presence or absence of accD have been observed within J. sambac. The calculation of nucleotide diversity (Pi) values for 19 cp genomes indicated that potential mutation hotspots were more likely to be located in LSC regions than in other regions, particularly in genes ycf2, rbcL, atpE, ndhK, and ndhC (Pi > 0.2). Ka/Ks values revealed strong selection pressure on the genes rps2, atpA, rpoA, rpoC1, and rpl33 when comparing J. sambac with the three most closely related species (J. auriculatum, J. multiflorum, and J. dichotomum). Additionally, SNP identification, along with the results of Structure, PCA, and phylogenetic tree analyses, divided the Jasminum cp genomes into six groups. Notably, J. polyanthum showed gene flow signals from both the G5 group (J. nudiflorum) and the G3 group (J. tortuosum and J. fluminense). Phylogenetic tree analysis reflected that most species from the same genus clustered together with robust support in Oleaceae, strongly supporting the monophyletic nature of cp genomes within the genus Jasminum. CONCLUSION Overall, this study provides comprehensive insights into the genomic composition, variation, and phylogenetic relationships among various Jasminum species. These findings enhance our understanding of the genetic diversity and evolutionary history of Jasminum.
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Affiliation(s)
- Xiuming Xu
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Hechen Huang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Linwei Zhou
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Yuchong Yi
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Enwen Lin
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Yu Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Aiting Lin
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, 350117, China.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
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Zhao S, Gao X, Yu X, Yuan T, Zhang G, Liu C, Li X, Wei P, Li X, Liu X. Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation. Int J Mol Sci 2024; 25:2193. [PMID: 38396871 PMCID: PMC10888623 DOI: 10.3390/ijms25042193] [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: 12/01/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.
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Affiliation(s)
- Shuqi Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoman Gao
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Xiaolei Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tao Yuan
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Guiyu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xinzhong Li
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan 430072, China;
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
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Xiao M, Hu X, Li Y, Liu Q, Shen S, Jiang T, Zhang L, Zhou Y, Li Y, Luo X, Bai L, Yan W. Comparative analysis of codon usage patterns in the chloroplast genomes of nine forage legumes. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:153-166. [PMID: 38623162 PMCID: PMC11016040 DOI: 10.1007/s12298-024-01421-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 04/17/2024]
Abstract
Leguminosae is one of the three largest families of angiosperms after Compositae and Orchidaceae. It is widely distributed and grows in a variety of environments, including plains, mountains, deserts, forests, grasslands, and even waters where almost all legumes can be found. It is one of the most important sources of starch, protein and oil in the food of mankind and also an important source of high-quality forage material for animals, which has important economic significance. In our study, the codon usage patterns and variation sources of the chloroplast genome of nine important forage legumes were systematically analyzed. Meanwhile, we also constructed a phylogenetic tree based on the whole chloroplast genomes and protein coding sequences of these nine forage legumes. Our results showed that the chloroplast genomes of nine forage legumes end with A/T bases, and seven identical high-frequency (HF) codons were detected among the nine forage legumes. ENC-GC3s mapping, PR2 analysis, and neutral analysis showed that the codon bias of nine forage legumes was influenced by many factors, among which natural selection was the main influencing factor. The codon usage frequency showed that the Nicotiana tabacum and Saccharomyces cerevisiae can be considered as receptors for the exogenous expression of chloroplast genes of these nine forage legumes. The phylogenetic relationships of the chloroplast genomes and protein coding genes were highly similar, and the nine forage legumes were divided into three major clades. Among the clades Melilotus officinalis was more closely related to Medicago sativa, and Galega officinalis was more closely related to Galega orientalis. This study provides a scientific basis for the molecular markers research, species identification and phylogenetic studies of forage legumes. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01421-0.
