COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOME OF THREE PROSOPIS SPECIES IN JORDAN

Authors

  • Hamad Adel Alkhatatbeh
  • Khaleel I Jawasreh
  • Maher J. Tadros

DOI:

https://doi.org/10.36103/mf941m18

Keywords:

DNA sequence, Tolerance, Ion S5, variable sec.

Abstract

Worldwide, Prosopis Genus is widely spread and well known to be of high tolerance to harsh conditions. The P. juliflora and P. cineraria species were introduced to the Mediterranean, while P. farcta is a native one. The genomic structure of the chloroplast of P. juliflora, P. cineraria and P. farcta were targeted in this study. The chloroplast DNA samples were sequenced by genetic analyzer sequencer “Ion S5™ System. The results indicated the size of the genome to be ranged between 162900 bp in P. farcta and 163667 bp in P. cineraria. The full chloroplast of P. juliflora and P. cineraria genome were reported for the first time nationally in Jordan, while globally P. farcta was the first to be analyzed genetically. The present study offers an important portfolio of Prosopis species chloroplast genome analyses, this could help with identification of species and speed up biological and genetic diversity researches.

References

Al-Soqeer, A.A., Q.D. Alsubaie, M. I. Motawei, H.M. Mousa and A.M. Abdel-Salam. 2017. Isolation and identification of allergens and biogenic amines of Prosopis juliflora genotypes. Electron J Biotechnol, 30: 24–32

Asaf, S, A. Khan, AL . Khan, A. Al-Harrasi, and A. Al-Rawahi. 2019. Complete chloroplast genomes of Vachellia nilotica and Senegalia senegal: comparative genomics and phylogenomic placement in a new generic system. PLoS One,14(11):e0225469

Asaf, S, AL. Khan, A. Khan, and A. Al-Harrasi. 2020. Unraveling the chloroplast genomes of two prosopis species to identify its genomic information, comparative analyses and phylogenetic relationship. Int J Mol Sci, 21(9):3280

Asaf, S, AL. Khan, A. Khan, and A. Al-harrasi. 2020. Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information, Comparative Analyses and Phylogenetic Relationship. International Journal of Molecular Sciences, 21(9), 3280

Asaf, S, AL. Khan, A. Khan, and A. Al-harrasi. 2020. Unraveling the Chloroplast Genomes of Two Prosopis Species to Identify Its Genomic Information , Comparative Analyses and Phylogenetic Relationship. International Journal of Molecular Sciences, 21(9), 3280

Asaf, S, AL. Khan, AR. Khan, M. Waqas, S-M. Kang, M.A. Khan, S-M. L. Lee and I. Lee. 2016. Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species. Frontiers in plant science, (7):843

Asaf, S, M. Waqas, A.L. Khan, M.A. Khan, S-M.Kang, Q.M. Imran, R. Shahzad, S. Bilal, B-W. Yun and I-J. Lee. 2017. The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species. Front Plant Sci, 8: 304

Beier, S., T. Thiel, T. Münch, U. Scholz, and M. Mascher. 2017. MISA-web: a web server for microsatellite prediction. Bioinformatics, 33(16):2583–5

Burkart, A. 1976. A monograph of the genus Prosopis (Leguminosae subfam. Mimosoideae). Catalogue of the recognized species of Prosopis. Journal of the Arnold arboretum, 57: 450-525

Chumley, T.W, J.D. Palmer, J.P. Mower, H.M. Fourcade, P.J Calie, J.L. Boore, and R.K. Jasen. 2006. The complete chloroplast genome sequence of Pelargonium× hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol,23 (11):2175–90

Daniell, H., C.S. Lin, M .Yu, and W.J Chang. 2016. Chloroplast genomes: Diversity, evolution, and applications in genetic engineering. Genome Biol [Internet], 17(1):1–30. Available from: http://dx.doi.org/10.1186/s13059-016-1004-2

de Souza, U.J.B, R . Nunes, C.P. Targueta, J.A.F. Diniz-Filho and M.P. de Campos Telles. 2019. The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae-caesalpinioideae): Comparative analysis with related Mimosoid species. Sci Rep, 9(1):1–12

Dong, W., C. Xu, C.Li, J. Sun, Y. Zuo and S. Shi.2015. ycf1, the most promising plastid DNA barcode of land plants. Sci Rep, 5 (1):1–5.

