Friday, October 11, 2024
No menu items!
HomeNatureTeosinte Pollen Drive guides maize diversification and domestication by RNAi

Teosinte Pollen Drive guides maize diversification and domestication by RNAi

  • Sandler, L. & Novitski, E. Meiotic drive as an evolutionary force. Am. Nat. 91, 105–110 (1957).

    Article 

    Google Scholar
     

  • Presgraves, D. C. The molecular evolutionary basis of species formation. Nat. Rev. Genet. 11, 175–180 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kistler, L. et al. Multiproxy evidence highlights a complex evolutionary legacy of maize in South America. Science 362, 1309–1313 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Schneider, K. L., Xie, Z., Wolfgruber, T. K. & Presting, G. G. Inbreeding drives maize centromere evolution. Proc. Natl Acad. Sci. USA 113, E987–E996 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Anderson, E. & Stebbins, G. L. Hybridization as an evolutionary stimulus. Evolution 8, 378–388 (1954).

    Article 

    Google Scholar
     

  • Arnold, M. L. Transfer and origin of adaptations through natural hybridization: were Anderson and Stebbins right? Plant Cell 16, 562–570 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bayes, J. J. & Malik, H. S. Altered heterochromatin binding by a hybrid sterility protein in Drosophila sibling species. Science 326, 1538–1541 (2009).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tang, S. & Presgraves, D. C. Evolution of the Drosophila nuclear pore complex results in multiple hybrid incompatibilities. Science 323, 779–782 (2009).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bomblies, K. et al. Autoimmune response as a mechanism for a Dobzhansky–Muller-type incompatibility syndrome in plants. PLoS Biol. 5, e236 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McLaughlin, R. N. Jr & Malik, H. S. Genetic conflicts: the usual suspects and beyond. J. Exp. Biol. 220, 6–17 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lindholm, A. K. et al. The ecology and evolutionary dynamics of meiotic drive. Trends Ecol. Evol. 31, 315–326 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Fishman, L. & Saunders, A. Centromere-associated female meiotic drive entails male fitness costs in monkeyflowers. Science 322, 1559–1562 (2008).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Chmátal, L. et al. Centromere strength provides the cell biological basis for meiotic drive and karyotype evolution in mice. Curr. Biol. 24, 2295–2300 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fishman, L. & McIntosh, M. Standard deviations: the biological bases of transmission ratio distortion. Annu. Rev. Genet. 53, 347–372 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Buckler, E. S. 4th et al. Meiotic drive of chromosomal knobs reshaped the maize genome. Genetics 153, 415–426 (1999).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dawe, R. K. et al. A kinesin-14 motor activates neocentromeres to promote meiotic drive in maize. Cell 173, 839–850.e18 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Lyon, M. F. Transmission ratio distortion in mice. Annu. Rev. Genet. 37, 393–408 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • McDermott, S. R. & Noor, M. A. F. The role of meiotic drive in hybrid male sterility. Phil. Trans. R. Soc. B 365, 1265–1272 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Herrmann, B. G., Koschorz, B., Wertz, K., McLaughlin, K. J. & Kispert, A. A protein kinase encoded by the t complex responder gene causes non-Mendelian inheritance. Nature 402, 141–146 (1999).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Bauer, H., Willert, J., Koschorz, B. & Herrmann, B. G. The t complex-encoded GTPase-activating protein Tagap1 acts as a transmission ratio distorter in mice. Nat. Genet. 37, 969–973 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hartl, D. L. Genetic dissection of segregation distortion. I. Suicide combinations of SD genes. Genetics 76, 477–486 (1974).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Larracuente, A. M. & Presgraves, D. C. The selfish segregation distorter gene complex of Drosophila melanogaster. Genetics 192, 33–53 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zanders, S. E. et al. Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast. eLife 3, e02630 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nuckolls, N. L. et al. wtf Genes are prolific dual poison–antidote meiotic drivers. eLife 6, e26033 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lewontin, R. C. & Dunn, L. C. The evolutionary dynamics of a polymorphism in the house mouse. Genetics 45, 705–722 (1960).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hurst, L. D. & Pomiankowski, A. Causes of sex ratio bias may account for unisexual sterility in hybrids: a new explanation of Haldane’s rule and related phenomena. Genetics 128, 841–858 (1991).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Coughlan, J. M. The role of conflict in shaping plant biodiversity. New Phytol. https://doi.org/10.1111/nph.19233 (2023).

