The genome of Eleocharis vivipara elucidates the genetics of C₃–C₄ photosynthetic plasticity and karyotype evolution in the Cyperaceae

Abstract

Eleocharis vivipara, an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C₃ photosynthesis underwater and C₄ photosynthesis on land. However, the absence of genomic data has hindered its utility for evolutionary and genetic research. Here, we present a high-quality genome for E. vivipara, representing the first chromosome-level genome for the Eleocharis genus, with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes. Its Hi–C pattern, chromosome clustering results, and one-to-one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n = 4x = 20. Phylogenetic analysis suggests that E. vivipara diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), and underwent a whole-genome duplication (WGD) about 3.5 Mya. Numerous fusion and fission events were identified between the chromosomes of E. vivipara and its close relatives. We demonstrate that E. vivipara has holocentromeres, a chromosomal feature which can maintain the stability of such chromosomal rearrangements. Experimental transplantation and cross-section studies showed its terrestrial culms developed C₄ Kranz anatomy with increased number of chloroplasts in the bundle sheath (BS) cells. Gene expression and weighted gene co-expression network analysis (WGCNA) showed overall elevated expression of core genes associated with the C₄ pathway, and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency. We found evidence of mixed nicotinamide adenine dinucleotide - malic enzyme and phosphoenolpyruvate carboxykinase type C₄ photosynthesis in E. vivipara, and hypothesize that the evolution of C₄ photosynthesis predates the WGD event. The mixed type is dominated by subgenome A and supplemented by subgenome B. Collectively, our findings not only shed light on the evolution of E. vivipara and karyotype within the Cyperaceae family, but also provide valuable insights into the transition between C₃ and C₄ photosynthesis, offering promising avenues for crop improvement and breeding.

Keywords

C ₄ photosynthesis / Cyperaceae / Eleocharis vivipara / evolution

References

[1] Adachi, S.,Stata, M.,Martin, D.G.,Cheng, S.,Liu, H.,Zhu, X.G., and Sage, R.F. (2023). The evolution of C4 photosynthesis in Flaveria (Asteraceae): Insights from the Flaveria linearis complex. Plant Physiol. 191:233–251.

[2] Allen, G.C.,Flores-Vergara, M.A.,Krasynanski, S.,Kumar, S., and Thompson, W.F. (2006). A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat. Protoc. 1:2320–2325.

[3] Alvarez, M.E.,Savouré A., and Szabados, L. (2022). Proline metabolism as regulatory hub. Trends Plant Sci. 27:39–55.

[4] Baksh, S.I., and Richards, J.H. (2006). An architectural model for Eleocharis: Morphology and development of Eleocharis cellulosa (Cyperaceae). Am. J. Bot. 93:707–715.

[5] Bardou, P.,Mariette, J.,Escudié F.,Djemiel, C., and Klopp, C. (2014). jvenn: An interactive Venn diagram viewer. BMC Bioinformatics 15:293.

[6] Bennetzen, J.L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42:251–269.

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

[8] Bianconi, M.E.,Dunning, L.T.,Moreno-Villena, J.J.,Osborne, C.P., and Christin, P.-A. (2018). Gene duplication and dosage effects during the early emergence of C4 photosynthesis in the grass genus Alloteropsis. J. Exp. Bot. 69:1967–1980.

[9] Bläsing, O.E.,Westhoff, P., and Svensson, P. (2000). Evolution of C4 phosphoenolpyruvate carboxylase in Flaveria, a conserved serine residue in the carboxyl-terminal part of the enzyme is a major determinant for C4-specific characteristics. J. Biol. Chem. 275:27917–27923.

[10] Bouckaert, R.,Vaughan, T.G.,Barido-Sottani, J.,Duchêne, S.,Fourment, M.,Gavryushkina, A.,Heled, J.,Jones, G.,Kühnert, D.,De Maio, N., et al. (2019). BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15: e1006650.

[11] Bremer, K. (2002). Gondwanan evolution of the grass alliance of families (Poales). Evolution 56:1374–1387.

[12] Brůna, T.,Hoff, K.J.,Lomsadze, A.,Stanke, M., and Borodovsky, M. (2021). BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom. Bioinform. 3: lqaa108.

[13] Buchfink, B.,Reuter, K., and Drost, H.-G. (2021). Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18:366–368.

[14] Burchardt, P.,Buddenhagen, C.E.,Gaeta, M.L.,Souza, M.D.,Marques, A., and Vanzela, A.L.L. (2020). Holocentric karyotype evolution in Rhynchospora is marked by intense numerical, structural, and genome size changes. Front. Plant Sci. 11:536507.

