Chloroplast genome: An important tool for inferring phylogenetic relationship

Paper Details

Research Paper 01/07/2019
Views (305) Download (19)
current_issue_feature_image
publication_file

Chloroplast genome: An important tool for inferring phylogenetic relationship

Samaila S. Yaradua, Dhafer A. Alzahrani
J. Bio. Env. Sci.15( 1), 94-100, July 2019.
Certificate: JBES 2019 [Generate Certificate]

Abstract

Chloroplast genome is an organelle characterized with definite DNA (cpDNA), whose primary function is to perform photosynthesis. The genome is reported to be derived from cyanobacterium in the process of endosymbiosis and co-evolution. The cp genome characteristic differs among different taxa, its size ranges from 135, 000 to 165, 000 base pairs (bp) with a pair of inverted repeats (IRa and IRb) separated by small single copy (SSC) and large single copy (LSC). Here, we discuss the importance and needs to utilize the chloroplast genome in phylogeny. Considering the taxonomic problem in various taxonomic levels, several studies have proven the viability of the cp genome in resolving taxonomic problems.

VIEWS 26

Blair JE, Ikeo K, Gojobori T, Hedges SB. 2002. The evolutionary position of nematodes. BMC Evolutionary Biology 2, 7.

Brinkmann H, Philippe H. 2008. Animal phylogeny and large-scale sequencing: progress and pitfalls. Journal of Systematic and Evolution 46, 274-286.

Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK. 2006. The complete chloroplast genome sequence of Pelargonium x hortorum: Organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Molecular Biology and Evolution 23, 2175-2190.

Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nature Review Genetics 6, 361-375.

Dong W, Liu J, Yu J, Wang L, Zhou S. 2012. Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding. PLoS One 7, e35071.

Eisen JA, Fraser CM. 2003. Phylogenomics: intersection of evolution and genomics. Science 300, 1706-1707.

Felsenstein J. 1978. Cases in which Parsimony or Compatibility Methods will be Positively Misleading. Systematic Biology 27, 401-410.

Galtier N, Gouy M. 1995. Inferring phylogenies from DNA sequences of unequal base compositions. Proceeding of the National Academy of Science of the United States of America 92, 11317-11321.

Gribaldo S, Philippe H. 2002. Ancient Phylogenetic Relationships. Theoretical Population Biology 61, 391-408.

Henriquez CL, Arias T, Pires JC, Croat TB, Schaal BA. 2014. Phylogenomics of the plant family Araceae. Molecular Phylogenetic and Evolution 75, 91-102.

Huang H, Shi C, Liu Y, Mao SY, Gao LZ. 2014. Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships. BMC Evolutionary Biology 14, 151.

Jansen RK, Cai Z, Raubeson LA, Daniell H, Depamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK. 2007. Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proceeding of the National Academy of Science of the United States of America 104, 19369-19374.

Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ. 2005. Methods for obtaining and analyzing whole chloroplast genome sequences. Methods in Enzymology 395, 348-384.

Jansen RK, Wee JL, Millie D. 1998. Molecular systematics of plants II. In: Soltis DE, Soltis PS, Doyle JJ, editors. Springer US. p. 87-100.

Jeffroy O, Brinkmann H, Delsuc F, Philippe H. 2006. Phylogenomics: the beginning of incongruence. Trends in Genetics 22, 225-231.

Kim KJ, Lee HL. 2004. Complete chloroplast genome sequences from Korean ginseng (Panaxschinseng nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Research 11, 247-261.

Lemmon EM, Lemmon AR. 2013. High-Throughput Genomic Data in Systematics and Phylogenetics. Annual Review of Ecology Evolution and Systematics 44, 99-121.

Li R, Ma PF, Wen J, Yi TS. 2013. Complete Sequencing of Five Araliaceae Chloroplast Genomes and the Phylogenetic Implications. PLoS One 8, 1-15.

