Abstract
The draft pineapple genome is a remarkable resource to breeders and plant biologists. The study of the gene repertoire involved in the crassulacean acid metabolism (CAM) photosynthetic pathway enables researchers to track down genomic and regulatory changes necessary for a shift from C3 metabolism, also shedding light on the evolution of the C4 metabolism. In addition to its unique photosynthetic pathway, pineapple occupies a unique evolutionary position on the monocot tree of life, making it an ideal genome proxy for the Poales clade. The lineage of pineapple, known as the bromeliads, serve as an excellent out-group to the well-studied cereal group while retaining a less complex genome that reflects a close-to-ancestral karyotype. Herein, we take an in-depth look on the genomic comparisons both on the whole-genome level and the local scale. On the whole-genome level, we have compared pineapple against several related monocot, eudicot, and basal angiosperm genomes providing a solid framework to study the patterns of macroscale genome evolution, in order to clarify the nature and dating of recurring genome duplication events. On the local scale, we have identified significant sequence conservation outside the coding regions that have so far remained underexplored yet critical to our understanding of the unique biology and physiology of the pineapple species.
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References
Amborella Genome P (2013) The Amborella genome and the evolution of flowering plants. Science 342(6165):1241089. https://doi.org/10.1126/science.1241089
Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12(7):1021–1029
Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AFA, Roskin KM et al (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res 14(4):708–715. https://doi.org/10.1101/Gr.1933104
Blanchette M, Bataille AR, Chen X, Poitras C, Laganière J, Lefèbvre C et al (2006) Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res 16(5):656–668
Bolouri H, Davidson EH (2002) Modeling DNA sequence-based cis-regulatory gene networks. Dev Biol 246(1):2–13
Bossolini E, Wicker T, Knobel PA, Keller B (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J 49(4):704–717
Buels R, Yao E, Diesh CM, Hayes RD, Munoz-Torres M, Helt G et al (2016) JBrowse: a dynamic web platform for genome visualization and analysis. Genome Biol 17:66. https://doi.org/10.1186/s13059-016-0924-1
Burgess D, Freeling M (2014) The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates. Plant Cell 26(3):946–961
Cai J, Liu X, Vanneste K, Proost S, Tsai WC, Liu KW et al (2015) The genome sequence of the orchid Phalaenopsis equestris. Nat Genet 47(1):65–72. https://doi.org/10.1038/ng.3149
Colinas J, Birnbaum K, Benfey PN (2002) Using cauliflower to find conserved non-coding regions in Arabidopsis. Plant Physiol 129(2):451–454
D’Hont A, Denoeud F, Aury J-M, Baurens F-C, Carreel F, Garsmeur O et al (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488(7410):213–217
Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12(5):637–646
Duret L, Bucher P (1997) Searching for regulatory elements in human noncoding sequences. Curr Opin Struct Biol 7(3):399–406
Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20(11):1470–1484
Freeling M, Subramaniam S (2009) Conserved noncoding sequences (CNSs) in higher plants. Curr Opin Plant Biol 12(2):126–132
Frith MC, Kawaguchi R (2015) Split-alignment of genomes finds orthologies more accurately. Genome Biol 16:106. https://doi.org/10.1186/S13059-015-0670-9
Gaut BS, Morton BR, McCaig BC, Clegg MT (1996) Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc Natl Acad Sci 93(19):10274–10279
Givnish TJ, Barfuss MH, Van Ee B, Riina R, Schulte K, Horres R et al (2014) Adaptive radiation, correlated and contingent evolution, and net species diversification in Bromeliaceae. Mol Phylogenet Evol 71:55–78
Guo H, Moose SP (2003) Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. Plant Cell 15(5):1143–1158
Haberer G, Mader MT, Kosarev P, Spannagl M, Yang L, Mayer KF (2006) Large-scale cis-element detection by analysis of correlated expression and sequence conservation between Arabidopsis and Brassica oleracea. Plant Physiol 142(4):1589–1602
Hardison RC (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet 16(9):369–372
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ et al (2013) An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 45(8):891–898
Higo K, Ugawa Y, Iwamoto M, Higo H (1998) PLACE: a database of plant cis-acting regulatory DNA elements. Nucleic Acids Res 26(1):358–359. https://doi.org/10.1093/nar/26.1.358
Hupalo D, Kern AD (2013) Conservation and functional element discovery in 20 angiosperm plant genomes. Mol Biol Evol 30(7):1729–1744
Inada DC, Bashir A, Lee C, Thomas BC, Ko C, Goff SA et al (2003) Conserved noncoding sequences in the grasses4. Genome Res 13(9):2030–2041
Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449(7161):463–467. https://doi.org/10.1038/nature06148
Jiao Y, Leebens-Mack J, Ayyampalayam S, Bowers JE, McKain MR, McNeal J et al (2012) A genome triplication associated with early diversification of the core eudicots. Genome Biol 13(1):R3. https://doi.org/10.1186/gb-2012-13-1-r3
