[1] |
McKinley KL, Cheeseman IM. 2016. The molecular basis for centromere identity and function. Nature Reviews Molecular Cell Biology 17:16−29 doi: 10.1038/nrm.2015.5 |
[2] |
Comai L, Maheshwari S, Marimuthu MPA. 2017. Plant centromeres. Current Opinion in Plant Biology 36:158−67 doi: 10.1016/j.pbi.2017.03.003 |
[3] |
Black BE, Jansen LET, Maddox PS, Foltz DR, Desai AB, et al. 2007. Centromere identity maintained by nucleosomes assembled with histone H3 containing the CENP-A targeting domain. Molecular Cell 25:309−22 doi: 10.1016/j.molcel.2006.12.018 |
[4] |
Musacchio A, Desai A. 2017. A molecular view of kinetochore assembly and function. Biology 6:5 doi: 10.3390/biology6010005 |
[5] |
Fukagawa T, Earnshaw WC. 2014. The Centromere: Chromatin Foundation for the Kinetochore Machinery. Developmental Cell 30:496−508 doi: 10.1016/j.devcel.2014.08.016 |
[6] |
Guo W, Comai L, Henry IM. 2023. Chromoanagenesis in plants: triggers, mechanisms, and potential impact. Trends in Genetics 39:34−45 doi: 10.1016/j.tig.2022.08.003 |
[7] |
Ravi M, Chan SWL. 2010. Haploid plants produced by centromere-mediated genome elimination. Nature 464:615−18 doi: 10.1038/nature08842 |
[8] |
Kelliher T, Starr D, Wang W, McCuiston J, Zhong H, et al. 2016. Maternal haploids are preferentially induced by CENH3-tailswap transgenic complementation in maize. Frontiers in Plant Science 7:414 doi: 10.3389/fpls.2016.00414 |
[9] |
Maheshwari S, Tan EH, West A, Franklin FC, Comai L, et al. 2015. Naturally occurring differences in CENH3 affect chromosome segregation in zygotic mitosis of hybrids. PLoS Genetics 11:e1004970 doi: 10.1371/journal.pgen.1004970 |
[10] |
Lv J, Yu K, Wei J, Gui H, Liu C, et al. 2020. Generation of paternal haploids in wheat by genome editing of the centromeric histone CENH3. Nature Biotechnology1397−401 doi: 10.1038/s41587-020-0728-4 |
[11] |
Kuppu S, Tan EH, Nguyen H, Rodgers A, Comai L, et al. 2015. Point Mutations in Centromeric Histone Induce Post-zygotic Incompatibility and Uniparental Inheritance. PLoS Genetics 11:e1005494 doi: 10.1371/journal.pgen.1005494 |
[12] |
Karimi-Ashtiyani R, Ishii T, Niessen M, Stein N, Heckmann S, et al. 2015. Point mutation impairs centromeric CENH3 loading and induces haploid plants. Proceedings of the National Academy of Sciences of the United States of America 112:11211−16 doi: 10.1073/pnas.1504333112 |
[13] |
Kuppu S, Ron M, Marimuthu MPA, Li G, Huddleson A, et al. 2020. A variety of changes, including CRISPR/Cas9-mediated deletions, in CENH3 lead to haploid induction on outcrossing. Plant Biotechnology Journal 18:2068−80 doi: 10.1111/pbi.13365 |
[14] |
Marimuthu MPA, Maruthachalam R, Bondada R, Kuppu S, Tan EH, et al. 2021. Epigenetically mismatched parental centromeres trigger genome elimination in hybrids. Science Advances 7:eabk1151 doi: 10.1126/sciadv.abk1151 |
[15] |
Wang N, Gent JI, Dawe RK. 2021. Haploid induction by a maize cenh3 null mutant. Science Advances 7:eabe2299 doi: 10.1126/sciadv.abe2299 |
[16] |
Demidov D, Lermontova I, Moebes M, Kochevenko A, Fuchs J, et al. 2022. Haploid induction by nanobody-targeted ubiquitin-proteasome-based degradation of EYFP-tagged CENH3 in Arabidopsis thaliana. Journal of Experimental Botany 73:7243−54 doi: 10.1093/jxb/erac359 |
[17] |
Li S, Wang J, Jia S, Wang K, Li H. 2023. Synthetic apomixis: from genetic basis to agricultural application. Seed Biology 2:10 doi: 10.48130/seedbio-2023-0010 |
[18] |
Sanei M, Pickering R, Kumke K, Nasuda S, Houben A. 2011. Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids. Proceedings of the National Academy of Sciences of the United States of America 108:E498−E505 doi: 10.1073/pnas.1103190108 |