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Affiliation(s)
- Mingkun Xiao
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Xiang Hu
- Tropical Eco-agricultural Research Institute, Yunnan Academy of Agricultural Sciences, Yuanmou, Yunnan China
| | - Yaqi Li
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Qian Liu
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Shaobin Shen
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Tailing Jiang
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Linhui Zhang
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Yingchun Zhou
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Yuexian Li
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Xin Luo
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Lina Bai
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
| | - Wei Yan
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan China
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Zhang K, Wang Y, Zhang Y, Shan X. Codon usage characterization and phylogenetic analysis of the mitochondrial genome in Hemerocallis citrina. BMC Genom Data 2024; 25:6. [PMID: 38218810 PMCID: PMC10788020 DOI: 10.1186/s12863-024-01191-4] [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: 05/25/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024] Open
Abstract
BACKGROUND Hemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and ornamental value. The phenomenon of codon usage bias (CUB) is prevalent in various genomes and provides excellent clues for gaining insight into organism evolution and phylogeny. Comprehensive analysis of the CUB of mitochondrial (mt) genes can provide rich genetic information for improving the expression efficiency of exogenous genes and optimizing molecular-assisted breeding programmes in H. citrina. RESULTS Here, the CUB patterns in the mt genome of H. citrina were systematically analyzed, and the possible factors shaping CUB were further evaluated. Composition analysis of codons revealed that the overall GC (GCall) and GC at the third codon position (GC3) contents of mt genes were lower than 50%, presenting a preference for A/T-rich nucleotides and A/T-ending codons in H. citrina. The high values of the effective number of codons (ENC) are indicative of fairly weak CUB. Significant correlations of ENC with the GC3 and codon counts were observed, suggesting that not only compositional constraints but also gene length contributed greatly to CUB. Combined ENC-plot, neutrality plot, and Parity rule 2 (PR2)-plot analyses augmented the inference that the CUB patterns of the H. citrina mitogenome can be attributed to multiple factors. Natural selection, mutation pressure, and other factors might play a major role in shaping the CUB of mt genes, although natural selection is the decisive factor. Moreover, we identified a total of 29 high-frequency codons and 22 optimal codons, which exhibited a consistent preference for ending in A/T. Subsequent relative synonymous codon usage (RSCU)-based cluster and mt protein coding gene (PCG)-based phylogenetic analyses suggested that H. citrina is close to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in evolutionary terms, reflecting a certain correlation between CUB and evolutionary relationships. CONCLUSIONS There is weak CUB in the H. citrina mitogenome that is subject to the combined effects of multiple factors, especially natural selection. H. citrina was found to be closely related to Asparagus officinalis, Chlorophytum comosum, Allium cepa, and Allium fistulosum in terms of their evolutionary relationships as well as the CUB patterns of their mitogenomes. Our findings provide a fundamental reference for further studies on genetic modification and phylogenetic evolution in H. citrina.
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Affiliation(s)
- Kun Zhang
- College of Agriculture and Life Sciences, Shanxi Datong University, Datong, Shanxi, China.
- Key Laboratory of Organic Dry Farming for Special Crops in Datong City, Datong, Shanxi, China.
| | - Yiheng Wang
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yue Zhang
- College of Agriculture and Life Sciences, Shanxi Datong University, Datong, Shanxi, China
| | - Xiaofei Shan
- College of Agriculture and Life Sciences, Shanxi Datong University, Datong, Shanxi, China
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Yang M, Liu J, Yang W, Li Z, Hai Y, Duan B, Zhang H, Yang X, Xia C. Analysis of codon usage patterns in 48 Aconitum species. BMC Genomics 2023; 24:703. [PMID: 37993787 PMCID: PMC10664653 DOI: 10.1186/s12864-023-09650-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 09/05/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The Aconitum genus is a crucial member of the Ranunculaceae family. There are 350 Aconitum species worldwide, with about 170 species found in China. These species are known for their various pharmacological effects and are commonly used to treat joint pain, cold abdominal pain, and other ailments. Codon usage bias (CUB) analysis contributes to evolutionary relationships and phylogeny. Based on protein-coding sequences (PCGs), we selected 48 species of Aconitum for CUB analysis. RESULTS The results revealed that Aconitum species had less than 50% GC content. Furthermore, the distribution of GC content was irregular and followed a trend of GC1 > GC2 > GC3, indicating a bias towards A/T bases. The relative synonymous codon usage (RSCU) heat map revealed the presence of conservative codons with slight variations within the genus. The effective number of codons (ENC)-Plot and the parity rule 2 (PR2)-bias plot analysis indicate that natural selection is the primary factor influencing the variation in codon usage. As a result, we screened various optimal codons and found that A/T bases were preferred as the last codon. Furthermore, our Maximum Likelihood (ML) analysis based on PCGs among 48 Aconitum species yielded results consistent with those obtained from complete chloroplast (cp.) genome data. This suggests that analyzing mutation in PCGs is an efficient method for demonstrating the phylogeny of species at the genus level. CONCLUSIONS The CUB analysis of 48 species of Aconitum was mainly influenced by natural selection. This study reveals the CUB pattern of Aconitum and lays the foundation for future genetic modification and phylogenetic analyses.
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Affiliation(s)
- Meihua Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Jiahao Liu
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Wanqing Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Zhen Li
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Yonglin Hai
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Baozhong Duan
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China
| | - Haizhu Zhang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China
- Western Yunnan Traditional Chinese Medicine and Ethnic Drug Engineering Center, Dali, Yunnan, 671000, China
| | - Xiaoli Yang
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China.
| | - Conglong Xia
- College of Pharmaceutical Science, Dali University, Dali, Yunnan, 671000, China.
- Key Laboratory of Yunnan Provincial Higher Education Institutions for Development of Yunnan Daodi Medicinal Materials Resources, Dali, Yunnan, 671000, China.