Jiao Y, Li J, Tang H, Paterson AH (2014) Integrated syntenic and phylogenomic analyses reveal an ancient genome duplication in monocots. Plant Cell 26(7):2792–2802. https://doi.org/10.1105/tpc.114.127597
Kaplinsky NJ, Braun DM, Penterman J, Goff SA, Freeling M (2002) Utility and distribution of conserved noncoding sequences in the grasses. Proc Natl Acad Sci 99(9):6147–6151
Kellogg EA (2001) Evolutionary history of the grasses. Plant Physiol 125(3):1198–1205
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D (2003) Evolution’s cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A 100(20):11484–11489. https://doi.org/10.1073/pnas.1932072100
Lee H, Golicz AA, Bayer PE, Jiao Y, Tang H, Paterson AH et al (2016) The genome of a southern hemisphere seagrass species (Zostera muelleri). Plant Physiol 172(1):272–283. https://doi.org/10.1104/pp.16.00868
Li X, Tan L, Wang L, Hu S, Sun C (2009) Isolation and characterization of conserved non-coding sequences among rice (Oryza sativa L.) paralogous regions. Mol Gen Genomics 281(1):11–18
Lyons E, Pedersen B, Kane J, Alam M, Ming R, Tang H et al (2008) Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant Physiol 148(4):1772–1781. https://doi.org/10.1104/pp.108.124867
Magallón S, Gómez-Acevedo S, Sánchez-Reyes LL, Hernández-Hernández T (2015) A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity. New Phytol 207(2):437–453
Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A et al (2007) Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res 17(6):760–774
Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE et al (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genet 47(12):1435–1442. https://doi.org/10.1038/ng.3435
Ming R, Wai CM, Guyot R (2016) Pineapple genome: a reference for monocots and CAM photosynthesis. Trends Genet 32(11):690–696. https://doi.org/10.1016/j.tig.2016.08.008
Panne D, Maniatis T, Harrison SC (2007) An atomic model of the interferon-β enhanceosome. Cell 129(6):1111–1123
Paterson AH, Bowers JE, Chapman BA (2004) Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci U S A 101(26):9903–9908. https://doi.org/10.1073/pnas.0307901101
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H et al (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556. https://doi.org/10.1038/nature07723
Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D et al (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429):423–427. https://doi.org/10.1038/nature11798
Pennacchio LA, Loots GG, Nobrega MA, Ovcharenko I (2007) Predicting tissue-specific enhancers in the human genome. Genome Res 17(2):201–211
Priest HD, Filichkin SA, Mockler TC (2009) Cis-regulatory elements in plant cell signaling. Curr Opin Plant Biol 12(5):643–649
Reineke AR, Bornberg-Bauer E, Gu J (2011) Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. Nucleic Acids Res 39(14):6029–6043
Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA et al (2007) Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci 104(27):11376–11381
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S et al (2012) A map of the cis-regulatory sequences in the mouse genome. Nature 488(7409):116–120
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K et al (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15(8):1034–1050
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW et al (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450(7167):219–232
Strähle U, Rastegar S (2008) Conserved non-coding sequences and transcriptional regulation. Brain Res Bull 75(2):225–230
Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH (2008) Synteny and collinearity in plant genomes. Science 320(5875):486–488. https://doi.org/10.1126/science.1153917
Tang H, Bowers JE, Wang X, Paterson AH (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A 107(1):472–477. https://doi.org/10.1073/pnas.0908007107
The Angiosperm Phylogeny G (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161(2):105–121. https://doi.org/10.1111/j.1095-8339.2009.00996.x
Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S et al (2009) FlyBase: enhancing Drosophila gene ontology annotations. Nucleic Acids Res 37(suppl 1):D555–D5D9
Wang W, Haberer G, Gundlach H, Glasser C, Nussbaumer T, Luo MC et al (2014) The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat Commun 5:3311. https://doi.org/10.1038/ncomms4311
Wolfe KH, Gouy M, Yang Y-W, Sharp PM, Li W-H (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci 86(16):6201–6205
Acknowledgment
We thank the Fujian provincial government for a Fujian “100 Talent Plan” award to HT. This work was supported by the National Key Research and Development Program of China (2016YFD0100305). Competing interests: the authors declare that they have no competing interests.
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Liang, P., Chen, X., Zhang, X., Tang, H. (2018). Comparative Genomics of Pineapple and Other Angiosperm Genomes. In: Ming, R. (eds) Genetics and Genomics of Pineapple. Plant Genetics and Genomics: Crops and Models, vol 22. Springer, Cham. https://doi.org/10.1007/978-3-030-00614-3_10
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