| [1] |
Trueman SJ. 2013. The reproductive biology of macadamia. Scientia Horticulturae 150:354−59 doi: 10.1016/j.scienta.2012.11.032 |
| [2] |
O'Connor K, Hayes B, Topp B. 2018. Prospects for increasing yield in macadamia using component traits and genomics. Tree Genetics & Genomes 14:7 doi: 10.1007/s11295-017-1221-1 |
| [3] |
Kilian B, Dempewolf H, Guarino L, Werner P, Coyne C, et al. 2021. Crop Science special issue: Adapting agriculture to climate change: A walk on the wild side. Crop Science 61(1):32−36 doi: 10.1002/csc2.20418 |
| [4] |
Nock CJ, Baten A, Mauleon R, Langdon KS, Topp B, et al. 2020. Chromosome-scale assembly and annotation of the macadamia genome (Macadamia integrifolia HAES 741). G3 Genes | Genomes | Genetics 10(10):3497−504 doi: 10.1534/g3.120.401326 |
| [5] |
Nock CJ, Baten A, Barkla BJ, Furtado A, Henry RJ, et al. 2016. Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae). BMC genomics 17:937 doi: 10.1186/s12864-016-3272-3 |
| [6] |
Murigneux V, Rai SK, Furtado A, Bruxner TJC, Tian W, et al. 2020. Comparison of long-read methods for sequencing and assembly of a plant genome. GigaScience 9:giaa146 doi: 10.1093/gigascience/giaa146 |
| [7] |
Sharma P, Murigneux V, Haimovitz J, Nock CJ, Tian W, et al. 2021. The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding. Plant Direct 5(12):e364 doi: 10.1002/pld3.364 |
| [8] |
Sharma P, Al-Dossary O, Alsubaie B, Al-Mssallem I, Nath O, et al. 2021a. Improvements in the sequencing and assembly of plant genomes. GigaByte 2021:gigabyte24 doi: 10.46471/gigabyte.24 |
| [9] |
Sharma P, Masouleh AK, Topp B, Furtado A, Henry RJ. 2022. De novo chromosome level assembly of a plant genome from long read sequence data. The Plant Journal 109(3):727−36 doi: 10.1111/tpj.15583 |
| [10] |
Xia C, Jiang S, Tan Q, Wang W, Zhao L, et al. 2022. Chromosomal-level genome of macadamia (Macadamia integrifolia). Tropical Plants 1:3 doi: 10.48130/tp-2022-0003 |
| [11] |
Lin J, Zhang W, Zhang X, Ma X, Zhang S, et al. 2022. Signatures of selection in recently domesticated macadamia. Nature communications 13:242 doi: 10.1038/s41467-021-27937-7 |
| [12] |
Niu Y, Li G, Ni S, He X, Zheng C, et al. 2022. The chromosome-scale reference genome of Macadamia tetraphylla provides insights into fatty acid biosynthesis. Frontiers in Genetics 13:835363 doi: 10.3389/fgene.2022.835363 |
| [13] |
Si X, Lyu S, Hussain Q, Ye H, Huang C, et al. 2023. Analysis of Delta (9) fatty acid desaturase gene family and their role in oleic acid accumulation in Carya cathayensis kernel. Frontiers in Plant Science 14:1193063 doi: 10.3389/fpls.2023.1193063 |
| [14] |
Hu W, Fitzgerald M, Topp B, Alam M, O'Hare TJ. 2022. Fatty acid diversity and interrelationships in macadamia nuts. LWT 154:112839 doi: 10.1016/j.lwt.2021.112839 |
| [15] |
Irmisch S, Clavijo McCormick A, Boeckler GA, Schmidt A, Reichelt M, et al. 2013. Two herbivore-induced cytochrome P450 enzymes CYP79D6 and CYP79D7 catalyze the formation of volatile aldoximes involved in poplar defense. The Plant Cell 25(11):4737−54 doi: 10.1105/tpc.113.118265 |
| [16] |
Hansen CC, Sørensen M, Veiga TA, Zibrandtsen JF, Heskes AM, et al. 2018. Reconfigured cyanogenic glucoside biosynthesis in Eucalyptus cladocalyx involves a cytochrome P450 CYP706C55. Plant Physiology 178(3):1081−95 doi: 10.1104/pp.18.00998 |
| [17] |
He X, Li JJ, Chen Y, Yang JQ, Chen XY. 2019. Genome-wide analysis of the WRKY gene family and its response to abiotic stress in buckwheat (Fagopyrum tataricum). Open Life Sciences 14(1):80−96 doi: 10.1515/biol-2019-0010 |
| [18] |
Tiley GP, Barker MS, Burleigh JG. 2018. Assessing the performance of Ks plots for detecting ancient whole genome duplications. Genome Biology and Evolution 10(11):2882−98 doi: 10.1093/gbe/evy200 |
| [19] |
Zwaenepoel A, Van de Peer Y. 2019. wgd—simple command line tools for the analysis of ancient whole-genome duplications. Bioinformatics 35(12):2153−55 doi: 10.1093/bioinformatics/bty915 |
| [20] |
Nakandala U, Masouleh AK, Smith MW, Furtado A, Mason P, et al. 2023. Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes. Horticulture Research 10(5):uhad058 doi: 10.1093/hr/uhad058 |
| [21] |
Zhang X, Chen S, Shi L, Gong D, Zhang S, et al. 2021. Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis. Nature Genetics 53(8):1250−59 doi: 10.1038/s41588-021-00895-y |
| [22] |
Cheng H, Concepcion GT, Feng X, Zhang H, Li H. 2021. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nature Methods 18(2):170−75 doi: 10.1038/s41592-020-01056-5 |
| [23] |
McManus AM, Nielsen KJ, Marcus JP, Harrison SJ, Green JL, et al. 1999. MiAMP1, a novel protein from Macadamia integrifolia adopts a Greek key β-barrel fold unique amongst plant antimicrobial proteins. Journal of Molecular Biology 293(3):629−38 doi: 10.1006/jmbi.1999.3163 |
| [24] |