  • Phadnis, N. & Orr, H. A. A single gene causes both male sterility and segregation distortion in Drosophila hybrids. Science 323, 376–379 (2009).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, L., Sun, T., Woldesellassie, F., Xiao, H. & Tao, Y. Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility. PLoS Genet. 11, e1005073 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kermicle, J. L. & Allen, J. P. Cross-incompatibility between maize and teosinte. Maydica 35, 399–408 (1990).


    Google Scholar
     

  • Lu, Y., Hokin, S. A., Kermicle, J. L., Hartwig, T. & Evans, M. M. S. A pistil-expressed pectin methylesterase confers cross-incompatibility between strains of Zea mays. Nat. Commun. 10, 2304 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hufford, M. B. et al. The genomic signature of crop-wild introgression in maize. PLoS Genet. 9, e1003477 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rojas-Barrera, I. C. et al. Contemporary evolution of maize landraces and their wild relatives influenced by gene flow with modern maize varieties. Proc. Natl Acad. Sci. USA 116, 21302–21311 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, C. et al. A natural gene drive system confers reproductive isolation in rice. Cell 186, 3577–3592.e18 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yang, Z. & Bielawski, J. P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15, 496–503 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yoshikawa, M., Peragine, A., Park, M. Y. & Poethig, R. S. A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. Genes Dev 19, 2164–2175 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Parent, J.-S., Bouteiller, N., Elmayan, T. & Vaucheret, H. Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing. Plant J. 81, 223–232 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Deleris, A. et al. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313, 68–71 (2006).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Bouché, N., Lauressergues, D., Gasciolli, V. & Vaucheret, H. An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J. 25, 3347–3356 (2006).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, Y.-Y. et al. DCL2- and RDR6-dependent transitive silencing of SMXL4 and SMXL5 in Arabidopsis dcl4 mutants causes defective phloem transport and carbohydrate over-accumulation. Plant J. 90, 1064–1078 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Taochy, C. et al. A genetic screen for impaired systemic RNAi highlights the crucial role of DICER-LIKE 2. Plant Physiol. 175, 1424–1437 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mlotshwa, S. et al. DICER-LIKE2 plays a primary role in transitive silencing of transgenes in Arabidopsis. PLoS ONE 3, e1755 (2008).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tagami, Y., Motose, H. & Watanabe, Y. A dominant mutation in DCL1 suppresses the hyl1 mutant phenotype by promoting the processing of miRNA. RNA 15, 450–458 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Welker, N. C. et al. Dicer’s helicase domain discriminates dsRNA termini to promote an altered reaction mode. Mol. Cell 41, 589–599 (2011).

    Article 
    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Aderounmu, A. M., Aruscavage, P. J., Kolaczkowski, B. & Bass, B. L. Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function. eLife 12, e85120 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Slotkin, R. K., Freeling, M. & Lisch, D. Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nat. Genet. 37, 641–644 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bhutani, K. et al. Widespread haploid-biased gene expression enables sperm-level natural selection. Science 371, eabb1723 (2021).

    Article 
    CAS 
    PubMed 

    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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ding, L.-N. et al. Advances in plant GDSL lipases: from sequences to functional mechanisms. Acta Physiol. Plant 41, 151 (2019).