[15] Cai, Y.,Zhang, Y.,Loh, Y.P.,Tng, J.Q.,Lim, M.C.,Cao, Z.,Raju, A.,Lieberman Aiden, E.,Li, S.,Manikandan, L., et al. (2021). H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions. Nat. Commun. 12:719.

[16] Can, M.,Wei, W.,Zi, H.,Bai, M.,Liu, Y.,Gao, D.,Tu, D.,Bao, Y.,Wang, L.,Chen, S., et al. (2020). Genome sequence of Kobresia littledalei, the first chromosome-level genome in the family Cyperaceae. Sci. Data 7:175.

[17] Cantalapiedra, C.P.,Hernández-Plaza, A.,Letunic, I.,Bork, P., and Huerta-Cepas, J. (2021). eggNOG-mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 38:5825–5829.

[18] Cantarel, B.L.,Korf, I.,Robb, S.M.C.,Parra, G.,Ross, E.,Moore, B.,Holt, C.,Sánchez Alvarado, A., and Yandell, M. (2008). MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18:188–196.

[19] Chen, C.,Chen, H.,Zhang, Y.,Thomas, H.R.,Frank, M.H.,He, Y., and Xia, R. (2020). TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data. Mol. Plant 13:1194–1202.

[20] Chen, M. (2014). Chlorophyll modifications and their spectral extension in oxygenic photosynthesis. Annu. Rev. Biochem. 83:317–340.

[21] Chen, T.,Ye, R.,Fan, X.,Li, X., and Lin, Y. (2011). Identification of C4 photosynthesis metabolism and regulatory-associated genes in Eleocharis vivipara by SSH. Photosynth. Res. 108:157–170.

[22] Chen, T.,Zhu, X.-G., and Lin, Y. (2014). Major alterations in transcript profiles between C3–C4 and C4 photosynthesis of an amphibious species Eleocharis baldwinii. Plant Mol. Biol. 86:93–110.

[23] Cho, S.K.,Ryu, M.Y.,Song, C.,Kwak, J.M., and Kim, W.T. (2008). Arabidopsis PUB22 and PUB23 are homologous U-Box E3 ubiquitin ligases that play combinatory roles in response to drought stress. Plant Cell 20:1899–1914.

[24] Christin, P.-A.,Salamin, N.,Savolainen, V.,Duvall, M.R., and Besnard, G. (2007). C4 photosynthesis evolved in grasses via parallel adaptive genetic changes. Curr. Biol. 17:1241–1247.

[25] Dávid, C.Z.,Hohmann, J., and Vasas, A. (2021). Chemistry and pharmacology of Cyperaceae stilbenoids: A review. Molecules 26:2794.

[26] Deng, Y.,Bartosovic, M.,Kukanja, P.,Zhang, D.,Liu, Y.,Su, G.,Enninful, A.,Bai, Z.,Castelo-Branco, G., and Fan, R. (2022). Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science 375:681–686.

[27] Dey, D.,Tanaka, R., and Ito, H. (2023). Structural characterization of the Chlorophyllide a oxygenase (CAO) enzyme through an in silico approach. J. Mol. Evol. 91:225–235.

[28] Ding, F.,Wang, M.,Zhang, S., and Ai, X. (2016). Changes in SBPase activity influence photosynthetic capacity, growth, and tolerance to chilling stress in transgenic tomato plants. Sci. Rep. 6:32741.

[29] Dudchenko, O.,Batra, S.S.,Omer, A.D.,Nyquist, S.K.,Hoeger, M.,Durand, N.C.,Shamim, M.S.,Machol, I.,Lander, E.S.,Aiden, A.P., et al. (2017). De novo assembly of the Aedes aegypti genome using Hi–C yields chromosome-length scaffolds. Science 356:92–95.

[30] Dunning, L.T.,Moreno-Villena, J.J.,Lundgren, M.R.,Dionora, J.,Salazar, P.,Adams, C.,Nyirenda, F.,Olofsson, J.K.,Mapaura, A.,Grundy, I.M., et al. (2019). Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata. J. Exp. Bot. 70:3255–3268.

[31] Durand, N.C.,Robinson, J.T.,Shamim, M.S.,Machol, I.,Mesirov, J.P.,Lander, E.S., and Aiden, E.L. (2016). Juicebox provides a visualization system for Hi–C contact maps with unlimited zoom. Cell Syst. 3:99–101.

[32] Edwards, E.J.,Osborne, C.P.,Strömberg, C.A.E.,Smith, S.A.,Consortium, C.G.,Bond, W.J.,Christin, P.-A.,Cousins, A.B.,Duvall, M.R.,Fox, D.L., et al. (2010). The origins of C4 grasslands: Integrating evolutionary and ecosystem science. Science 328:587–591.

[33] Emms, D.M., and Kelly, S. (2019). OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol. 20:238.

