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

Abstract Cuphea hookeriana Walp. is an ornamental plant belonging to the Lythraceae. In this study, we reported the complete chloroplast (cp) genome sequence here and analyzed the phylogenetic relationship among Lythraceae plants. The length of the cp genome was 158,999 bp, including a large single-copy (LSC, 89,311 bp) region and a small single-copy (SSC, 18,436 bp) region separated by a pair of inverted repeats (IRs, 25,626 bp). There were 72 unique protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes in the cp genome of C. hookeriana. A total of 223 simple sequence repeats (SSRs) and 34 long repeat sequences were identified. Phylogenetic analyses using maximum-likelihood (ML) revealed that C. hookeriana was close to C. hyssopifolia. In addition, the two Cuphea species were the sister group of Woodfordia fruticosa.

[1]  Chang Liu,et al.  CPGView: A package for visualizing detailed chloroplast genome structures , 2023, Molecular ecology resources.

[2]  Jing Ma,et al.  Phylogeny, molecular evolution, and dating of divergences in Lagerstroemia using plastome sequences , 2022, Horticultural Plant Journal.

[3]  Xiuling Li,et al.  Fifteen complete chloroplast genomes of Trapa species (Trapaceae): insight into genome structure, comparative analysis and phylogenetic relationships , 2022, BMC plant biology.

[4]  L. Lin,et al.  Chloroplast genome of Trapa bispinosa Roxb. (Trapa, Lythraceae) , 2021, Mitochondrial DNA. Part B, Resources.

[5]  Zhiqiang Wu,et al.  Characterization of the chloroplast genome of Lagerstroemia villosa Wall. ex Kurz. (Lagerstroemia, Lythraceae) , 2021, Mitochondrial DNA. Part B, Resources.

[6]  Trevor Bedford,et al.  Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California , 2020, Science.

[7]  Zhiqiang Wu,et al.  Complete chloroplast genome sequence of Punica granatum ‘Nana’ (Lythraceae) and phylogenetic analysis , 2020, Mitochondrial DNA. Part B, Resources.

[8]  Zhiqiang Wu,et al.  The complete chloroplast genome sequence of Cuphea hyssopifolia , 2020 .

[9]  Yixiang Wang,et al.  Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales , 2019, BMC Plant Biology.

[10]  H. Ren,et al.  The complete chloroplast genome sequence of Pemphis acidula (Lythraceae) , 2019, Mitochondrial DNA Part B.

[11]  Liang Xu,et al.  The Complete Chloroplast Genome of Heimia myrtifolia and Comparative Analysis within Myrtales , 2018, Molecules.

[12]  Song Xue,et al.  Tuning of acyl-ACP thioesterase activity directed for tailored fatty acid synthesis , 2018, Applied Microbiology and Biotechnology.

[13]  K. Ma,et al.  The complete chloroplast DNA sequence of Trapa maximowiczii Korsh. (Trapaceae), and comparative analysis with other Myrtales species , 2017 .

[14]  Kazutaka Katoh,et al.  MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization , 2017, Briefings Bioinform..

[15]  Axel Fischer,et al.  GeSeq – versatile and accurate annotation of organelle genomes , 2017, Nucleic Acids Res..

[16]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[17]  Uwe Scholz,et al.  MISA-web: a web server for microsatellite prediction , 2017, Bioinform..

[18]  Dong Zhang,et al.  Characterize the complete chloroplast genome of Lagerstroemia floribunda (Lythraceae), a narrow endemic crape myrtle native to Southeast Asia , 2017, Conservation Genetics Resources.

[19]  Zhiqiang Wu,et al.  The complete chloroplast genome of Lagerstroemia intermedia (Lythraceae), a threatened species endemic to southwestern Yunnan province, China , 2017, Conservation Genetics Resources.

[20]  Wenpan Dong,et al.  Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes , 2017, Front. Plant Sci..

[21]  Yan Li,et al.  SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation , 2016, PloS one.

[22]  Mark P. Simmons,et al.  The Complete Plastid Genome of Lagerstroemia fauriei and Loss of rpl2 Intron from Lagerstroemia (Lythraceae) , 2016, PloS one.

[23]  Justin Zobel,et al.  Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.

[24]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[25]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[26]  Gerard Talavera,et al.  Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.

[27]  J. Stoye,et al.  REPuter: the manifold applications of repeat analysis on a genomic scale. , 2001, Nucleic acids research.

[28]  P. Edwards,et al.  Overexpression of 3-ketoacyl-acyl-carrier protein synthase IIIs in plants reduces the rate of lipid synthesis. , 2001, Plant physiology.

[29]  D. Mulcahy,et al.  Identification of plastid genotypes in Oenothera subsect. Munzia by restriction fragment length polymorphisms (RFLPs) , 1999, Theoretical and Applied Genetics.

[30]  Duss,et al.  Flore Phanérogamique des Antilles Françaises, Guadeloupe et Martinique . Par le R. P. Duss, Professeur au Collège de la Basse-Terre. Macon. 1897. 8vo. Pp. xxviii + 656. , 1898, Science.