Dugas, D.V, D. Hernandez, E.J.M. Koenen, E. Schwarz, S. Straub and C.E. Hughes. 2015. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions and accelerated rate of evolution in clpP. Sci Rep,5 (1):1–13

Ebert, D. and R.O.D. Peakall. 2009. Chloroplast simple sequence repeats (cpSSRs): technical resources and recommendations for expanding cpSSR discovery and applications to a wide array of plant species. Mol Ecol Resour, 9 (3):673–90

Falconer, D.S and T.F.C. Mackay. 1996. Introduction to quantitative genetics. Longmans Green, Harlow, Essex, UK. Introd to Quant Genet 4th ed Longmans Green, Harlow, Essex, UK, Essex, England, 254-256

Felker, P., G.H. Cannell, P.R. Clark, J.F. Osborn and P. Nash. 1983. Biomass production of Prosopis species ( mesquite), leucaena, and other leguminous trees grown under heat/ drought stress. For Sci, 29 (3):592–606

Frailey, D.C., S.R. Chaluvadi, J.N. Vaughn, C.G. Coatney and J.L. Bennetzen. 2018. Gene loss and genome rearrangement in the plastids of five Hemiparasites in the family Orobanchaceae. BMC Plant Biol, 18 (1):30

Frazer, K.A., L. Pachter, A. Poliakov, E.M. Rubin and I. Dubchak. 2004. VISTA: computational tools for comparative genomics. Nucleic Acids Res, 32 (suppl_2):W273–9

Gascuel, O. 1997. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol, 14 (7):685–95

Hohmann, N., R. Schmickl, T-Y.Chiang, M. Lučanová, F. Kolář and K. Marhold. 2014. Taming the wild: resolving the gene pools of non-model Arabidopsis lineages. BMC Evol Biol, 14 (1):1–21.

Karaman, M.W. and J.G. Hacia. 2003. Genomes. Oxford University Press, 432-433

Katoh, K. and H. Toh. 2010. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics, 26 (15):1899–900

Kearse, M., R. Moir, A.Wilson, S. Stones-Havas, M. Cheung and S. Sturrock. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 28 (12):1647–9

Khan, A., S. Asaf, AL Khan, A. Al-Harrasi, O. Al-Sudairy and N.M. AbdulKareem. 2019. First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. Foliacea: Myrrh producing trees, PLoS One, 14(1), e0208511

Kikuchi, S., J. Bédard, M. Hirano, Y. Hirabayashi, M. Oishi and M. Imai. 2013. Uncovering the protein translocon at the chloroplast inner envelope membrane. Science, 339(6119):571–4

Kumar, S., M. Nei, J. Dudley and K. Tamura. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinformatics, 9 (4), 299-306

Kurtz, S., J.V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye and R. Giegerich. 2001. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 29 (22):4633–42

Küster, E. and S.T. Williams. 1964. Selection of media for isolation of streptomycetes. Nature, 202 (4935):928–9

Langmead, B. and S.L. Salzberg. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods, 9 (4):357

Liu, D., Y. Cui, S. Li, G. Bai, Q. Li and Z. Zhao.2019. A New Chloroplast DNA Extraction Protocol Significantly Improves the Chloroplast Genome Sequence Quality of Foxtail Millet (Setaria italica (L.) P. Beauv.). Sci Rep, 9 (1):1–9

Lohse, M., O. Drechsel and R. Bock. 2007. Organellar Genome DRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Curr Genet, 52 (5–6):267–74

Martin, G., F-C. Baurens,C. Cardi, J-M. Aury and A. D’Hont. 2013. The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution. PLoS One, 8 (6):e67350

Melotto-Passarin, D.M., E.V. Tambarussi, K. Dressano, V.F. De Martin and H .Carrer. 2011. Characterization of chloroplast DNA microsatellites from Saccharum spp and related species. Genet Mol Res, 10 (3):2024–33

Menezes, A.P.A., L. C. Resende-Moreira, R.S.O. Buzatti, A.G. Nazareno, M. Carlsen and F.P. Lobo. 2018. Chloroplast genomes of Byrsonima species (Malpighiaceae): comparative analysis and screening of high divergence sequences. Sci Rep, 8 (1):1–12

Merilä. J. and P. Crnokrak. 2001. Comparison of genetic differentiation at marker loci and quantitative traits. Journal of Evolutionary Biology, 14 (6), 892-903

Michel-López, C. Y., D. González-Mendoza and O. Grimaldo-Juarez. 2013. Fast protocol for extraction of DNA from Prosopis spp leaves (plant adapted to arid environment) without liquid nitrogen. Genetics and Molecular Research, 12 (3):4090–4

