Phylogenomics of tomato chloroplasts using assembly and alignment-free method

References

• Adachi J, Waddell PJ, Martin W, Hasegawa M. 2000. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J Mol Evol. 50:348–358.
   PubMed Web of Science ®Google Scholar
• Aflitos S, Schijlen E, De Jong H, De Ridder D, Smit S, Finkers R, Wang J, Zhang G, Li N, Mao L, et al. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J. 80:136–148.
   PubMed Web of Science ®Google Scholar
• Chan CX, Ragan MA. 2013. Next-generation phylogenomics. Biol Direct. 8:3.
   PubMed Web of Science ®Google Scholar
• Chu KH, Qi J, Yu ZG, Anh VO. 2004. Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol Biol Evol. 21:200–206.
   PubMed Web of Science ®Google Scholar
• Daniell H, Kumar S, Dufourmantel N. 2010. Breakthrough in chloroplast genetic engineering of agronomically important crops. TRENDS Biotechnol. 23:238–245.
   Google Scholar
• De Las Rivas J, Lozano JJ, Ortiz AR. 2002. Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns. Genome Res. 12:567–583.
   PubMed Web of Science ®Google Scholar
• Dodsworth S, Chase MW, Arkinen TS, Knapp S, Leitch AR. 2016. Using genomic repeats for phylogenomics: a case study in wild tomatoes (Solanum section Lycopersicon: Solanaceae). Biol J Linn Soc. 117:96–105.
   Web of Science ®Google Scholar
• Fan H, Ives AR, Surget-Groba Y, Cannon CH. 2015. An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data. BMC Genomics. 16:522.
   PubMed Web of Science ®Google Scholar
• Fitz-Gibbon ST, House CH. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27:4218–4222.
   PubMed Web of Science ®Google Scholar
• Grandillo S, Chetelat R, Knapp S, Spooner D, Peralta I, Cammareri M, Perez O, Termolino P, Tripodi P, Chiusano ML, et al. 2011. Solanum sect. Lycopersicon. In: Wild crop relatives: genomic and breeding resources. Berlin (Germany): Springer; p. 129–215.
   Google Scholar
• Haubold B. 2014. Alignment-free phylogenetics and population genetics. Brief Bioinformatics. 15:407–418.
   PubMed Web of Science ®Google Scholar
• Hollingsworth PM, Forrest LL, Spouge JL, Hajibabaei M, Ratnasingham S, van der Bank M, Chase MW, Cowan RS, Erickson DL, Fazekas AJ, et al. 2009. A DNA barcode for land plants. Proc Natl Acad Sci. 106:12794–12797.
   PubMed Web of Science ®Google Scholar
• Hollingsworth PM, Graham SW, Little DP. 2011. Choosing and using a plant DNA barcode. PLoS One. 6:e19254.
   PubMed Web of Science ®Google Scholar
• Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254–267.
   PubMed Web of Science ®Google Scholar
• Jablonska B, Ammiraju JS, Bhattarai KK, Mantelin S, de Ilarduya O, Roberts PA, Kaloshian I. 2007. The Mi-9 gene from Solanum arcanum conferring heat-stable resistance to root-knot nematodes is a homolog of Mi-1. Plant Physiol. 143:1044–1054.
   PubMed Web of Science ®Google Scholar
• Kress WJ, Erickson DL. 2008. DNA barcodes: genes, genomics, and bioinformatics. Proc Natl Acad Sci USA. 105:2761–2762.
   PubMed Web of Science ®Google Scholar
• Lahaye R, van der Bank M, Bogarin D, Warner J, Pupulin F, Gigot G, Maurin O, Duthoit S, Barraclough TG, Savolainen V. 2008. DNA barcoding the oras of biodiversity hotspots. Proc Natl Acad Sci USA. 105:2923–2928.
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9:357–359.
   PubMed Web of Science ®Google Scholar
• Lemieux C, Otis C, Turmel M. 2000. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature. 403:649–652.
   PubMed Web of Science ®Google Scholar
• Li CP, Han GS, Chu KH. 2012. Analyzing multi-locus plant barcoding datasets with a composition vector method based on adjustable weighted distance. PLoS One. 7:e42154.