    Article 

    Google Scholar
     

  • An, X. et al. ZmMs30 encoding a novel GDSL lipase is essential for male fertility and valuable for hybrid breeding in maize. Mol. Plant 12, 343–359 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Huo, Y. et al. IRREGULAR POLLEN EXINE2 encodes a GDSL lipase essential for male fertility in maize. Plant Physiol. 184, 1438–1454 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhao, J. et al. RMS2 encoding a GDSL lipase mediates lipid homeostasis in anthers to determine rice male fertility. Plant Physiol. 182, 2047–2064 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tsugama, D., Fujino, K., Liu, S. & Takano, T. A GDSL-type esterase/lipase gene, GELP77, is necessary for pollen dissociation and fertility in Arabidopsis. Biochem. Biophys. Res. Commun. 526, 1036–1041 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu, H. et al. Plant 22-nt siRNAs mediate translational repression and stress adaptation. Nature 581, 89–93 (2020).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Borges, F. & Martienssen, R. A. The expanding world of small RNAs in plants. Nat. Rev. Mol. Cell Biol. 16, 727–741 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fang, X. & Qi, Y. RNAi in plants: an Argonaute-centered view. Plant Cell 28, 272–285 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Axtell, M. J., Westholm, J. O. & Lai, E. C. Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biol. 12, 221 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Manavella, P. A., Koenig, D. & Weigel, D. Plant secondary siRNA production determined by microRNA-duplex structure. Proc. Natl Acad. Sci. USA 109, 2461–2466 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nelms, B. & Walbot, V. Gametophyte genome activation occurs at pollen mitosis I in maize. Science 375, 424–429 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Wongpalee, S. P. et al. CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation. Nat. Commun. 10, 3916 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jauvion, V., Rivard, M., Bouteiller, N., Elmayan, T. & Vaucheret, H. RDR2 partially antagonizes the production of RDR6-dependent siRNA in sense transgene-mediated PTGS. PLoS ONE 7, e29785 (2012).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Creasey, K. M. et al. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature 508, 411–415 (2014).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Romero Navarro, J. A. et al. A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat. Genet. 49, 476–480 (2017).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen, L. et al. Genome sequencing reveals evidence of adaptive variation in the genus Zea. Nat. Genet. 54, 1736–1745 (2022).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lu, Y., Kermicle, J. L. & Evans, M. M. S. Genetic and cellular analysis of cross-incompatibility in Zea mays. Plant Reprod. 27, 19–29 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hartl, D. L. Population dynamics of sperm and pollen killers. Theor. Appl. Genet. 42, 81–88 (1972).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sweigart, A. L., Brandvain, Y. & Fishman, L. Making a murderer: the evolutionary framing of hybrid gamete-killers. Trends Genet. 35, 245–252 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bravo Núñez, M. A., Lange, J. J. & Zanders, S. E. A suppressor of a wtf poison–antidote meiotic driver acts via mimicry of the driver’s antidote. PLoS Genet. 14, e1007836 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Barnes, A. C. et al. An adaptive teosinte mexicana introgression modulates phosphatidylcholine levels and is associated with maize flowering time. Proc. Natl Acad. Sci. USA 119, e2100036119 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McClintock, B., Kato Yamakake, T. A., Blumenschein, A. & Escuela Nacional de Agricultura (Mexico). Chromosome Constitution of Races of Maize: Its Significance in the Interpretation of Relationships between Races and Varieties in the Americas (Colegio de Postgraduados, 1981).

  • Borges, F. et al. Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis. Nat. Genet. 50, 186–192 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martinez, G. et al. Paternal easiRNAs regulate parental genome dosage in Arabidopsis. Nat. Genet. 50, 193–198 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Durand, E. et al. Dominance hierarchy arising from the evolution of a complex small RNA regulatory network. Science 346, 1200–1205 (2014).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Czech, B. et al. An endogenous small interfering RNA pathway in Drosophila. Nature 453, 798–802 (2008).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wen, J. et al. Adaptive regulation of testis gene expression and control of male fertility by the Drosophila hairpin RNA pathway. Mol. Cell 57, 165–178 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tao, Y. et al. A sex-ratio meiotic drive system in Drosophila simulans. II: an X-linked distorter. PLoS Biol. 5, e293 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lin, C.-J. et al. The hpRNA/RNAi pathway is essential to resolve intragenomic conflict in the Drosophila male germline. Dev. Cell 46, 316–326.e5 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Flemr, M. et al. A retrotransposon-driven Dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell 155, 807–816 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Tam, O. H. et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453, 534–538 (2008).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Su, R. et al. Global profiling of RNA-binding protein target sites by LACE-seq. Nat. Cell Biol. 23, 664–675 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Begcy, K. & Dresselhaus, T. Tracking maize pollen development by the leaf collar method. Plant Reprod. 30, 171–178 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bass, H. W. et al. A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development. J. Exp. Bot. 65, 2747–2756 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kalkar, S. A. & Neha, K. Evaluation of FDA staining technique in stored maize pollen. Middle East J. Sci. Res. 12, 560–562 (2012).