[34] Etchells, J.P.,Provost, C.M., and Turner, S.R. (2012). Plant vascular cell division is maintained by an interaction between PXY and ethylene signalling. PLoS Genet. 8: e1002997.

[35] Feller, A.,Machemer, K.,Braun, E.L., and Grotewold, E. (2011). Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Plant J. 66:94–116.

[36] Fisher, A.E.,McDade, L.A.,Kiel, C.A.,Khoshravesh, R.,Johnson, M.A.,Stata, M.,Sage, T.L., and Sage, R.F. (2015). Evolutionary history of Blepharis (Acanthaceae) and the origin of C4 photosynthesis in section Acanthodium. Int. J. Plant Sci. 176:770–790.

[37] Flynn, J.M.,Hubley, R.,Goubert, C.,Rosen, J.,Clark, A.G.,Feschotte, C., and Smit, A.F. (2020). RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. U.S.A. 117:9451–9457.

[38] Foyer, C.H.,Bloom, A.J.,Queval, G., and Noctor, G. (2009). Photorespiratory metabolism: Genes, mutants, energetics, and redox signaling. Annu. Rev. Plant. Biol. 60:455–484.

[39] Gabriel, L.,Brůna, T.,Hoff, K.J.,Ebel, M.,Lomsadze, A.,Borodovsky, M., and Stanke, M. (2024). BRAKER3: Fully automated genome annotation using RNA-Seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA. Genome Res. 34:769–777.

[40] Gaut, B.S.,Morton, B.R.,McCaig, B.C., and Clegg, M.T. (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. U.S.A. 93:10274–10279.

[41] Grabherr, M.G.,Haas, B.J.,Yassour, M.,Levin, J.Z.,Thompson, D.A.,Amit, I.,Adiconis, X.,Fan, L.,Raychowdhury, R., and Zeng, Q. (2011). Trinity: Reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat. Biotechnol. 29:644.

[42] Guan, D.,McCarthy, S.A.,Wood, J.,Howe, K.,Wang, Y., and Durbin, R. (2020). Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics 36:2896–2898.

[43] Haas, B.J.,Delcher, A.L.,Mount, S.M.,Wortman, J.R.,Smith Jr., R.K.,Hannick, L.I.,Maiti, R.,Ronning, C.M.,Rusch, D.B.,Town, C.D., et al. (2003). Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31:5654–5666.

[44] Harada, D.,Yamato, K.T.,Izui, K., and Akita, M. (2018). De novo short read assembly and functional annotation of Eleocharis vivipara, a C3/C4 interconvertible sedge plant. Environ. Control Biol. 56:81–87.

[45] He, W.,Yang, J.,Jing, Y.,Xu, L.,Yu, K., and Fang, X. (2023). NGenomeSyn: An easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes. Bioinformatics 39: btad121.

[46] Heyduk, K.,Moreno-Villena, J.J.,Gilman, I.S.,Christin, P.-A., and Edwards, E.J. (2019). The genetics of convergent evolution: Insights from plant photosynthesis. Nat. Rev. Genet. 20:485–493.

[47] Higgisson, W.,Broadhurst, L.,Shams, F.,Gruber, B., and Dyer, F. (2022). Reproductive strategies and population genetic structure in two dryland river floodplain plants,Marsilea drummondii and Eleocharis acuta. Genes 13:1506.

[48] Hipp, A.L.,Rothrock, P.E., and Roalson, E.H. (2009). The evolution of chromosome arrangements in Carex (Cyperaceae). Bot. Rev. 75:96–109.

[49] Hofstatter, P.G.,Thangavel, G.,Lux, T.,Neumann, P.,Vondrak, T.,Novak, P.,Zhang, M.,Costa, L.,Castellani, M.,Scott, A., et al. (2022). Repeat-based holocentromeres influence genome architecture and karyotype evolution. Cell 185:3153–3168.e18.

[50] Huang, Y.,Jiao, Y.,Xie, N.,Guo, Y.,Zhang, F.,Xiang, Z.,Wang, R.,Wang, F.,Gao, Q.,Tian, L., et al. (2019). OsNCED5, a 9-cis-epoxycarotenoid dioxygenase gene, regulates salt and water stress tolerance and leaf senescence in rice. Plant Sci. 287:110188.

[51] Hufford, M.B.,Seetharam, A.S.,Woodhouse, M.R.,Chougule, K.M.,Ou, S.,Liu, J.,Ricci, W.A.,Guo, T.,Olson, A.,Qiu, Y., et al. (2021). De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373:655–662.

[52] Jia, K.-H.,Wang, Z.-X.,Wang, L.,Li, G.-Y.,Zhang, W.,Wang, X.-L.,Xu, F.-J.,Jiao, S.-Q.,Zhou, S.-S.,Liu, H., et al. (2022). SubPhaser: A robust allopolyploid subgenome phasing method based on subgenome-specific k-mers. New Phytol. 235:801–809.