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9
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Fu Y, Liang F, Li C, Warren A, Shin MK, Li L. Codon Usage Bias Analysis in Macronuclear Genomes of Ciliated Protozoa. Microorganisms 2023; 11:1833. [PMID: 37513005 PMCID: PMC10384029 DOI: 10.3390/microorganisms11071833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Ciliated protozoa (ciliates) are unicellular eukaryotes, several of which are important model organisms for molecular biology research. Analyses of codon usage bias (CUB) of the macronuclear (MAC) genome of ciliates can promote a better understanding of the genetic mode and evolutionary history of these organisms and help optimize codons to improve gene editing efficiency in model ciliates. In this study, the following indices were calculated: the guanine-cytosine (GC) content, the frequency of the nucleotides at the third position of codons (T3, C3, A3, G3), the effective number of codons (ENc), GC content at the 3rd position of synonymous codons (GC3s), and the relative synonymous codon usage (RSCU). Parity rule 2 plot analysis, Neutrality plot analysis, ENc plot analysis, and correlation analysis were employed to explore the main influencing factors of CUB. The results showed that the GC content in the MAC genomes of each of 21 ciliate species, the genomes of which were relatively complete, was lower than 50%, and the base compositions of GC and GC3s were markedly distinct. Synonymous codon analysis revealed that the codons in most of the 21 ciliates ended with A or T and four codons were the general putative optimal codons. Collectively, our results indicated that most of the ciliates investigated preferred using the codons with anof AT-ending and that codon usage bias was affected by gene mutation and natural selection.
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Affiliation(s)
- Yu Fu
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Fasheng Liang
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Congjun Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Mann Kyoon Shin
- Department of Biology, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Lifang Li
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
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10
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Gan J, Li Y, Tang D, Guo B, Li D, Cao F, Sun C, Yu L, Yan Z. The Complete Chloroplast Genomes of Gynostemma Reveal the Phylogenetic Relationships of Species within the Genus. Genes (Basel) 2023; 14:genes14040929. [PMID: 37107687 PMCID: PMC10138119 DOI: 10.3390/genes14040929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/06/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Gynostemma is an important medicinal and food plant of the Cucurbitaceae family. The phylogenetic position of the genus Gynostemma in the Cucurbitaceae family has been determined by morphology and phylogenetics, but the evolutionary relationships within the genus Gynostemma remain to be explored. The chloroplast genomes of seven species of the genus Gynostemma were sequenced and annotated, of which the genomes of Gynostemma simplicifolium, Gynostemma guangxiense and Gynostemma laxum were sequenced and annotated for the first time. The chloroplast genomes ranged from 157,419 bp (Gynostemma compressum) to 157,840 bp (G. simplicifolium) in length, including 133 identical genes: 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. Phylogenetic analysis showed that the genus Gynostemma is divided into three primary taxonomic clusters, which differs from the traditional morphological classification of the genus Gynostemma into the subgenus Gynostemma and Trirostellum. The highly variable regions of atpH-atpL, rpl32-trnL, and ccsA-ndhD, the repeat unilts of AAG/CTT and ATC/ATG in simple sequence repeats (SSRs) and the length of overlapping regions between rps19 and inverted repeats(IRb) and between ycf1 and small single-copy (SSC) were found to be consistent with the phylogeny. Observations of fruit morphology of the genus Gynostemma revealed that transitional state species have independent morphological characteristics, such as oblate fruit and inferior ovaries. In conclusion, both molecular and morphological results showed consistency with those of phylogenetic analysis.
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Affiliation(s)
- Jiaxia Gan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Ying Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Deying Tang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Jinghong 666100, China
| | - Baolin Guo
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Doudou Li
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Feng Cao
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Chao Sun
- Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Key Laboratory of Ministry of Education, Beijing 100193, China
| | - Liying Yu
- Guangxi Botanical Garden of Medicinal Plant, Guangxi TCM Resources General Survey and Data Collection Key Laboratory, Nanning 530023, China
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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11
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Koo H, Shin AY, Hong S, Kim YM. The complete chloroplast genome of Hibiscus syriacus using long-read sequencing: Comparative analysis to examine the evolution of the tribe Hibisceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1111968. [PMID: 36818825 PMCID: PMC9931742 DOI: 10.3389/fpls.2023.1111968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Hibiscus syriacus, a member of the tribe Hibisceae, is considered an important ornamental and medicinal plant in east Asian countries. Here, we sequenced and assembled the complete chloroplast genome of H. syriacus var. Baekdansim using the PacBio long-read sequencing platform. A quadripartite structure with 161,026 base pairs was obtained, consisting of a pair of inverted repeats (IRA and IRB) with 25,745 base pairs, separated by a large single-copy region of 89,705 base pairs and a short single-copy region of 19,831 base pairs. This chloroplast genome had 79 protein-coding genes, 30 transfer RNA genes, 4 ribosomal RNA genes, and 109 simple sequence repeat regions. Among them, ndhD and rpoC1, containing traces of RNA-editing events associated with adaptive evolution, were identified by analysis of putative RNA-editing sites. Codon usage analysis revealed a preference for A/U-terminated codons. Furthermore, the codon usage pattern had a clustering tendency similar to that of the phylogenetic analysis of the tribe Hibisceae. This study provides clues for understanding the relationships and refining the taxonomy of the tribe Hibisceae.