Ma PF, Zhang YX, Zeng CX, Guo ZH, Li DZ. 2014. Chloroplast phylogenomic analyses resolve deep-level relationships of an intractable bamboo tribe

Moore MJ, Bel CD, Soltis PS, Soltis DE. 2007. Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proceeding of the National Academy of Science of the United States of America 104, 19363-19368.

Mullet JE. 1988. Chloroplast Development and Gene Expression 1967, 475-502.

Nock CJ, Waters DLE, Edwards MA, Bowen SG, Rice N, Cordeiro GM, Henry RJ. 2011. Chloroplast genome sequences from total DNA for plant identification. Plant Biotechnology Journal 9, 328-333.

Olmstead RG, Palmer JD. 1994. Chloroplast DNA systematics: A review of methods and data analysis. American Journal of Botany 81, 1205-1224.

Palmer JD, Nugent JM, Herbon LA. 1987. Unusual structure of geranium chloroplast DNA: A triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families. Proceeding of the National Academy of Science of the United States of America 84, 769-773.

Palmer JD. 1985. Chloroplast DNA and molecular phylogeny. Bio Essays 2, 263-267.

Perry AS, Wolfe KH. 2002. Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat. Journal of Molecular Evolution 55, 501-508.

Philippe H, Delsuc F, Brinkmann H, Lartillot N. 2005. Phylogenomics. Phylogenomics. Annual Review in Ecology, Evolution and Systematic 36, 541-562.

Pyron RA, Hendry CR, Chou VM, Lemmon EM, Lemmon AR, Burbrink FT. 2014. Effectiveness of phylogenomic data and coalescent species-tree methods for resolving difficult nodes in the phylogeny of advanced snakes (Serpentes: Caenophidia). Molecular Phylogenetic and Evolution 81, 221-231.

Ravi V, Khurana JP, Tyagi AK, Khurana P. 2008. An update on chloroplast genomes. Plant Systematic and Evolution 271, 101-122.

Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang BF, Philippe H. 2007. Detecting and overcoming systematic errors in genome-scale phylogenies. Systematic Biology 56, 389-399.

Rokas A, Holland PWH. 2000. Rare genomic changes as a tool for phylogenetics. Trends in Ecology and Evolution 15, 454-459.

Saski C, Lee SB, Daniell H, Wood TC, Tomkins J, Kim HG, Jansen RK. 2005. Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes. Plant Molecular Biology 59, 309-322.

Teichmann SA, Mitchison G. 1999. Is there a phylogenetic signal in prokaryote proteins? Journal of Molecular Evolution 49, 98-107.

Timmis JN, Ayliffe MA, Huang CY, Martin W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature Review Genetics 5, 123, 135.

Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D. 2011. The evolution of the plastid chromosome in land plants: Gene content, gene order, gene function. Plant Molecular Biology 76, 273-297.

Wolf YI, Rogozin IB, Koonin EV. 2004. Coelomata and not ecdysozoa: Evidence from genome-wide phylogenetic analysis. Genome Research 14, 29-36.

Wu FH, Chan MT, Liao DC, Hsu CT, Lee YW, Daniell H, Duvall MR, Lin CS. 2010. Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae. BMC Plant Biology 10, 68.

Yang JB, Li DZ, Li HT. 2014. Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs. Molecular Ecology Resources 5, 1024-1031.

Yang JB, Tang M, Li HT, Zhang ZR, Li DZ. 2013. Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. BMC Evolutionary Biology 13, 84.

Yi DK, Kim KJ. 2012. Complete chloroplast genome sequences of important oilseed crop Sesamum indicum L. PLoS One 7. Arundinarieae (poaceae). Systematic Biology 63, 933-950.

Zhang Y, Ma J, Yang B, Li R, Zhu W, Sun L, Tian J, Zhang L. 2014. The complete chloroplast genome sequence of Taxuschinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species. Gene 540, 201-209.