[53] Keeley, J.E. (1998). C4 photosynthetic modifications in the evolutionary transition from land to water in aquatic grasses. Oecologia 116:85–97.

[54] Kim, D.,Paggi, J.M.,Park, C.,Bennett, C., and Salzberg, S.L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37:907–915.

[55] Koren, S.,Walenz, B.P.,Berlin, K.,Miller, J.R.,Bergman, N.H., and Phillippy, A.M. (2017). Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27:722–736.

[56] Koteyeva, N.K.,Voznesenskaya, E.V.,Roalson, E.H., and Edwards, G.E. (2011). Diversity in forms of C4 in the genus Cleome Cleomaceae). Ann. Bot. 107:269–283.

[57] Krzywinski, M.,Schein, J.,Birol, I.,Connors, J.,Gascoyne, R.,Horsman, D.,Jones, S.J., and Marra, M.A. (2009). Circos: An information aesthetic for comparative genomics. Genome Res. 19:1639–1645.

[58] Külahoglu, C.,Denton, A.K.,Sommer, M.,Maß J.,Schliesky, S.,Wrobel, T.J.,Berckmans, B.,Gongora-Castillo, E.,Buell, C.R.,Simon, R., et al. (2014). Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species. Plant Cell 26:3243–3260.

[59] Kumar, S.,Stecher, G.,Li, M.,Knyaz, C., and Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35:1547–1549.

[60] Kumar, S.,Stecher, G.,Suleski, M., and Hedges, S.B. (2017). TimeTree: A resource for timelines, timetrees, and divergence times. Mol. Biol. Evol. 34:1812–1819.

[61] Kurowska, M., and Daszkowska-Golec, A. (2023). Molecular mechanisms of SNAC1 (stress-responsive NAC1) in conferring the abiotic stress tolerance. Plant Sci. 337:111894.

[62] Lamesch, P.,Berardini, T.Z.,Li, D.,Swarbreck, D.,Wilks, C.,Sasidharan, R.,Muller, R.,Dreher, K.,Alexander, D.L., and Garcia-Hernandez, M. (2012). The Arabidopsis information resource (TAIR): Improved gene annotation and new tools. Nucleic Acids Res. 40: D1202–D1210.

[63] Langfelder, P., and Horvath, S. (2008). WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics 9:559.

[64] Larridon, I.,Bauters, K.,Reynders, M.,Huygh, W.,Muasya, A.M.,Simpson, D.A., and Goetghebeur, P. (2013). Towards a new classification of the giant paraphyletic genus Cyperus (Cyperaceae): Phylogenetic relationships and generic delimitation in C4 Cyperus. Bot. J. Linn. Soc. 172:106–126.

[65] Larridon, I.,Zuntini, A.R.,Léveillé-Bourret, É.,Barrett, R.L.,Starr, J.R.,Muasya, A.M.,Villaverde, T.,Bauters, K.,Brewer, G.E.,Bruhl, J.J., et al. (2021). A new classification of Cyperaceae (Poales) supported by phylogenomic data. J. Syst. Evol. 59:852–895.

[66] Lauterbach, M.,Billakurthi, K.,Kadereit, G.,Ludwig, M.,Westhoff, P., and Gowik, U. (2017). C3 cotyledons are followed by C4 leaves: Intra-individual transcriptome analysis of Salsola soda (Chenopodiaceae). J. Exp. Bot. 68:161–176.

[67] Lehti-Shiu, M.D.,Panchy, N.,Wang, P.,Uygun, S., and Shiu, S.-H. (2017). Diversity, expansion, and evolutionary novelty of plant DNA-binding transcription factor families. Biochim. Biophys. Acta Gene Regul. Mech. 1860:3–20.

[68] Leitch, A.R., and Leitch, I.J. (2012). Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol. 194:629–646.

[69] Li, H. (2018). Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100.

[70] Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760.

[71] Li, H.-T.,Yi, T.-S.,Gao, L.-M.,Ma, P.-F.,Zhang, T.,Yang, J.-B.,Gitzendanner, M.A.,Fritsch, P.W.,Cai, J.,Luo, Y., et al. (2019). Origin of angiosperms and the puzzle of the Jurassic gap. Nat. Plants 5:461–470.

[72] Li, W.,Dong, X.,Zhang, X.,Cao, J.,Liu, M.,Zhou, X.,Long, H.,Cao, H.,Lin, H., and Zhang, L. (2024). Genome assembly and resequencing shed light on evolution, population selection, and sex identification in Vernicia montana. Hortic. Res. 11: uhae141.