  • Nagar, R. & Schwessinger, B. DNA size selection (>3–4 kb) and purification of DNA using an improved homemade SPRIbeads solution. Protocols.io https://doi.org/10.17504/protocols.io.n7hdhj6 (2018).

  • Schalamun, M., Nagar, R. & Kainer, D. Harnessing the MinION: an example of how to establish long‐read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora. Mol. Ecol. https://doi.org/10.1111/1755-0998.12938 (2018).

  • Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shafin, K. et al. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nat. Methods 18, 1322–1332 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Vasimuddin, M., Misra, S., Li, H. & Aluru, S. Efficient architecture-aware acceleration of BWA-MEM for multicore systems. In 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) 314–324 (IEEE, 2019).

  • Hu, J., Fan, J., Sun, Z. & Liu, S. NextPolish: a fast and efficient genome polishing tool for long read assembly. Bioinformatics https://doi.org/10.1093/bioinformatics/btz891 (2019).

  • Aury, J.-M. & Istace, B. Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads. NAR Genom. Bioinform. 3, lqab034 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99–101 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Springer, N. M. et al. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat. Genet. 50, 1282–1288 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639–1643 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10 (2011).

    Article 

    Google Scholar
     

  • Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997 (2013).

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. Preprint at https://arxiv.org/abs/1207.3907 (2012).

  • Takagi, H. et al. QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J. 74, 174–183 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J. & Delaneau, O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 53, 120–126 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2014).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alexa, A. & Rahnenfuhrer, J. topGO: enrichment analysis for gene ontology. R package version 2.42.0 (2023).

  • Sayols, S. rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. MicroPubl. Biol. https://doi.org/10.17912/micropub.biology.000811 (2023).

  • Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, 160–165 (2016).

    Article 

    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
     

  • Axtell, M. J. ShortStack: comprehensive annotation and quantification of small RNA genes. RNA 19, 740–751 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R. & Hofacker, I. L. The Vienna RNA websuite. Nucleic Acids Res. 36, W70–W74 (2008).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • German, M. A., Luo, S., Schroth, G., Meyers, B. C. & Green, P. J. Construction of parallel analysis of RNA ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat. Protoc. 4, 356–362 (2009).

    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
     

  • Dai, X., Zhuang, Z. & Zhao, P. X. psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 46, W49–W54 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Szpiech, Z. A. selscan 2.0: scanning for sweeps in unphased data. Bioinformatics 40, btae006 (2024).

  • Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grzybowski, M. W. et al. A common resequencing-based genetic marker data set for global maize diversity. Plant J. 113, 1109–1121 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yang, N. et al. Two teosintes made modern maize. Science 382, eadg8940 (2023).

  • Browning, B. L., Tian, X., Zhou, Y. & Browning, S. R. Fast two-stage phasing of large-scale sequence data. Am. J. Hum. Genet. 108, 1880–1890 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Portwood, J. L. II et al. MaizeGDB 2018: the maize multi-genome genetics and genomics database. Nucleic Acids Res. 47, D1146–D1154 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Stitzer, M. C. & Ross-Ibarra, J. Maize domestication and gene interaction. New Phytol. 220, 395–408 (2018).

    Article 
    PubMed 

    Google Scholar
     

  • Walley, J. W. et al. Integration of omic networks in a developmental atlas of maize. Science 353, 814–818 (2016).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, L. & Li, J. Communications between the endoplasmic reticulum and other organelles during abiotic stress response in plants. Front. Plant Sci. 10, 749 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Taurino, M. et al. SEIPIN proteins mediate lipid droplet biogenesis to promote pollen transmission and reduce seed dormancy. Plant Physiol. 176, 1531–1546 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Beissinger, T. M. et al. Recent demography drives changes in linked selection across the maize genome. Nat. Plants 2, 16084 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • RELATED ARTICLES

    Most Popular

    Recent Comments