[19] |
Kenworthy WJ, Brim CA, Wernsman EA. 1973. Polyembryony in soybeans. Crop Science 13:637−39 doi: 10.2135/cropsci1973.0011183X001300060015x |
[20] |
Clarke JD. 2009. Cetyltrimethyl ammonium bromide (CTAB) DNA miniprep for plant DNA isolation. Cold Spring Harbor protocols 2009:pdb.prot5177 doi: 10.1101/pdb.prot5177 |
[21] |
Concordet JP, Haeussler M. 2018. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Research 46:W242−W245 doi: 10.1093/nar/gky354 |
[22] |
Sun B, Wang Y, Yang Q, Gao H, Niu H, et al. 2023. A high-resolution transcriptomic atlas depicting nitrogen fixation and nodule development in soybean. Journal of Integrative Plant Biology 65:1536−52 doi: 10.1111/jipb.13495 |
[23] |
Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal 17:10−12 doi: 10.14806/ej.17.1.200 |
[24] |
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754−60 doi: 10.1093/bioinformatics/btp324 |
[25] |
Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, et al. 2021. Twelve years of SAMtools and BCFtools. GigaScience 10:giab008 doi: 10.1093/gigascience/giab008 |
[26] |
Van der Auwera GA & O'Connor BD. 2020. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (1st Edition). |
[27] |
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, et al. 2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6:80−92 doi: 10.4161/fly.19695 |
[28] |
Ishii T, Juranić M, Maheshwari S, de Oliveira Bustamante F, Vogt M, et al. 2020. Unequal contribution of two paralogous CENH3 variants in cowpea centromere function. Communications Biology 3:775 doi: 10.1038/s42003-020-01507-x |
[29] |
Bassett EA, DeNizio J, Barnhart-Dailey MC, Panchenko T, Sekulic N, et al. 2012. HJURP Uses Distinct CENP-A Surfaces to Recognize and to Stabilize CENP-A/Histone H4 for Centromere Assembly. Developmental Cell 22:749−62 doi: 10.1016/j.devcel.2012.02.001 |
[30] |
Black BE, Foltz DR, Chakravarthy S, Luger K, Woods VL, et al. 2004. Structural determinants for generating centromeric chromatin. Nature 430:578−82 doi: 10.1038/nature02766 |
[31] |
Pan D, Walstein K, Take A, Bier D, Kaiser N, et al. 2019. Mechanism of centromere recruitment of the CENP-A chaperone HJURP and its implications for centromere licensing. Nature Communications 10:4046 doi: 10.1038/s41467-019-12019-6 |
[32] |
Neumann P, Pavlíková Z, Koblížková A, Fuková I, Jedličková V, et al. 2015. Centromeres off the hook: Massive changes in centromere size and structure following duplication of CenH3 gene in Fabeae species. Molecular Biology and Evolution 32:1862−79 doi: 10.1093/molbev/msv070 |
[33] |
De Rop V, Padeganeh A, Maddox PS. 2012. CENP-A: the key player behind centromere identity, propagation, and kinetochore assembly. Chromosoma 121:527−38 doi: 10.1007/s00412-012-0386-5 |
[34] |
Ravi M, Kwong PN, Menorca RMG, Valencia JT, Ramahi JS, et al. 2010. The rapidly evolving centromere-specific histone has stringent functional requirements in Arabidopsis thaliana. Genetics 186:461−71 doi: 10.1534/genetics.110.120337 |
[35] |
Hoffmann S, Izquierdo HM, Gamba R, Chardon F, Dumont M, et al. 2020. A genetic memory initiates the epigenetic loop necessary to preserve centromere position. The EMBO Journal 39:e105505 doi: 10.15252/embj.2020105505 |
[36] |
Liu Y, Yi C, Fan C, Liu Q, Liu S, et al. 2023. Pan-centromere reveals widespread centromere repositioning of soybean genomes. Proceedings of the National Academy of Sciences of the United States of America 120:e2310177120 doi: 10.1073/pnas.2310177120 |