[73] Li, Y.,Huang, Y.,Sun, H.,Wang, T.,Ru, W.,Pan, L.,Zhao, X.,Dong, Z.,Huang, W., and Jin, W. (2022). Heat shock protein 101 contributes to the thermotolerance of male meiosis in maize. Plant Cell 34:3702–3717.

[74] Liu, B.,Shi, Y.,Yuan, J.,Hu, X.,Zhang, H.,Li, N.,Li, Z.,Chen, Y.,Mu, D., and Fan, W. (2013). Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. arXiv:1308.2012.

[75] Liu, H.,Shi, J.,Cai, Z.,Huang, Y.,Lv, M.,Du, H.,Gao, Q.,Zuo, Y.,Dong, Z.,Huang, W., et al. (2020). Evolution and domestication footprints uncovered from the genomes of coix. Mol. Plant 13:295–308.

[76] Liu, R., and Dickerson, J. (2017). Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq. PLoS Comput. Biol. 13: e1005851.

[77] Liu, S.,Lin, L.,Jiang, P.,Wang, D., and Xing, Y. (2011). A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Res. 39:578–588.

[78] Liu, Y.,Wang, J.,Liu, B., and Xu, Z.-Y. (2022). Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. J. Integr. Plant Biol. 64:2252–2274.

[79] Love, M.I.,Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq. 2. Genome Biol. 15:550.

[80] Lukhtanov, V.A.,Dincă V.,Friberg, M.,Šíchová J.,Olofsson, M.,Vila, R.,Marec, F., and Wiklund, C. (2018). Versatility of multivalent orientation, inverted meiosis, and rescued fitness in holocentric chromosomal hybrids. Proc. Natl. Acad. Sci. U.S.A. 115: E9610–E9619.

[81] Lundgren, M.R.,Christin, P.-A.,Escobar, E.G.,Ripley, B.S.,Besnard, G.,Long, C.M.,Hattersley, P.W.,Ellis, R.P.,Leegood, R.C., and Osborne, C.P. (2016). Evolutionary implications of C3–C4 intermediates in the grass Alloteropsis semialata. Plant Cell Environ. 39:1874–1885.

[82] Maier, A.,Zell, M.B., and Maurino, V.G. (2011). Malate decarboxylases: Evolution and roles of NADP)-ME isoforms in species performing C4 and C3 photosynthesis. J. Exp. Bot. 62:3061–3069.

[83] Mallmann, J.,Heckmann, D.,Bräutigam, A.,Lercher, M.J.,Weber, A.P.M.,Westhoff, P., and Gowik, U. (2014). The role of photorespiration during the evolution of C4 photosynthesis in the genus Flaveria. eLife 3: e02478.

[84] Mandrioli, M., and Manicardi, G.C. (2020). Holocentric chromosomes. PLoS Genet. 16: e1008918.

[85] Manicardi, G.C.,Nardelli, A., and Mandrioli, M. (2015). Fast chromosomal evolution and karyotype instability: Recurrent chromosomal rearrangements in the peach potato aphid Myzus persicae Hemiptera: Aphididae). Biol. J. Linn. Soc. 116:519–529.

[86] Mapleson, D.,Venturini, L.,Kaithakottil, G., and Swarbreck, D. (2018). Efficient and accurate detection of splice junctions from RNA-seq with Portcullis. Gigascience 7: giy131.

[87] Marçais, G.,Delcher, A.L.,Phillippy, A.M.,Coston, R.,Salzberg, S.L., and Zimin, A. (2018). MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol. 14: e1005944.

[88] Marques, A.,Ribeiro, T.,Neumann, P.,Macas, J.,Novák, P.,Schubert, V.,Pellino, M.,Fuchs, J.,Ma, W.,Kuhlmann, M., et al. (2015). Holocentromeres in Rhynchospora are associated with genome-wide centromere-specific repeat arrays interspersed among euchromatin. Proc. Natl. Acad. Sci. U.S.A. 112:13633–13638.

[89] Mattei, A.L.,Bailly, N., and Meissner, A. (2022). DNA methylation: A historical perspective. Trends Genet. 38:676–707.

[90] Melters, D.P.,Paliulis, L.V.,Korf, I.F., and Chan, S.W.L. (2012). Holocentric chromosomes: Convergent evolution, meiotic adaptations, and genomic analysis. Chromosome Res. 20:579–593.

[91] Mendes, F.K.,Vanderpool, D.,Fulton, B., and Hahn, M.W. (2021). CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36:5516–5518.

[92] Monti, V.,Lombardo, G.,Loxdale, H.D.,Manicardi, G.C., and Mandrioli, M. (2012). Continuous occurrence of intra-individual chromosome rearrangements in the peach potato aphid,Myzus persicae (Sulzer) (Hemiptera: Aphididae). Genetica 140:93–103.

