Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

Zhu, Y.-X. & Li, F.G. The Gossypium raimondii genome, a huge leap forward in cotton genomics. J. Integr. Plant Biol. 55, 570–571 (2013).

Chen, Z.J. et al. Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 145, 1303–1310 (2007).

Wendel, J., Brubaker, C., Alvarez, I., Cronn, R. & Stewart, J.M. in Genetics and Genomics of Cotton, vol. 3 (ed. Paterson, A.H.) 3–22 (Springer, New York, 2009).

Paterson, A.H. et al. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492, 423–427 (2012).

Li, F.G. et al. Genome sequence of the cultivated cotton Gossypium arboreum. Nat. Genet. 46, 567–572 (2014).

Wang, K. et al. The draft genome of a diploid cotton Gossypium raimondii. Nat. Genet. 44, 1098–1103 (2012).

Wendel, J.F. & Albert, V.A. Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Syst. Bot. 17, 115–143 (1992).

Wendel, J.F. New world tetraploid cottons contain old-world cytoplasm. Proc. Natl. Acad. Sci. USA 86, 4132–4136 (1989).

The International Wheat Genome Sequencing Consortium. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345, 1251788 (2014).

Chalhoub, B. et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345, 950–953 (2014).

Kohel, R.J., Richmond, T.R. & Lewis, C.F. Texas Marker-1. Description of a genetic standard for Gossypium hirsutum. Crop Sci. 10, 670–671 (1970).

Yu, J.Z. et al. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. G3 (Bethesda) 2, 43–58 (2012).

Arumuganathan, K. & Earle, E.D. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208–218 (1991).

Hendrix, B. & Stewart, J.M. Estimation of the nuclear DNA content of Gossypium species. Ann. Bot. 95, 789–797 (2005).

Li, R. et al. The sequence and de novo assembly of the giant panda genome. Nature 463, 311–317 (2010).

Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010).

Wendel, J.F. & Cronn, R.C. in Advances in Agronomy (ed. Sparks, D.L.) 139–186 (Academic Press, 2003).

Zhang, H.B., Li, Y., Wang, B. & Chee, P.W. Recent advances in cotton genomics. Int. J. Plant Genomics 2008, 742304 (2008).

Jaillon, O. et al. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467 (2007).

Argout, X. et al. The genome of Theobroma cacao. Nat. Genet. 43, 101–108 (2011).

Myburg, A.A. et al. The genome of Eucalyptus grandis. Nature 510, 356–362 (2014).

The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).

Schmutz, J. et al. Genome sequence of the palaeopolyploid soybean. Nature 463, 178–183 (2010).

Tang, H. et al. Unravelling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res. 18, 1944–1954 (2008).

Oliver, K.R., McComb, J.A. & Greene, W.K. Transposable elements: powerful contributors to angiosperm evolution and diversity genome. Genome Biol. Evol. 5, 1886–1901 (2013).

Bennetzen, J.L. & Wang, H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu. Rev. Plant Biol. 65, 505–530 (2014).

Ossowski, S. et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327, 92–94 (2010).

Zhang, T. et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol. doi: 10.1038/nbt.3207 (20 April 2015).

Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486–488 (2008).

Udall, J.A., Quijada, P.A. & Osborn, T.C. Detection of chromosomal rearrangements derived from homeologous recombination in four mapping populations of Brassica napus L. Genetics 169, 967–979 (2005).

Wright, R.J., Thaxton, P.M., El-Zik, K.M. & Paterson, A.H. D-subgenome bias of Xcm resistance genes in tetraploid Gossypium (cotton) suggests that polyploid formation has created novel venues for evolution. Genetics 149, 1987–1996 (1998).

Yu, J. et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3, e38 (2005).

Small, R.L. & Wendel, J.F. Differential evolutionary dynamics of duplicated paralogous Adh loci in allotetraploid cotton (Gossypium). Mol. Biol. Evol. 19, 597–607 (2002).

Shi, Y.H. et al. Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fibre cell elongation. Plant Cell 18, 651–664 (2006).

Qin, Y.M. et al. Saturated very-long-chain fatty acids promote cotton fibre and Arabidopsis cell elongation by activating ethylene biosynthesis. Plant Cell 19, 3692–3704 (2007).

Qin, Y.M. & Zhu, Y.-X. How cotton fibres elongate: a tale of linear cell-growth mode. Curr. Opin. Plant Biol. 14, 106–111 (2011).

Pang, C.Y. et al. Comparative proteomics indicates that biosynthesis of pectic precursors is important for cotton fibre and Arabidopsis root hair elongation. Mol. Cell. Proteomics 9, 2019–2033 (2010).

Peng, L.C., Kawagoe, Y., Hogan, P. & Delmer, D. Sitosterol-β-glucoside as primer for cellulose synthesis in plants. Science 295, 147–150 (2002).

McFarlane, H.E., Doring, A. & Persson, S. The cell biology of cellulose synthesis. Annu. Rev. Plant Biol. 65, 69–94 (2014).

Rozen, S. et al. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423, 873–876 (2003).

You, M. et al. A heterozygous moth genome provides insights into herbivory and detoxification. Nat. Genet. 45, 220–225 (2013).

Boetzer, M., Henkel, C.V., Jansen, H.J., Butler, D. & Pirovano, W. Scaffolding pre-assembled contigs using SSPACE. Bioinformatics 27, 578–579 (2011).

Stam, P. Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J. 3, 739–744 (1993).

Xie, W. et al. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc. Natl. Acad. Sci. USA 107, 10578–10583 (2010).

Jurka, J. Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet. 16, 418–420 (2000).

Edgar, R.C. & Myers, E.W. PILER: identification and classification of genomic repeats. Bioinformatics 21 (suppl. 1), i152–i158 (2005).

Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007).

Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics. Chapter 4, Unit 4.10 (2009).

Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).

Elsik, C.G. et al. Creating a honey bee consensus gene set. Genome Biol. 8, R13 (2007).

Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).

Majoros, W., Pertea, M. & Salzberg, S. TigrScan and GlimmerHMM: Twoopen source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004).

Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Genome Res. 14, 988–995 (2004).

Kent, W.J. BLAT: The BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).

Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997).

Remm, M., Storm, C.E. & Sonnhammer, E.L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol. 314, 1041–1052 (2001).

Finn, R.D., Clements, J. & Eddy, S.R. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 39, W29–W37 (2011).

Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739 (2011).