Yan, N. et al. Morphological characteristics, nutrients, and bioactive compounds of Zizania latifolia, and health benefits of its seeds. Molecules 23, 1561 (2018).
Google Scholar
Yan, N. et al. A comparative UHPLC-QqQ-MS-based metabolomics approach for evaluating Chinese and North American wild rice. Food Chem. 275, 618–627 (2019).
Google Scholar
Yu, X. et al. Wild rice (Zizania spp.): A review of its nutritional constituents, phytochemicals, antioxidant activities, and health-promoting effects. Food Chem. 331, 127293 (2020).
Google Scholar
Zhai, C. K., Tang, W. L., Jang, X. L. & Lorenz, K. J. Studies of the safety of Chinese wild rice. Food Chem. Toxicol. 34, 347–352 (1996).
Google Scholar
Chu, M. J. et al. Partial purification, identification, and quantitation of antioxidants from wild rice (Zizania latifolia). Molecules 23, 2782 (2018).
Google Scholar
Chu, M. J. et al. Extraction of proanthocyanidins from Chinese wild rice (Zizania latifolia) and analyses of structural composition and potential bioactivities of different fractions. Molecules 24, 1681 (2019).
Google Scholar
Yu, X. et al. Comparison of the contents of phenolic compounds including flavonoids and antioxidant activity of rice (Oryza sativa) and Chinese wild rice (Zizania latifolia). Food Chem. 344, 128600 (2021).
Google Scholar
Li, J. et al. Transcriptome analysis reveals the symbiotic mechanism of Ustilago esculenta-induced gall formation of Zizania latifolia. Mol. Plant Microbe . 34, 168–185 (2021).
Google Scholar
Wang, Z. D. et al. RNA-seq analysis provides insight into reprogramming of culm development in Zizania latifolia induced by Ustilago esculenta. Plant Mol. Biol. 95, 533–547 (2017).
Google Scholar
Wang, Z. H. et al. Gene expression in the smut fungus Ustilago esculenta governs swollen gall metamorphosis in Zizania latifolia. Microb. Pathogenesis 143, 104107 (2020).
Google Scholar
Ye, C. Y. & Fan, L. Orphan crops and their wild relatives in the genomic era. Mol. Plant 14, 27–39 (2021).
Google Scholar
Wang, M. et al. Purification, characterization and immunomodulatory activity of water extractable polysaccharides from the swollen culms of Zizania latifolia. Int. J. Biol. Macromol. 107, 882–890 (2018).
Google Scholar
Yang, Z., Davy, A. J., Liu, X., Yuan, S. & Wang, H. Responses of an emergent macrophyte, Zizania latifolia, to water-level changes in lakes with contrasting hydrological management. Ecol. Eng. 151, 105814 (2020).
Xu, X. W. et al. Phylogeny and biogeography of the eastern Asian–North American disjunct wild-rice genus (Zizania L., Poaceae). Mol. Phylogenet. Evol. 55, 1008–1017 (2010).
Google Scholar
Xu, X. W. et al. Comparative phylogeography of the wild-rice genus Zizania (Poaceae) in eastern Asia and North America. Am. J. Bot. 102, 239–247 (2015).
Google Scholar
Mao, L. et al. RiceRelativesGD: a genomic database of rice relatives for rice research. Database 2019, baz110 (2019).
Google Scholar
Dong, Z. Y. et al. Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb. Theor. Appl. Genet. 113, 196–205 (2006).
Google Scholar
Shan, X. et al. Mobilization of the active MITE transposons mPing and Pong in rice by introgression from wild rice (Zizania latifolia Griseb.). Mol. Biol. Evol. 22, 976–990 (2005).
Google Scholar
Wang, N. et al. Transpositional reactivation of the Dart transposon family in rice lines derived from introgressive hybridization with Zizania latifolia. BMC Plant Biol. 10, 190 (2010).
Google Scholar
Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 1309–1321 (2006).
