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Mitogenome Announcement

The chloroplast genome of Cuphea hookeriana Walp. (Lythraceae), a Mexico ornamental plant

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Pages 522-526 | Received 17 Oct 2022, Accepted 12 Apr 2023, Published online: 24 Apr 2023

References

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 19(5):455–477.
  • Beier S, Thiel T, Münch T, Scholz U, Mascher M. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics. 33(16):2583–2585.
  • Chapman MJ, Mulcahy DL, Stein DB. 1999. Identification of plastid genotypes in Oenothera subsect. Munzia by restriction fragment length polymorphisms (RFLPs). Theor Appl Genet. 98(1):47–53.
  • Dehesh K, Tai H, Edwards P, Byrne J, Jaworski JG. 2001. Overexpression of 3-ketoacyl-acyl-carrier protein synthase IIIs in plants reduces the rate of lipid synthesis. Plant Physiol. 125(2):1103–1114.
  • Deng X, Gu W, Federman S, Du Plessis L, Pybus OG, Faria NR, Wang C, Yu G, Bushnell B, Pan C-Y, et al. 2020. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science. 369(6503):582–587.
  • Duss R-PA. 1897. Flore phanérogamique des Antilles françaises.
  • Fan X, Wang W, Wagutu GK, Li W, Li X, Chen Y. 2022. Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships. BMC Plant Biol. 22(1):230.
  • Feng Y, Zhang Y, Wang Y, Liu J, Liu Y, Cao X, Xue S. 2018. Tuning of acyl-ACP thioesterase activity directed for tailored fatty acid synthesis. Appl Microbiol Biotechnol. 102(7):3173–3182.
  • Gu C, Dong B, Xu L, Tembrock LR, Zheng S, Wu Z. 2018. The complete chloroplast genome of Heimia myrtifolia and comparative analysis within Myrtales. Molecules. 23(4):846.
  • Gu C, Ma L, Wu Z, Chen K, Wang Y. 2019. Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales. BMC Plant Biol. 19(1):281.
  • Gu C, Tembrock LR, Johnson NG, Simmons MP, Wu Z. 2016. The complete plastid genome of Lagerstroemia fauriei and loss of rpl2 intron from Lagerstroemia (Lythraceae). PLOS One. 11(3):e0150752.
  • Gu C, Tembrock LR, Wu Z. 2017. The complete chloroplast genome of Lagerstroemia intermedia (Lythraceae), a threatened species endemic to southwestern Yunnan province, China. Conserv Genet Resour. 9(3):357–360.
  • Gu C, Tembrock LR, Zhang D, Wu Z. 2017. Characterize the complete chloroplast genome of Lagerstroemia floribunda (Lythraceae), a narrow endemic crape myrtle native to Southeast Asia. Conserv Genet Resour. 9(1):91–94.
  • Jian S, Ren H. 2019. The complete chloroplast genome sequence of Pemphis acidula (Lythraceae). Mitochondrial DNA B. 4(1):912–913.
  • Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 14(6):587–589.
  • Katoh K, Rozewicki J, Yamada KD. 2019. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 20(4):1160–1166.
  • Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 29(22):4633–4642.
  • Lin L, Wang J, Zhao YX, Ma L, Gu CH, Wu ZQ. 2021. Chloroplast genome of Trapa bispinosa Roxb. (Trapa, Lythraceae). Mitochondrial DNA B Resour. 6(2):333–334.
  • Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H, Liu C. 2023. CPGView: a package for visualizing detailed chloroplast genome structures. Mol Ecol Resour. 23(3):694–704.
  • Ma L, He Y-Z, Yu J-Y, Gu C-H, Liao X-Z, Wu Z-Q. 2020. The complete chloroplast genome sequence of Cuphea hyssopifolia. Mitochondrial DNA B. 5(2):1415–1416.
  • Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 32(1):268–274.
  • Shen W, Le S, Li Y, Hu F. 2016. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLOS One. 11(10):e0163962.
  • Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56(4):564–577.
  • Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S. 2017. GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 45(W1):W6–W11.
  • Wang J, He W, Liao X, Ma J, Gao W, Wang H, Wu D, Tembrock LR, Wu Z, Gu C. 2023. Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences. Hortic Plant J. 9(2):345–355.
  • Wang J, Wu Z, Ma L, Gu C. 2021. Characterization of the chloroplast genome of Lagerstroemia villosa Wall. ex Kurz. (Lagerstroemia, Lythraceae). Mitochondrial DNA B Resour. 6(1):19–20.
  • Wang J, Wu ZQ, Ma L, Gu CH. 2020. Complete chloroplast genome sequence of Punica granatum 'Nana’ (Lythraceae) and phylogenetic analysis. Mitochondrial DNA B Resour. 5(3):2070–2071.
  • Wick RR, Schultz MB, Zobel J, Holt KE. 2015. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 31(20):3350–3352.
  • Xu C, Dong W, Li W, Lu Y, Xie X, Jin X, Shi J, He K, Suo Z. 2017. Comparative analysis of six Lagerstroemia complete chloroplast genomes. Front Plant Sci. 8:15.
  • Xue Z-Q, Xue J-H, Victorovna KM, Ma K-P. 2017. The complete chloroplast DNA sequence of Trapa maximowiczii Korsh. (Trapaceae), and comparative analysis with other Myrtales species. Aquat Bot. 143:54–62.