Amiryousefi A, Hyvönen J, Poczai P. IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics. 2018;34(17):3030–1.

Article  PubMed  Google Scholar 

Cao X, Liu S, Mu Z, Qiao Z. Characteration and comparative analysis of the whole chloroplast genomes of five common millet (Panicum miliaceum). Mitochondrial DNA Part B. 2021;6(3):738–44.

Article  PubMed  PubMed Central  Google Scholar 

Cao X, Wang J, Wang H, Liu S, Chen L, Tian X, et al. The complete chloroplast genome of Panicum miliaceum. Mitochondrial DNA Part B. 2017;2(1):43–5.

Article  PubMed  PubMed Central  Google Scholar 

Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–202.

Article  PubMed  Google Scholar 

Cui Y, Nie L, Sun W, Xu Z, Wang Y, Yu J, et al. Comparative and phylogenetic analyses of ginger (Zingiber officinale) in the family Zingiberaceae based on the complete chloroplast genome. Plants. 2019;8(8):283.

Article  PubMed  PubMed Central  Google Scholar 

Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004;14(7):1394–403.

Article  PubMed  PubMed Central  Google Scholar 

Deng Y, Luo Y, He Y, Qin X, Li C, Deng X. Complete chloroplast genome of Michelia shiluensis and a comparative analysis with four Magnoliaceae species. Forests. 2020;11(3):267.

Article  Google Scholar 

Du L, Zhang C, Liu Q, Zhang X, Yue B. Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics. 2018;34(4):681–3.

Article  PubMed  Google Scholar 

Huang Y-Y, Cho S-T, Haryono M, Kuo C-H. Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae. PloS One. 2017;12(6):e0179055.

Krause K. Piecing together the puzzle of parasitic plant plastome evolution. Planta. 2011;234(4):647–56.

Article  PubMed  Google Scholar 

Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics. 2007;23(1):127–8.

Article  PubMed  Google Scholar 

Liu F, Zhao Y, Luo D, Hong D, Li R. The complete chloroplast genome sequence of Oryza eichingeri (Poaceae). Mitochondrial DNA Part B. 2017;2(2):465–6.

Article  PubMed  PubMed Central  Google Scholar 

McInerney JO. GCUA: general codon usage analysis. Bioinformatics (Oxford, England). 1998;14(4):372–3.

PubMed  Google Scholar 

Nie X, Zhao X, Wang S, Zhang T, Li C, Liu H, et al. Complete chloroplast genome sequence of Broomcorn Millet (Panicum miliaceum L.) and comparative analysis with other Panicoideae species. Agronomy. 2018;8(9):159.

Parameswaran KP, Sadasivam S. Changes in the carbohydrates and nitrogenous components during germination of proso millet, Panicum miliaceum. Plant Foods Hum Nutr. 1994;45:97–102.

Article  PubMed  Google Scholar 

Paschapur AU, Joshi D, Mishra K, Kant L, Kumar V, Kumar A. Millets for life: a brief introduction. Millets Millet Technol. 2021:1–32.

Powell W, Morgante M, Andre C, McNicol J, Machray G, Doyle J, et al. Hypervariable microsatellites provide a general source of polymorphic DNA markers for the chloroplast genome. Curr Biol. 1995;5(9):1023–9.

Article  PubMed  Google Scholar 

Powell W, Morgante M, McDevitt R, Vendramin G, Rafalski J. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proc Natl Acad Sci. 1995;92(17):7759–63.

Article  ADS  PubMed  PubMed Central  Google Scholar 

Puigbò P, Bravo IG, Garcia-Vallve S. CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct. 2008;3(1):1–8.

Article  Google Scholar 

Rao BR, Nagasampige MH, Ravikiran M. Evaluation of nutraceutical properties of selected small millets. J Pharm Bioallied Sci. 2011;3(2):277.

Article  PubMed  PubMed Central  Google Scholar 

Raveendar S, Lee G, Lee K, Shin M, Lee J, Lee S, et al. The complete chloroplast genome of pearl millet (Pennisetum glaucum (L.) R. Br.) and comparative analysis within the family Poaceae. Cereal Res Commun. 2019;47(1):1–10.

