Analysis of chloroplast genome characteristics and codon usage bias in 14 species of Annonaceae

Abdullah MF, Shahzadi I, Waseem S, Mirza B, Ahmed I, Waheed MT (2020) Chloroplast genome of Hibiscus rosa-sinensis (Malvaceae): comparative analyses and identification of mutational hotspots. Genomics 112(1):581–591. https://doi.org/10.1016/j.ygeno.2019.04.010

Article  CAS  PubMed  Google Scholar 

Almutairi MM (2021) Analysis of chromosomes and nucleotides in rice to predict gene expression through codon usage pattern. Saudi J Biol Sci 28(8):4569–4574. https://doi.org/10.1016/j.sjbs.2021.04.059

Article  CAS  PubMed  PubMed Central  Google Scholar 

Campbell WH, Gowri G (1990) Codon usage in higher plant, green algae, and cyanobacteria. Plant Physiol 92(1):1–11. https://doi.org/10.1104/pp.92.1.1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cao Z, Yang L, Xin Y, Xu W, Li Q, Zhang H, Tu Y, Song Y, Xin P (2023) Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae). Front Plant Sci 14:1205051. https://doi.org/10.3389/fpls.2023.1205051

Article  PubMed  PubMed Central  Google Scholar 

Chakraborty S, Yengkhom S, Uddin A (2020) Analysis of codon usage bias of chloroplast genes in Oryza species: Codon usage of chloroplast genes in Oryza species. Planta 252(4):67. https://doi.org/10.1007/s00425-020-03470-7

Article  CAS  PubMed  Google Scholar 

Chakraborty S, Sophiarani Y, Uddin A (2021) Free energy of mRNA positively correlates with GC content in chloroplast transcriptomes of edible legumes. Genomics 113(4):2826–2838. https://doi.org/10.1016/j.ygeno.2021.06.026

Article  CAS  PubMed  Google Scholar 

Chen J, Ma W, Hu X, Zhou K (2023) Synonymous Codon usage Bias in the Chloroplast genomes of 13 Oil-Tea Camellia Samples from South China. Forests 14(4):794. https://doi.org/10.3390/F14040794

Article  Google Scholar 

Chi X, Chen R, Zhang F, Chen S (2023) Comparative plastomes of species from Phrymaceae and Mazaceae: insights into adaptive evolution, Codon usage Bias and phylogenetic relationships. https://doi.org/10.1139/gen-2023-0014. Genome

Dehlinger B, Jurss J, Lychuk K, Putonti C (2021) The dynamic Codon Biaser: calculating prokaryotic codon usage biases. Microb Genomics 7(10):000663. https://doi.org/10.1099/mgen.0.000663

Article  CAS  Google Scholar 

Finkeldey R, Gailing O (2013) Chloroplasts. Brenner’s Encyclopedia of Genetics (Second Edition). Academic Press. 525–527

Geng X, Huang N, Zhu Y, Qin L, Hui L (2022) Codon usage bias analysis of the chloroplast genome of cassava. South African Journal of Botany 151(PA): 970–975. https://doi.org/10.1016/J.SAJB.2022.11.022

Guo X, Wang Y, Wang S (2020) Complete chloroplast genome sequences from yellowhorn (Xanthoceras sorbifolia) and evolution analysis based on codon usage bias. Int J Agric Biology 24(4):676–684. https://doi.org/10.17957/IJAB/15.1487

Article  CAS  Google Scholar 

Hershberg R, Petrov DA (2008) Selection on codon bias. Annu Rev Genet 42:287–299. https://doi.org/10.1146/annurev.genet.42.110807.091442

Article  CAS  PubMed  Google Scholar 

Jiang Y, Li BT (1979) Flora Reipublicae Popularis Sinicae. Sci Press 30(2):10–175

Google Scholar 

Konhar R, Debnath M, Vishwakarma S, Bhattacharjee A, Sundar D, Tandon P, Biswal DK (2019) The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobium species. PeerJ 7:e7756. https://doi.org/10.7717/peerj.7756

Article  PubMed  PubMed Central  Google Scholar 

Larranaga N, Albertazzi FJ, Hormaza JI (2019) Phylogenetics of Annona cherimola (Annonaceae) and some of its closest relatives. J Syst Evol 57(3):211–221. https://doi.org/10.1111/jse.12473

Article  Google Scholar 

Larranaga N, Fontecha G, Albertazzi FJ, Palmieri M, Hormaza JI (2022) Amplification of Cherimoya (Annona cherimola Mill.) With chloroplast-specific markers: geographical implications on diversity and dispersion studies. Horticulturae 8(9):807. https://doi.org/10.3390/HORTICULTURAE8090807

Article  Google Scholar 

Lei JM, Liang ZR, Zhang H, Li YQ, Xue BE (2022) Advances in exploitation and utilization of wild fruit resources of Annonaceae in China. J Fruit Sci 39(01):121–130. https://doi.org/10.13925/j.cnki.gsxb.20210301

Article  Google Scholar 

Li BT, Michael GG (2012) Flora of China, vol 19. Science, pp 672–713

Li N, Sun MH, Jiang ZS, Shu HR, Zhang SZ (2016) Genome-wide analysis of the synonymous codon usage patterns in apple. J Integr Agric 15(5):983–991. https://doi.org/10.3390/ijms17081304