   PubMed Web of Science ®Google Scholar
• Li D-Z, Gao L-M, Li H-T, Wang H, Ge X-J, Liu J-Q, Liu JQ, Chen ZD, Zhou SL, Chen SL, et al. 2011. From the cover: comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc Natl Acad Sci. 108:19641–19646.
   PubMed Web of Science ®Google Scholar
• Lin J, Gerstein M. 2000. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res. 10:808–818.
   PubMed Web of Science ®Google Scholar
• Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, et al. 2014. Genomic analyses provide insights into the history of tomato breeding. Nat Genet. 46:1220–1226.
   PubMed Web of Science ®Google Scholar
• Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D. 2002. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci. 99:12246–12251.
   PubMed Web of Science ®Google Scholar
• Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, Kowallik KV. 1998. Gene transfer to the nucleus and the evolution of chloroplasts. Nature. 393:162–165.
   PubMed Web of Science ®Google Scholar
• McElroy KE, Luciani F, Thomas T. 2012. GemSIM: general, error-model based simulator of next-generation sequencing data. BMC Genomics. 13:74.
   PubMed Web of Science ®Google Scholar
• Palmer JD, Zamir D. 1982. Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon. Proc Natl Acad Sci U S A. 79:5006–5010. America.
   PubMed Web of Science ®Google Scholar
• Peralta IE, Knapp S, Spooner DM. 2008. Taxonomy of wild tomatoes and their relatives. (Solanum sect. Lycopersoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae). Syst Bot Monographs. 84:1–186.
   Google Scholar
• Peralta IE, Spooner DM. 2005. Morphological characterization and relationships of wild tomatoes (Solanum L. sect. Lycopersicon). Monographs Syst Bot. 104:227–257.
   Google Scholar
• Qi W, Yu Z-G, Yang J. 2017. DLTree: a web server for phylogeny reconstruction using dynamical language method. Bioinformatics. 33:2214–2215.
   PubMed Web of Science ®Google Scholar
• Rodriguez F, Wu F, Ané C, Tanksley S, Spooner DM. 2009. Do potatoes and tomatoes have a single evolutionary history, and what proportion of the genome supports this history? BMC Evol Biol. 9:191.
   PubMed Web of Science ®Google Scholar
• Sankoff D, Leduc G, Antoine N, Paquin B, Lang BF, Cedergren R. 1992. Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc Natl Acad Sci. 89:6575–6579.
   PubMed Web of Science ®Google Scholar
• Small RL, Cronn RC, Wendel JF. 2004. L. A. S. JOHNSON REVIEW No. 2. Use of nuclear genes for phylogeny reconstruction in plants. Aust Syst Bot. 17:145–170.
   Web of Science ®Google Scholar
• Song K, Ren J, Zhai Z, Liu X, Deng M, Sun F. 2013. Alignment-free sequence comparison based on next-generation sequencing reads. J Comput Biol. 20:64–79.
   PubMed Web of Science ®Google Scholar
• Stiller JW. 2011. Experimental design and statistical rigor in phylogenomics of horizontal and endosymbiotic gene transfer. BMC Evol Biol. 11:259.
   PubMed Web of Science ®Google Scholar
• Stuart GW, Moffett K, Baker S. 2002. Integrated gene and species phylogenies from unaligned whole genome protein sequences. Bioinformatics. 18:100–108.
   PubMed Web of Science ®Google Scholar
• Tekaia F, Lazcano A, Dujon B. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9:550–557.
   PubMed Web of Science ®Google Scholar
• Turmel M, Otis C, Lemieux C. 1999. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc Natl Acad Sci. 96:10248–10253.
   PubMed Web of Science ®Google Scholar
• Turmel M, Otis C, Lemieux C. 2002. The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc Natl Acad Sci. 99:11275–11280.
   PubMed Web of Science ®Google Scholar
• Wong KM, Suchard MA, Huelsenbeck JP. 2008. Alignment uncertainty and genomic analysis. Science. 319:473–476.
   PubMed Web of Science ®Google Scholar
• Wu Z. 2015. The completed eight chloroplast genomes of tomato from Solanum genus. Mitochondrial DNA. 27:1–3.
   Web of Science ®Google Scholar
• Yi H, Jin L. 2013. Co-phylog: an assembly-free phylogenomic approach for closely related organisms. Nucleic Acids Res. 41:e75.
   PubMed Web of Science ®Google Scholar