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 2017;34(12):3299–302.

Article  PubMed  Google Scholar 

Saski C, Lee S-B, Fjellheim S, Guda C, Jansen RK, Luo H, et al. Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. Theor Appl Genet. 2007;115:571–90.

Article  PubMed  PubMed Central  Google Scholar 

Sebastin R, Lee G-A, Lee KJ, Shin M-J, Cho G-T, Lee J-R, et al. The complete chloroplast genome sequences of little millet (Panicum sumatrense Roth ex Roem. and Schult.)(Poaceae). Mitochondrial DNA Part B. 2018;3(2):719–20.

Sharp PM, Tuohy TM, Mosurski KR. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res. 1986;14(13):5125–43.

Article  PubMed  PubMed Central  Google Scholar 

Singh BP, Kumar A, Kaur H, Singh H, Nagpal AK. CpGDB: a comprehensive database of chloroplast genomes. Bioinformation. 2020;16(2):171.

Article  PubMed  PubMed Central  Google Scholar 

Song C, Shen W, Du L, Wen J, Lin J, Li R. Development and chemical characterization of Casparian strips in the roots of Chinese fir (Cunninghamia lanceolata). Trees. 2019;33:827–36.

Article  Google Scholar 

Song W, Chen Z, He L, Feng Q, Zhang H, Du G, et al. Comparative chloroplast genome analysis of wax gourd (Benincasa hispida) with three Benincaseae species, revealing evolutionary dynamic patterns and phylogenetic implications. Genes. 2022;13(3):461.

Article  PubMed  PubMed Central  Google Scholar 

Song W, Chen Z, Shi W, Han W, Feng Q, Shi C, et al. Comparative analysis of complete chloroplast genomes of nine species of Litsea (Lauraceae): Hypervariable regions, positive selection, and phylogenetic relationships. Genes. 2022;13(9):1550.

Article  PubMed  PubMed Central  Google Scholar 

Song W, Ji C, Chen Z, Cai H, Wu X, Shi C, et al. Comparative analysis the complete chloroplast genomes of nine Musa species: genomic features, comparative analysis, and phylogenetic implications. Front Plant Sci. 2022;13: 832884.

Article  PubMed  PubMed Central  Google Scholar 

Song Y, Chen Y, Lv J, Xu J, Zhu S, Li M. Comparative chloroplast genomes of Sorghum species: sequence divergence and phylogenetic relationships. BioMed Research International. 2019;2019.

Tadele Z. Drought adaptation in millets: InTech; 2016.

Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular biology and evolution. 2007;24(8):1596–9.

Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, et al. GeSeq–versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017;45(W1):W6–11.

Article  PubMed  PubMed Central  Google Scholar 

Wang S, Gao L-Z. The complete chloroplast genome of an irreplaceable dietary and model crop, foxtail millet (Setaria italica). Mitochondrial DNA Part A. 2016;27(6):4442–3.

Article  MathSciNet  Google Scholar 

Xue S, Shi T, Luo W, Ni X, Iqbal S, Ni Z, et al. Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca, and P. salicina. Horticulture research. 2019;6:89.

Yadav O, Rai K. Genetic improvement of pearl millet in India. Agricultural Research. 2013;2:275–92.

Article  Google Scholar 

Yang Z, Zhao T, Ma Q, Liang L, Wang G. Comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and interspecific relationships of Corylus (Betulaceae) species. Front Plant Sci. 2018;9:927.

Article  PubMed  PubMed Central  Google Scholar 

Yap J-YS, Rohner T, Greenfield A, Van Der Merwe M, McPherson H, Glenn W, et al. Complete chloroplast genome of the wollemi pine (Wollemia nobilis): structure and evolution. PloS one. 2015;10(6):e0128126.

Zhang Y, Nie X, Jia X, Zhao C, Biradar SS, Wang L, et al. Analysis of codon usage patterns of the chloroplast genomes in the Poaceae family. Aust J Bot. 2012;60(5):461–70.

Article  Google Scholar 

Zhou M, Long W, Li X. Patterns of synonymous codon usage bias in chloroplast genomes of seed plants. For Stud China. 2008;10:235–42.

Article  Google Scholar