Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication (original) (raw)

• Gross, B.L. & Olsen, K.M. Genetic perspectives on crop domestication. Trends Plant Sci. 15, 529–537 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Varshney, R.K., Terauchi, R. & McCouch, S.R. Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol. 12, e1001883 (2014).
  Article PubMed PubMed Central Google Scholar
• Crossa, J. et al. Genomic prediction in CIMMYT maize and wheat breeding programs. Heredity (Edinb) 112, 48–60 (2014).
  Article CAS Google Scholar
• Chen, Z.J. et al. Toward sequencing cotton (Gossypium) genomes. Plant Physiol. 145, 1303–1310 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Senchina, D.S. et al. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol. Biol. Evol. 20, 633–643 (2003).
  Article CAS PubMed Google Scholar
• Stewart, J.M., Oosterhuis, D., Heitholt, J.J. & Mauney, J.R. Physiology of Cotton (Springer, 2010).
• Rapp, R.A. et al. Gene expression in developing fibres of Upland cotton (Gossypium hirsutum L.) was massively altered by domestication. BMC Biol. 8, 139 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Yoo, M.J. & Wendel, J.F. Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum) fiber transcriptome. PLoS Genet. 10, e1004073 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, T. et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat. Biotechnol. 33, 531–537 (2015).
  Article CAS PubMed Google Scholar
• Li, F. et al. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat. Biotechnol. 33, 524–530 (2015).
  Article CAS PubMed Google Scholar
• Nie, X. et al. Genome-wide SSR-based association mapping for fiber quality in nation-wide upland cotton inbreed cultivars in China. BMC Genomics 17, 352 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Zhou, S.H. Genogram of Cotton Varieties in China (Sichuan Science and Technology Press, 2000).
• Huang, Z.K. Cotton Varieties and their Genealogy in China (Chinese Agricultural Press, 2007).
• Doebley, J.F., Gaut, B.S. & Smith, B.D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006).
  Article CAS PubMed Google Scholar
• Hufford, M.B. et al. Comparative population genomics of maize domestication and improvement. Nat. Genet. 44, 808–811 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961–967 (2010).
  Article CAS PubMed Google Scholar
• Zhou, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408–414 (2015).
  Article CAS PubMed Google Scholar
• Lin, T. et al. Genomic analyses provide insights into the history of tomato breeding. Nat. Genet. 46, 1220–1226 (2014).
  Article CAS PubMed Google Scholar
• Said, J.I. et al. A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific G. hirsutum × G. barbadense populations. Mol. Genet. Genomics 290, 1003–1025 (2015).
  Article CAS PubMed Google Scholar
• Han, L.B. et al. The dual functions of WLIM1a in cell elongation and secondary wall formation in developing cotton fibers. Plant Cell 25, 4421–4438 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Applequist, W.L., Cronn, R. & Wendel, J.F. Comparative development of fiber in wild and cultivated cotton. Evol. Dev. 3, 3–17 (2001).
  Article CAS PubMed Google Scholar
• Hovav, R. et al. The evolution of spinnable cotton fiber entailed prolonged development and a novel metabolism. PLoS Genet. 4, e25 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Cheng, F. et al. Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat. Genet. 48, 1218–1224 (2016).
  Article CAS PubMed Google Scholar
• Banno, H. & Chua, N.H. Characterization of the Arabidopsis formin-like protein AFH1 and its interacting protein. Plant Cell Physiol. 41, 617–626 (2000).
  Article CAS PubMed Google Scholar
• Deeks, M.J., Hussey, P.J. & Davies, B. Formins: intermediates in signal-transduction cascades that affect cytoskeletal reorganization. Trends Plant Sci. 7, 492–498 (2002).
  Article CAS PubMed Google Scholar
• Bischoff, V. et al. TRICHOME BIREFRINGENCE and its homolog AT5G01360 encode plant-specific DUF231 proteins required for cellulose biosynthesis in Arabidopsis. Plant Physiol. 153, 590–602 (2010).
  Article PubMed PubMed Central Google Scholar
• Brown, D.M., Zeef, L.A., Ellis, J., Goodacre, R. & Turner, S.R. Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17, 2281–2295 (2005).
  Article CAS PubMed PubMed Central Google Scholar
• Guo, K. et al. Fibre elongation requires normal redox homeostasis modulated by cytosolic ascorbate peroxidase in cotton (Gossypium hirsutum). J. Exp. Bot. 67, 3289–3301 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Feng, H. et al. Molecular analysis of proanthocyanidins related to pigmentation in brown cotton fibre (Gossypium hirsutum L.). J. Exp. Bot. 65, 5759–5769 (2014).
  Article CAS PubMed Google Scholar
• Xiao, Y.H. et al. Transcriptome and biochemical analyses revealed a detailed proanthocyanidin biosynthesis pathway in brown cotton fiber. PLoS One 9, e86344 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Maurano, M.T. et al. Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo. Nat. Genet. 47, 1393–1401 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Wittkopp, P.J. & Kalay, G. _Cis_-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat. Rev. Genet. 13, 59–69 (2011).
  Article CAS PubMed Google Scholar
• Burgess, D.G., Xu, J. & Freeling, M. Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics. Curr. Opin. Plant Biol. 27, 141–147 (2015).