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Affiliation(s)
- Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Seongmin Hong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioinformatics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
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12
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Li C, Zhou L, Nie J, Wu S, Li W, Liu Y, Liu Y. Codon usage bias and genetic diversity in chloroplast genomes of Elaeagnus species (Myrtiflorae: Elaeagnaceae). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:239-251. [PMID: 36875724 PMCID: PMC9981860 DOI: 10.1007/s12298-023-01289-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Codon usage bias (CUB) reveals the characteristics of species and can be utilized to understand their evolutionary relationship, increase the target genes' expression in the heterologous receptor plants, and further provide theoretic assistance for correlative study on molecular biology and genetic breeding. The chief aim of this work was to analyze the CUB in chloroplast (cp.) genes in nine Elaeagnus species to provide references for subsequent studies. The codons of Elaeagnus cp. genes preferred to end with A/T bases rather than with G/C bases. Most of the cp. genes were prone to mutation, while the rps7 genes were identical in sequences. Natural selection was inferred to have a powerful impact on the CUB in Elaeagnus cp. genomes, and their CUB was extremely strong. In addition, the optimal codons were identified in the nine cp. genomes based on the relative synonymous codon usage (RSCU) values, and the optimal codon numbers were between 15 and 19. The clustering analyses based on RSCU were contrasted with the maximum likelihood (ML)-based phylogenetic tree derived from coding sequences, suggesting that the t-distributed Stochastic Neighbor Embedding clustering method was more appropriate for evolutionary relationship analysis than the complete linkage method. Moreover, the ML-based phylogenetic tree based on the conservative matK genes and the whole cp. genomes had visible differences, indicating that the sequences of specific cp. genes were profoundly affected by their surroundings. Following the clustering analysis, Arabidopsis thaliana was considered the optimal heterologous expression receptor plant for the Elaeagnus cp. genes. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01289-6.
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Affiliation(s)
- Changle Li
- College of Forestry, Northwest A&F University, Yangling, 712100 China
| | - Ling Zhou
- College of Forestry, Northwest A&F University, Yangling, 712100 China
| | - Jiangbo Nie
- College of Forestry, Northwest A&F University, Yangling, 712100 China
| | - Songping Wu
- College of Forestry, Northwest A&F University, Yangling, 712100 China
| | - Wei Li
- Academy of Agriculture and Forestry Science, Qinghai University, Xining, 810016 China
| | - Yonghong Liu
- College of Forestry, Northwest A&F University, Yangling, 712100 China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, 712100 China
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13
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Comparative Analysis of Chloroplast Genomes within Saxifraga (Saxifragaceae) Takes Insights into Their Genomic Evolution and Adaption to the High-Elevation Environment. Genes (Basel) 2022; 13:genes13091673. [PMID: 36140840 PMCID: PMC9498722 DOI: 10.3390/genes13091673] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Saxifraga species are widely distributed in alpine and arctic regions in the Northern hemisphere. Highly morphological diversity within this genus brings great difficulties for species identification, and their typical highland living properties make it interesting how they adapt to the extreme environment. Here, we newly generated the chloroplast (cp) genomes of two Saxifraga species and compared them with another five Saxifraga cp genomes to understand the characteristics of cp genomes and their potential roles in highland adaptation. The genome size, structure, gene content, GC content, and codon usage pattern were found to be highly similar. Cp genomes ranged from 146,549 bp to 151,066 bp in length, most of which comprised 130 predicted genes. Yet, due to the expansion of IR regions, the second copy of rps19 in Saxifraga stolonifera was uniquely kept. Through sequence divergence analysis, we identified seven hypervariable regions and detected some signatures of regularity associated with genetic distance. We also identified 52 to 89 SSRs and some long repeats among seven Saxifraga species. Both ML and BI phylogenetic analyses confirmed that seven Saxifraga species formed a monophyletic clade in the Saxifragaceae family, and their intragenus relationship was also well supported. Additionally, the ndhI and ycf1 genes were considered under positive selection in species inhabiting relatively high altitudes. Given the conditions of intense light and low CO2 concentration in the highland, the products of these two genes might participate in the adaptation to the extreme environment.
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