Google Scholar
Chen, Q., Li, W., Tan, L. & Tian, F. Harnessing knowledge from maize and rice domestication for new crop breeding. Mol. Plant 14, 9–26 (2021).
Google Scholar
Yu, H. et al. A route to de novo domestication of wild allotetraploid rice. Cell 184, 1156–1170 (2021).
Google Scholar
Kennard, W., Phillips, R. & Porter, R. Genetic dissection of seed shattering, agronomic, and color traits in American wildrice (Zizania palustris var. interior L.) with a comparative map. Theor. Appl. Genet. 105, 1075–1086 (2002).
Google Scholar
Guo, L. et al. Genomic clues for crop—weed interactions and evolution. Trends Plant Sci. 23, 1102–1115 (2018).
Google Scholar
Kitaoka, N. et al. Interdependent evolution of biosynthetic gene clusters for momilactone production in rice. Plant Cell 33, 290–305 (2021).
Google Scholar
Swaminathan, S., Morrone, D., Wang, Q., Fulton, D. B. & Peters, R. J. CYP76M7 is an ent-cassadiene C11α-hydroxylase defining a second multifunctional diterpenoid biosynthetic gene cluster in rice. Plant Cell 21, 3315–3325 (2009).
Google Scholar
Shimura, K. et al. Identification of a biosynthetic gene cluster in rice for momilactones. J. Biol. Chem. 282, 34013–34018 (2007).
Google Scholar
Hasegawa, M. et al. Phytoalexin accumulation in the interaction between rice and the blast fungus. Mol. Plant Microbe. 23, 1000–1011 (2010).
Google Scholar
Mennan, H. et al. Quantification of momilactone B in rice hulls and the phytotoxic potential of rice extracts on the seed germination of Alisma plantago-aquatica. Weed Biol. Manag. 12, 29–39 (2012).
Google Scholar
Kato-noguchi, H. & Peters, R. J. The role of momilactones in rice allelopathy. J. Chem. Ecol. 39, 175–185 (2013).
Google Scholar
Guo, L. et al. A host plant genome (Zizania latifolia) after a century‐long endophyte infection. Plant J. 83, 600–609 (2015).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061–1067 (2007).
Google Scholar
Ou, S., Chen, J. & Jiang, N. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 46, e126–e126 (2018).
Google Scholar
Du, H. et al. Sequencing and de novo assembly of a near complete indica rice genome. Nat. Commun. 8, 15324 (2017).
Google Scholar
Haas, M. W. et al. Whole-genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole-genome duplication in the Zizania genus. Plant J. 107, 1802–1818 (2021).
Google Scholar
Paterson, A. H., Bowers, J. E. & Chapman, B. A. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. P. Natl Acad. Sci. Usa. 101, 9903–9908 (2004).
Google Scholar
Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009).
Google Scholar
Kennard, W. C., Phillips, R. L., Porter, R. A. & Grombacher, A. W. A comparative map of wild rice (Zizania palustris L. 2n= 2x= 30). Theor. Appl. Genet. 101, 677–684 (2000).
Google Scholar
Hass, B. L., Pires, J. C., Porter, R., Phillips, R. L. & Jackson, S. A. Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris). Theor. Appl. Genet. 107, 773–782 (2003).
Google Scholar
Estornell, L. H., Agustí, J., Merelo, P., Talón, M. & Tadeo, F. R. Elucidating mechanisms underlying organ abscission. Plant Sci. 199, 48–60 (2013).
Google Scholar
Fernie, A. R. & Yan, J. De novo domestication: an alternative route toward new crops for the future. Mol. Plant 12, 615–631 (2019).
Google Scholar
Zhang, Y., Pribil, M., Palmgren, M. & Gao, C. A CRISPR way for accelerating improvement of food crops. Nat. Food 1, 200–205 (2020).
Miyamoto, K. et al. Evolutionary trajectory of phytoalexin biosynthetic gene clusters in rice. Plant J. 87, 293–304 (2016).
Google Scholar
Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).
Google Scholar
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
Google Scholar
Bruce, J. et al. Pilon: An integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
Google Scholar
Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).