  Article CAS PubMed Google Scholar
• Zhang, W. et al. High-resolution mapping of open chromatin in the rice genome. Genome Res. 22, 151–162 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Hobo, T., Kowyama, Y. & Hattori, T. A bZIP factor, TRAB1, interacts with VP1 and mediates abscisic acid-induced transcription. Proc. Natl. Acad. Sci. USA 96, 15348–15353 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, S. et al. Control of plant trichome development by a cotton fiber MYB gene. Plant Cell 16, 2323–2334 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Koini, M.A. et al. High temperature-mediated adaptations in plant architecture require the bHLH transcription factor PIF4. Curr. Biol. 19, 408–413 (2009).
  Article CAS PubMed Google Scholar
• Cook, P.R. The organization of replication and transcription. Science 284, 1790–1795 (1999).
  Article CAS PubMed Google Scholar
• Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Fullwood, M.J. et al. An oestrogen-receptor-α-bound human chromatin interactome. Nature 462, 58–64 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, Y. et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504, 306–310 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–501 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 489, 83–90 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Villar, D. et al. Enhancer evolution across 20 mammalian species. Cell 160, 554–566 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, W., Zhang, T., Wu, Y. & Jiang, J. Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis. Plant Cell 24, 2719–2731 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Wang, C. et al. Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res. 25, 246–256 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Zhou, Y. et al. Cotton (Gossypium hirsutum) 14-3-3 proteins participate in regulation of fibre initiation and elongation by modulating brassinosteroid signalling. Plant Biotechnol. J. 13, 269–280 (2015).
  Article CAS PubMed Google Scholar
• Jakoby, M.J. et al. Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106. Plant Physiol. 148, 1583–1602 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Bueso, E. et al. ARABIDOPSIS THALIANA HOMEOBOX25 uncovers a role for gibberellins in seed longevity. Plant Physiol. 164, 999–1010 (2014).
  Article CAS PubMed Google Scholar
• He, X.C., Qin, Y.M., Xu, Y., Hu, C.Y. & Zhu, Y.X. Molecular cloning, expression profiling, and yeast complementation of 19 beta-tubulin cDNAs from developing cotton ovules. J. Exp. Bot. 59, 2687–2695 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Tan, J. et al. A genetic and metabolic analysis revealed that cotton fiber cell development was retarded by flavonoid naringenin. Plant Physiol. 162, 86–95 (2013).
  Article CAS PubMed PubMed Central Google Scholar
• Nakajima, K., Furutani, I., Tachimoto, H., Matsubara, H. & Hashimoto, T. SPIRAL1 encodes a plant-specific microtubule-localized protein required for directional control of rapidly expanding Arabidopsis cells. Plant Cell 16, 1178–1190 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Cheng, Q., Liu, H.T., Bombelli, P., Smith, A. & Slabas, A.R. Functional identification of AtFao3, a membrane bound long chain alcohol oxidase in Arabidopsis thaliana. FEBS Lett. 574, 62–68 (2004).
  Article CAS PubMed Google Scholar
• Szumlanski, A.L. & Nielsen, E. The Rab GTPase RabA4d regulates pollen tube tip growth in Arabidopsis thaliana. Plant Cell 21, 526–544 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Paterson, A.H., Brubaker, C.L. & Wendel, J.F. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol. Biol. Report. 11, 122–127 (1993).
  Article CAS Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  CAS PubMed PubMed Central Google Scholar
• McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  PubMed PubMed Central Google Scholar
• Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6, 80–92 (2012).
  CAS Google Scholar
• Chen, K. et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods 6, 677–681 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333–i339 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Zhuang, J. & Weng, Z. Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes. Nucleic Acids Res. 43, 8146–8156 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Felsenstein, J. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5, 164–166 (1989).
  Google Scholar
• Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).
  Article CAS PubMed Google Scholar
• Falush, D., Stephens, M. & Pritchard, J.K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567–1587 (2003).
  CAS PubMed PubMed Central Google Scholar
• Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393–402 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Bradbury, P.J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23, 2633–2635 (2007).
  Article CAS PubMed Google Scholar
• Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Liu, D., Zhang, X., Tu, L., Zhu, L. & Guo, X. Isolation by suppression-subtractive hybridization of genes preferentially expressed during early and late fiber development stages in cotton. Mol. Biol. (Mosk.) 40, 825–834 (2006).
  CAS Google Scholar
• Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• 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).
  Article CAS PubMed PubMed Central Google Scholar
• Bolger, A.M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Krueger, F. & Andrews, S.R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571–1572 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, W. & Jiang, J. Genome-wide mapping of DNase I hypersensitive sites in plants. Methods Mol. Biol. 1284, 71–89 (2015).
  Article CAS PubMed Google Scholar
• Wang, M. et al. Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation. Nucleic Acids Res. 44, 4067–4079 (2016).
  Article CAS PubMed PubMed Central Google Scholar
• Langmead, B. & Salzberg, S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Boyle, A.P., Guinney, J., Crawford, G.E. & Furey, T.S. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24, 2537–2538 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X.S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).
  Article CAS PubMed Google Scholar
• Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime _cis_-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Xie, T. et al. De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. Mol. Plant 8, 489–492 (2015).
  Article CAS PubMed Google Scholar
• Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
  Article CAS PubMed PubMed Central Google Scholar
• Ay, F., Bailey, T.L. & Noble, W.S. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 24, 999–1011 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Shin, H. et al. TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic Acids Res. 44, e70 (2016).
  Article CAS PubMed Google Scholar