Article  CAS  Google Scholar 

Liu L, Du J, Liu Z, Zuo W, Wang Z, Li J, Zeng Y (2023) Comparative and phylogenetic analyses of nine complete chloroplast genomes of Orchidaceae. Sci Rep 13(1):21403. https://doi.org/10.1038/s41598-023-48043-2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mehmood F, Abdullah, Shahzadi I, Ahmed I, Waheed MT, Mirza B (2020) Characterization of Withania somnifera chloroplast genome and its comparison with other selected species of Solanaceae. Genomics 112(2):1522–1530. https://doi.org/10.1016/j.ygeno.2019.08.024

Article  CAS  PubMed  Google Scholar 

Morton BR (2021) Context-dependent Mutation dynamics, not selection, explains the Codon usage Bias of Most Angiosperm Chloroplast genes. J Mol Evol 90(1):17–29. https://doi.org/10.1007/s00239-021-10038-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Morton BR (2022) Context-dependent mutation dynamics, not selection, explains the codon usage bias of most angiosperm chloroplast genes. J Mol Evol 90(1):17–29. https://doi.org/10.1007/s00239-021-10038-w

Article  CAS  PubMed  Google Scholar 

Nogueira BBAP, Mendes DS, Mendes RB, Pimenta S, Pereira MCT, Azevedo AM, Nietsche S (2022) Selection in half-sib progenies of Annona squamosa L.: an important step in the development of new cultivars. Sci Hort 302:111173. https://doi.org/10.1016/j.scienta.2022.111173

Article  CAS  Google Scholar 

Parmar R, Cattonaro F, Phillips C, Vassiliev S, Morgante M, Rajora OP (2022) Assembly and annotation of Red Spruce (Picea rubens) chloroplast genome, identification of simple sequence repeats, and phylogenetic analysis in Picea. Int J Mol Sci 23(23):15243. https://doi.org/10.3390/IJMS232315243

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rawal HC, Borchetia S, Bera B, Soundararajan S, Ilango RVJ, Barooah AK, Sharma TR, Singh NK, Mondal TK (2021) Comparative analysis of chloroplast genomes indicated different origin for Indian tea (Camellia Assamica Cv TV1) as compared to Chinese tea. Sci Rep 11(1):110. https://doi.org/10.1038/s41598-020-80431-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rehman U, Sultana N, Abdullah, Jamal A, Muzaffar M, Poczai P (2021) Comparative chloroplast genomics in Phyllanthaceae species. Diversity 13(9):403. https://doi.org/10.3390/D13090403

Article  CAS  Google Scholar 

Sadhu L, Kumar K, Kumar S, Dass A, Pathak R, Bhardwaj A, Reddy VS (2023) Chloroplasts evolved an additional layer of translational regulation based on non-AUG start codons for proteins with different turnover rates. Sci Rep 13(1):896. https://doi.org/10.1038/S41598-022-27347-9

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sahoo S, Rakshit R (2022) The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family. Genomics Inf 20(4):e43. https://doi.org/10.5808/gi.22045

Article  Google Scholar 

Senapati A, Chetri BK, Mitra S, Shelke RG, Rangan L (2023) Decoding the complete chloroplast genome of Cissus quadrangularis: insights into molecular structure, comparative genome analysis and mining of mutational hotspot regions. Physiol Mol Biology Plants 29(5):709–724. https://doi.org/10.1007/S12298-023-01312-W

Article  CAS  Google Scholar 

Shahzadi I, Abdullah, Mehmood F, Ali Z, Ahmed I, Mirza B (2020) Chloroplast genome sequences of Artemisia maritima and Artemisia absinthium: comparative analyses, mutational hotspots in genus Artemisia and phylogeny in family Asteraceae. Genomics 112(2):1454–1463. https://doi.org/10.1016/j.ygeno.2019.08.016

Article  CAS  PubMed  Google Scholar 

Simmonds SE, Smith JF, Davidson C, Buerki S (2021) Phylogenetics and comparative plastome genomics of two of the largest genera of angiosperms, Piper and Peperomia. Mol Phylogenet Evol 163:107229. https://doi.org/10.1016/J.YMPEV.2021.107229

Article  PubMed  Google Scholar 

Somaratne Y, Guan DL, Wang WQ, Zhao L, Xu SQ (2019) The complete chloroplast genomes of two Lespedeza species: insights into codon usage bias, RNA editing sites, and phylogenetic relationships in Desmodieae (Fabaceae: Papilionoideae). Plants 9(1):51. https://doi.org/10.3390/plants9010051

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tyagi S, Jung JA, Kim JS, Won SY (2020) Comparative analysis of the complete chloroplast genome of mainland Aster spathulifolius and other Aster species. Plants 9(5): 568. https://doi.org/

Uckele KA, Adams RP, Schwarzbach AE, Parchman TL (2021) Genome-wide RAD sequencing resolves the evolutionary history of serrate leaf Juniperus and reveals discordance with chloroplast phylogeny. Mol Phylogenet Evol 156:107022. https://doi.org/10.1016/j.ympev.2020.107022

Article  PubMed  Google Scholar 

Wang Z, Cai Q, Wang Y, Li M, Wang C, Wang Z, Jiao C, Xu C, Wang H, Zhang Z (2022) Comparative Analysis of Codon Bias in the Chloroplast genomes of Theaceae Species. Front Genet 13:824610. https://doi.org/10.3389/fgene.2022.824610

Article  PubMed  PubMed Central  Google Scholar 

Wanichthanarak K, Nookaew I, Pasookhush P, Khoomrung S (2023) Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae. BMC Plant Biol 23(1):59. https://doi.org/10.1186/s12870-023-04074-5

Article  CAS  PubMed  PubMed Central  Google Scholar 

留言 (0)

沒有登入
gif