[93] Moore, L.D.,Le, T., and Fan, G. (2013). DNA methylation and its basic function. Neuropsychopharmacology 38:23–38.

[94] Murphy, L.R.,Barroca, J.,Franceschi, V.R.,Lee, R.,Roalson, E.H.,Edwards, G.E., and Ku, M.S.B. (2007). Diversity and plasticity of C4 photosynthesis in Eleocharis (Cyperaceae). Funct. Plant Biol. 34:571–580.

[95] Nijalingappa, B.H.M. (1974). Cytological studies in Scirpus (Cyperaceae). Proc. Indian Acad. Sci. 80:134–138.

[96] Ning, Y.,Li, Y.,Dong, S.B.,Yang, H.G.,Li, C.Y.,Xiong, B.,Yang, J.,Hu, Y.K.,Mu, X.Y., and Xia, X.F. (2023). The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau. DNA Res. 30: dsac049.

[97] Ning, Y.,Li, Y.,Lin, H.Y.,Kang, E.Z.,Zhao, Y.X.,Dong, S.B.,Li, Y.,Xia, X.F.,Wang, Y.F., and Li, C.Y. (2024). Chromosome-scale genome assembly for clubrush (Bolboschoenus planiculmis) indicates a karyotype with high chromosome number and heterogeneous centromere distribution. Genome Biol. Evol. 16: evae039.

[98] Ou, S.,Su, W.,Liao, Y.,Chougule, K.,Agda, J.R.A.,Hellinga, A.J.,Lugo, C.S.B.,Elliott, T.A.,Ware, D.,Peterson, T., et al. (2019). Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 20:275.

[99] Ouyang, S.,Zhu, W.,Hamilton, J.,Lin, H.,Campbell, M.,Childs, K.,Thibaud-Nissen, F.,Malek, R.L.,Lee, Y., and Zheng, L. (2007). The TIGR rice genome annotation resource: Improvements and new features. Nucleic Acids Res. 35: D883–D887.

[100] Ozeki, K.,Miyazawa, Y., and Sugiura, D. (2022). Rapid stomatal closure contributes to higher water use efficiency in major C4 compared to C3 Poaceae crops. Plant Physiol. 189:188–203.

[101] Pardo, J., and VanBuren, R. (2021). Evolutionary innovations driving abiotic stress tolerance in C4 grasses and cereals. Plant Cell 33:3391–3401.

[102] Park, P.J. (2009). ChIP–seq: Advantages and challenges of a maturing technology. Nat. Rev. Genet. 10:669–680.

[103] Pertea, M.,Pertea, G.M.,Antonescu, C.M.,Chang, T.-C.,Mendell, J.T., and Salzberg, S.L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33:290–295.

[104] Planta, J.,Liang, Y.-Y.,Xin, H.,Chansler, M.T.,Prather, L.A.,Jiang, N.,Jiang, J., and Childs, K.L. (2022). Chromosome-scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus. G3 12: jkac211.

[105] Puranik, S.,Sahu, P.P.,Srivastava, P.S., and Prasad, M. (2012). NAC proteins: Regulation and role in stress tolerance. Trends Plant Sci. 17:369–381.

[106] Pyankov, V.I.,Voznesenskaya, E.V.,Kuz’min, A.N.,Ku, M.S.B.,Ganko, E.,Franceschi, V.R.,Black, C.C., and Edwards, G.E. (2000). Occurrence of C3 and C4 photosynthesis in cotyledons and leaves of Salsola species Chenopodiaceae). Photosynth. Res. 63:69–84.

[107] Qu, G.,Bao, Y.,Liao, Y.,Liu, C.,Zi, H.,Bai, M.,Liu, Y.,Tu, D.,Wang, L.,Chen, S., et al. (2022). Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes. Sci. Rep. 12:4970.

[108] Rao, S.S.P.,Huntley, M.H.,Durand, N.C.,Stamenova, E.K.,Bochkov, I.D.,Robinson, J.T.,Sanborn, A.L.,Machol, I.,Omer, A.D.,Lander, E.S., et al. (2014). A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159:1665–1680.

[109] Rao, X.,Lu, N.,Li, G.,Nakashima, J.,Tang, Y., and Dixon, R.A. (2016). Comparative cell-specific transcriptomics reveals differentiation of C4 photosynthesis pathways in switchgrass and other C4 lineages. J. Exp. Bot. 67:1649–1662.

[110] Roalson, E.H. (2008). A synopsis of chromosome number variation in the Cyperaceae. Bot. Rev. 74:209–393.

[111] Robinson, J.T.,Thorvaldsdóttir, H.,Winckler, W.,Guttman, M.,Lander, E.S.,Getz, G., and Mesirov, J.P. (2011). Integrative genomics viewer. Nat. Biotechnol. 29:24–26.