Nazir, A., Z. Dong, J. Liu, X. Zhang, R.A. Tahir and N. Ashraf. 2020. Sequence Analysis of a Jumbo Bacteriophage, Xoo-sp14, That Infects Xanthomonas oryzae pv. oryzae. Microbiology Resource Announcements, 9 (48), e01072-20

Neuhaus, H.E and M.J. Emes. 2000. Nonphotosynthetic metabolism in plastids. Annual review of plant biology, 51, 111.=40. Pasiecznik, N.M., P. Felker, P.J.C. Harris, L.n. Harsh, G. Cruz and J.C. Tewari. 2001. The Prosopis juliflora-Prosopis pallida complex: a monograph, (172). HDRA Coventry

Posada, D. 2008. jModelTest: phylogenetic model averaging. Molecular biology and evolution, 25 (7), 1253-1256

Qian, J., J. Song, H. Gao, Y. Zhu, J. Xu and X. Pang. 2013. The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza. PLoS One, 8 (2), e57607

Rodríguez-Ezpeleta, N., H. Brinkmann, S.C. Burey, B. Roure, G. Burger and W. Löffelhardt. 2005. Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes. Current biology, 15 (14):1325–30.

Ronquist, F. and J.P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19 (12), 1572-1574

Shi, C., N. Hu, H. Huang, J. Gao, Y-J. Zhao and L-Z. Gao.2012. An improved chloroplast DNA extraction procedure for whole plastid genome sequencing. PLoS One, 7 (2):e31468

Shinozaki, K., M. Ohme, M. Tanaka, T. Wakasugi, N. Hayashida and T. Matsubayashi. 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. The EMBO journal, 5 (9), 2043-2049

Su, Q., L. Liu, M. Zhao, C. Zhang, D. Zhang and Y. Li. 2020. The complete chloroplast genomes of seventeen Aegilops tauschii: genome comparative analysis and phylogenetic inference. PeerJ, 8:e8678

Swofford, D. L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4.,(Sinauer Associates Inc.: Sunderland, MA, USA.).

Tadros, M.J., A. Al-Assaf, Y.A. Othman, Z. Makhamreh and H. Taifoure.2020. Evaluating the Effect of Prosopis juliflora, an Alien Invasive Species, on Land Cover Change Using Remote Sensing Approach. Sustainability, 12 (15):5887

Tian, S., P. Lu, Z. Zhang, J.Q. Wu, H. Zhang and H. Shen. 2021. Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes. BMC Genomics, 22 (1):1–15.

Wang, Y-H., X-J. Qu, S-Y. Chen, D-Z. Li, and S. Yi. 2017. Plastomes of Mimosoideae: structural and size variation, sequence divergence, and phylogenetic implication. Tree Genet genomes, 13 (2):41

Wicke, S., G. M. Schneeweiss, C. W. Depamphilis, K. F. Müller, and D. Quandt. 2011. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant molecular biology, 76 (3), 273-297

Williams, A.V., L.M. Boykin, K.A. Howell, P.G. Nevill and I. Small. 2015. The complete sequence of the Acacia ligulata chloroplast genome reveals a highly divergent clpP1 gene. PLoS One, 10 (5):e0125768

Wyman, S, K., R. K. Jansen, and J. L. Boore. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20 (17):3252–5

Yang, Z., T. Zhao, Q. Ma, L. Liang and G. Wang. 2018. Comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and interspecific relationships of Corylus (Betulaceae) species. Frontiers in plant science, 9, 927

Yi, X., L. Gao, B. Wang, Y-J. Su and T. Wang. 2013. The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of Cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms. Genome biology and evolution, 5 (4), 688-698

Yue, X., Y. Yu, W. Gao, S. Chen, Z. Weng, and G. Ye. 2021. Complete chloroplast genome sequence of Acacia crassicarpa (Fabaceae). Mitochondrial DNA Part B, 6(8), 2249-2250.

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Published

2024-06-26

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How to Cite

Hamad Adel Alkhatatbeh, Khaleel I Jawasreh, & Maher J. Tadros. (2024). COMPARATIVE ANALYSIS OF THE COMPLETE CHLOROPLAST GENOME OF THREE PROSOPIS SPECIES IN JORDAN. IRAQI JOURNAL OF AGRICULTURAL SCIENCES, 55(3), 984-1000. https://doi.org/10.36103/mf941m18

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