Google Scholar
Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007).
Google Scholar
Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21, i351–i358 (2005).
Google Scholar
Hoede, C. et al. PASTEC: an automatic transposable element classification tool. PLoS ONE 9, e91929 (2014).
Google Scholar
Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005).
Google Scholar
Tarailo‐Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinforma. 25, 4.10.1–4.10.14 (2009).
Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol. 20, 275 (2019).
Google Scholar
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).
Google Scholar
Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Boil. 268, 78–94 (1997).
Google Scholar
Stanke, M. & Waack, S. Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19, ii215–ii225 (2003).
Google Scholar
Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004).
Google Scholar
Blanco, E., Parra, G. & Guigó, R. Using geneid to identify genes. Curr. Protoc. Bioinforma. 18, 4.3.1–4.3.28 (2007).
Korf, I. Gene finding in novel genomes. BMC Bioinforma. 5, 59 (2004).
Keilwagen, J. et al. Using intron position conservation for homology-based gene prediction. Nucleic Acids Res. 44, e89–e89 (2016).
Google Scholar
Keilwagen, J., Hartung, F., Paulini, M., Twardziok, S. O. & Grau, J. Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi. BMC Bioinforma. 19, 189 (2018).
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
Google Scholar
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Google Scholar
Tang, S., Lomsadze, A. & Borodovsky, M. Identification of protein coding regions in RNA transcripts. Nucleic Acids Res. 43, e78–e78 (2015).
Google Scholar
Grabherr, M. G. et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat. Biotechnol. 29, 644–652 (2011).
Google Scholar
Campbell, M. A., Haas, B. J., Hamilton, J. P., Mount, S. M. & Buell, C. R. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7, 327 (2006).
Google Scholar
Griffiths-Jones, S. et al. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33, D121–D124 (2005).
Google Scholar
Lowe, T. M. & Eddy, S. R. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964 (1997).
Google Scholar
She, R., Chu, J. S. C., Wang, K., Pei, J. & Chen, N. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 19, 143–149 (2009).
Google Scholar
Birney, E. et al. GeneWise and genomewise. Genome Res. 14, 988–995 (2004).
Google Scholar
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. J. Mol. Boil. 215, 403–410 (1990).
Google Scholar
Marchler-Bauer, A. et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res. 39, D225–D229 (2010).
Google Scholar
Koonin, E. V. et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5, R7 (2004).
Google Scholar
Dimmer, E. C. et al. The UniProt-GO annotation database in 2011. Nucleic Acids Res. 40, D565–D570 (2012).
Google Scholar
Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).
Google Scholar
Boeckmann, B. et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370 (2003).
Google Scholar
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Google Scholar
Mi, H., Muruganujan, A., Ebert, D., Huang, X. & Thomas, P. D. PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res. 47, D419–D426 (2019).
Google Scholar
Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Google Scholar
Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–W612 (2006).
Google Scholar
Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).
Google Scholar
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
Google Scholar
Yang, Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556 (1997).
Google Scholar
Puttick, M. N. MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees. Bioinformatics 35, 5321–5322 (2019).
Google Scholar
Han, M. V., Thomas, G. W., Lugo-Martinez, J. & Hahn, M. W. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. Mol. Biol. Evol. 30, 1987–1997 (2013).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
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).
Google Scholar
Zwaenepoel, A. & Van de Peer, Y. wgd-simple command line tools for the analysis of ancient whole-genome duplications. Bioinformatics 35, 2153–2155 (2019).
Google Scholar
Yan, N. et al. RNA sequencing provides insights into the regulation of solanesol biosynthesis in Nicotiana tabacum induced by moderately high temperature. Biomolecules 8, 165 (2018).
Google Scholar
Mao, X., Cai, T., Olyarchuk, J. G. & Wei, L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21, 3787–3793 (2005).
Google Scholar
Krzywinski, M. et al. Circos: An information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).
Google Scholar
Wei, T. et al. Package ‘corrplot’. Statistician 56, 316–324 (2017).