[112] Sage, R.F.,Christin, P.-A., and Edwards, E.J. (2011). The C4 plant lineages of planet Earth. J. Exp. Bot. 62:3155–3169.

[113] Saito, S.,Hirai, N.,Matsumoto, C.,Ohigashi, H.,Ohta, D.,Sakata, K., and Mizutani, M. (2004). Arabidopsis CYP707As encode (+)-abscisic acid 8′-hydroxylase, a key enzyme in the oxidative catabolism of Abscisic cid. Plant Physiol. 134:1439–1449.

[114] SanMiguel, P.,Gaut, B.S.,Tikhonov, A.,Nakajima, Y., and Bennetzen, J.L. (1998). The paleontology of intergene retrotransposons of maize. Nat. Genet. 20:43–45.

[115] Shi, J.,Ma, X.,Zhang, J.,Zhou, Y.,Liu, M.,Huang, L.,Sun, S.,Zhang, X.,Gao, X.,Zhan, W., et al. (2019). Chromosome conformation capture resolved near complete genome assembly of broomcorn millet. Nat. Commun. 10:464.

[116] Simpson, D.A.,Furness, C.A.,Hodkinson, T.R.,Muasya, A.M., and Chase, M.W. (2003). Phylogenetic relationships in Cyperaceae subfamily Mapanioideae inferred from pollen and plastid DNA sequence data. Am. J. Bot. 90:1071–1086.

[117] Smoot, M.E.,Ono, K.,Ruscheinski, J.,Wang, P.-L., and Ideker, T. (2011). Cytoscape 2.8: New features for data integration and network visualization. Bioinformatics 27:431–432.

[118] Song L.,Sabunciyan S.,Florea L. (2016) CLASS2: Accurate and efficient splice variant annotation from RNA-seq reads. Nucleic Acids Res. 44: e98.

[119] Stanke, M.,Keller, O.,Gunduz, I.,Hayes, A.,Waack, S., and Morgenstern, B. (2006). AUGUSTUS: Ab initio prediction of alternative transcripts. Nucleic Acids Res. 34: W435–W439.

[120] Stata, M.,Sage, T.L., and Sage, R.F. (2019). Mind the gap: The evolutionary engagement of the C4 metabolic cycle in support of net carbon assimilation. Curr. Opin. Plant Biol. 49:27–34.

[121] Surender Reddy, P.,Jogeswar, G.,Rasineni, G.K.,Maheswari, M.,Reddy, A.R.,Varshney, R.K., and Kavi Kishor, P.B. (2015). Proline over-accumulation alleviates salt stress and protects photosynthetic and antioxidant enzyme activities in transgenic sorghum [Sorghum bicolor (L.) Moench]. Plant Physiol. Biochem. 94:104–113.

[122] Tian, T.,Liu, Y.,Yan, H.,You, Q.,Yi, X.,Du, Z.,Xu, W., and Su, Z. (2017). agriGO v2.0: A GO analysis toolkit for the agricultural community, 2017 update. Nucleic Acids Res. 45: W122–W129.

[123] Trapnell, C.,Williams, B.A.,Pertea, G.,Mortazavi, A.,Kwan, G.,Van Baren, M.J.,Salzberg, S.L.,Wold, B.J., and Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28:511–515.

[124] Ueno, O. (1998). Induction of Kranz anatomy and C4-like biochemical characteristics in a submerged amphibious plant by abscisic acid. Plant Cell 10:571–583.

[125] Ueno, O. (2001). Environmental regulation of C3 and C4 differentiation in the amphibious sedge eleocharis vivipara. Plant Physiol. 127:1524–1532.

[126] Ueno, O.,Samejima, M.,Muto, S., and Miyachi, S. (1988). Photosynthetic characteristics of an amphibious plant,Eleocharis vivipara: Expression of C4 and C3 modes in contrasting environments. Proc. Natl. Acad. Sci. U.S.A. 85:6733–6737.

[127] Upadhyay, R.K.,Soni, D.K.,Singh, R.,Dwivedi, U.N.,Pathre, U.V.,Nath, P., and Sane, A.P. (2013). SlERF36, an EAR-motif-containing ERF gene from tomato, alters stomatal density and modulates photosynthesis and growth. J. Exp. Bot. 64:3237–3247.

[128] Vahisalu, T.,Kollist, H.,Wang, Y.-F.,Nishimura, N.,Chan, W.-Y.,Valerio, G.,Lamminmäki, A.,Brosché M.,Moldau, H.,Desikan, R., et al. (2008). SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling. Nature 452:487–491.

[129] VanBuren, R.,Man Wai, C.,Wang, X.,Pardo, J.,Yocca, A.E.,Wang, H.,Chaluvadi, S.R.,Han, G.,Bryant, D.,Edger, P.P., et al. (2020). Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff. Nat. Commun. 11:884.

[130] Venturini, L.,Caim, S.,Kaithakottil, G.G.,Mapleson, D.L., and Swarbreck, D. (2018). Leveraging multiple transcriptome assembly methods for improved gene structure annotation. Gigascience 7: giy093.

[131] Walker, B.J.,Abeel, T.,Shea, T.,Priest, M.,Abouelliel, A.,Sakthikumar, S.,Cuomo, C.A.,Zeng, Q.,Wortman, J.,Young, S.K., et al. (2014). Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9: e112963.

[132] Wang, X.,Elling, A.A.,Li, X.,Li, N.,Peng, Z.,He, G.,Sun, H.,Qi, Y.,Liu, X.S., and Deng, X.W. (2009). Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 21:1053–1069.

[133] Wang, Y.,Bräutigam, A.,Weber, A.P.M., and Zhu, X.-G. (2014). Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis. J. Exp. Bot. 65:3567–3578.

[134] Wang, Y.,Tang, H.,DeBarry, J.D.,Tan, X.,Li, J.,Wang, X.,Lee, T.-h,Jin, H.,Marler, B.,Guo, H., et al. (2012). MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40: e49.

[135] Way, D.A.,Katul, G.G.,Manzoni, S., and Vico, G. (2014). Increasing water use efficiency along the C3 to C4 evolutionary pathway: A stomatal optimization perspective. J. Exp. Bot. 65:3683–3693.

[136] Wei, L.Q.,Xu, W.Y.,Deng, Z.Y.,Su, Z.,Xue, Y., and Wang, T. (2010). Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa. BMC Genomics 11:338.

[137] Westhoff, P., and Gowik, U. (2010). Evolution of C4 photosynthesis—Looking for the master switch. Plant Physiol. 154:598–601.

[138] Wingler, A.,Lea, P.J.,Quick, W.P., and Leegood, R.C. (2000). Photorespiration: Metabolic pathways and their role in stress protection. Philos. Trans. R. Soc. London. Ser. B. 355:1517–1529.

[139] Wrensch, D.L.,Kethley, J.B., and Norton, R.A. (1994). Cytogenetics of holokinetic chromosomes and inverted meiosis: Keys to the evolutionary success of mites, with generalizations on eukaryotes. In Mites. Houck, M.A (ed). Boston, MA: Springer.

[140] Yang, Z. (2007). PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586–1591.

[141] Zedek, F.,Šmerda, J.,Šmarda, P., and Bureš P. (2010). Correlated evolution of LTR retrotransposons and genome size in the genus eleocharis. BMC Plant Biol. 10:265.

[142] Zhang, J.,Zhang, X.,Tang, H.,Zhang, Q.,Hua, X.,Ma, X.,Zhu, F.,Jones, T.,Zhu, X.,Bowers, J., et al. (2018). Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat. Genet. 50:1565–1573.

[143] Zhang, L.,Liu, M.,Long, H.,Dong, W.,Pasha, A.,Esteban, E.,Li, W.,Yang, X.,Li, Z.,Song, A., et al. (2019). Tung tree Vernicia fordii) genome provides a resource for understanding genome evolution and improved oil production. Genomics Proteomics Bioinformatics 17:558–575.

[144] Zhao, X.,Yi, L.,Ren, Y.,Li, J.,Ren, W.,Hou, Z.,Su, S.,Wang, J.,Zhang, Y.,Dong, Q., et al. (2023). Chromosome-scale genome assembly of the yellow nutsedge Cyperus esculentus). Genome Biol. Evol. 15: evad027.

[145] Zhao, Y.,Li, M.-C.,Konaté M.M.,Chen, L.,Das, B.,Karlovich, C.,Williams, P.M.,Evrard, Y.A.,Doroshow, J.H., and McShane, L.M. (2021). TPM, FPKM, or normalized counts? A comparative study of quantification measures for the analysis of RNA-seq data from the NCI patient-derived models repository. J. Transl. Med. 19:269.

[146] Zhao, Y.-Y.,Lyu, M.A.,Miao, F.,Chen, G., and Zhu, X.-G. (2022). The evolution of stomatal traits along the trajectory toward C4 photosynthesis. Plant Physiol. 190:441–458.

[147] Zuo, Y.,Liu, H.,Li, B.,Zhao, H.,Li, X.,Chen, J.,Wang, L.,Zheng, Q.,He, Y.,Zhang, J., et al. (2024). The Idesia polycarpa genome provides insights into its evolution and oil biosynthesis. Cell Rep. 43:113909.

RIGHTS & PERMISSIONS

2024 The Author(s). Journal of Integrative Plant Biology published by John Wiley & Sons Australia, Ltd on behalf of Institute of Botany, Chinese Academy of Sciences.