Li J, Hu S, Jian W, Xie C, Yang X. 2021. Plant antimicrobial peptides: structures, functions, and applications. Botanical Studies 62:5 doi: 10.1186/s40529-021-00312-x |
| [25] |
Campos ML, de Souza CM, de Oliveira KBS, Dias SC, Franco OL. 2018. The role of antimicrobial peptides in plant immunity. Journal of Experimental Botany 69(21):4997−5011 doi: 10.1093/jxb/ery294 |
| [26] |
Furtado A. 2014. DNA extraction from vegetative tissue for next-generation sequencing. In Cereal Genomics. Methods in Molecular Biology, eds. Henry R, Furtado A. Totowa, NJ: Humana Press. pp. 1−5 . doi: 10.1007/978-1-62703-715-0_1 |
| [27] |
Rubio-Piña JA, Zapata-Pérez O. 2011. Isolation of total RNA from tissues rich in polyphenols and polysaccharides of mangrove plants. Electronic Journal of Biotechnology 14(5):1−8 doi: 10.2225/vol14-issue5-fulltext-10 |
| [28] |
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, et al. 2019. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biology 20:224 doi: 10.1186/s13059-019-1829-6 |
| [29] |
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31(19):3210−12 doi: 10.1093/bioinformatics/btv351 |
| [30] |
Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072−75 doi: 10.1093/bioinformatics/btt086 |
| [31] |
Galbraith DW, Harkins KR, Maddox JM, Ayres NM, Sharma DP, et al. 1983. Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science 220(4601):1049−51 doi: 10.1126/science.220.4601.1049 |
| [32] |
Arumuganathan K, Earle ED. 1991. Estimation of nuclear DNA content of plants by flow cytometry. Plant Molecular Biology Reporter 9:229−41 doi: 10.1007/BF02672073 |
| [33] |
Sadhu A, Bhadra S, Bandyopadhyay M. 2016. Novel nuclei isolation buffer for flow cytometric genome size estimation of Zingiberaceae: a comparison with common isolation buffers. Annals of Botany 118(6):1057−70 doi: 10.1093/aob/mcw173 |
| [34] |
Doležel J, Greilhuber J, Suda J. 2007. Estimation of nuclear DNA content in plants using flow cytometry. Nature Protocols 2(9):2233−44 doi: 10.1038/nprot.2007.310 |
| [35] |
International Rice Genome Sequencing Project, Sasaki T. 2005. The map-based sequence of the rice genome. Nature 436:793−800 doi: 10.1038/nature03895 |
| [36] |
Marçais G, Kingsford C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27(6):764−70 doi: 10.1093/bioinformatics/btr011 |
| [37] |
Ranallo-Benavidez TR, Jaron KS, Schatz MC. 2020. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications 11:1432 doi: 10.1038/s41467-020-14998-3 |
| [38] |
Pérez-Wohlfeil E, Diaz-del-Pino S, Trelles O. 2019. Ultra-fast genome comparison for large-scale genomic experiments. Scientific Reports 9:10274 doi: 10.1038/s41598-019-46773-w |
| [39] |
Brůna T, Hoff KJ, Lomsadze A, Stanke M, Borodovsky M. 2021. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics and Bioinformatics 3(1):lqaa108 doi: 10.1093/nargab/lqaa108 |
| [40] |
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37(8):907−15 doi: 10.1038/s41587-019-0201-4 |
| [41] |
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078−79 doi: 10.1093/bioinformatics/btp352 |
| [42] |
Conesa A, Götz S. 2008. Blast2GO: a comprehensive suite for functional analysis in plant genomics. International Journal of Plant Genomics 1:619832 doi: 10.1155/2008/619832 |
| [43] |
Jones P, Binns D, Chang HY, Fraser M, Li W, et al. 2014. InterProScan 5: genome-scale protein function classification. Bioinformatics 30(9):1236−40 doi: 10.1093/bioinformatics/btu031 |
| [44] |
Naithani S, Gupta P, Preece J, D'Eustachio P, Elser JL, et al. 2020. Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Research 48(D1):D1093−D1103 doi: 10.1093/nar/gkz996 |
| [45] |
Kanehisa M, Goto S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28(1):27−30 doi: 10.1093/nar/28.1.27 |
| [46] |
Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238 doi: 10.1186/s13059-019-1832-y |
| [47] |
Sun J, Lu F, Luo Y, Bie L, Xu L, et al. 2023. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Research 51(W1):W397−W403 doi: 10.1093/nar/gkad313 |
| [48] |
Chapman BA, Bowers JE, Schulze SR, Paterson AH. 2004. A comparative phylogenetic approach for dating whole genome duplication events. Bioinformatics 20(2):180−85 doi: 10.1093/bioinformatics/bth022 |
| [49] |
Goel M, Sun H, Jiao WB, Schneeberger K. 2019. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biology 20:277 doi: 10.1186/s13059-019-1911-0 |
| [50] |
Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094−100 doi: 10.1093/bioinformatics/bty191 |
| [51] |
Goel M, Schneeberger K, et al. 2022. Plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics 38(10):2922−26 doi: 10.1093/bioinformatics/btac196 |
| [52] |
Wang Y, Tang H, DeBarry JD, Tan X, Li J, et al. 2012. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research 40(7):e49 doi: 10.1093/nar/gkr1293 |
| [53] |
Bandi V, Gutwin C. 2020. Interactive exploration of genomic conservation. Proceedings of Graphics Interface 2020, University of Toronto, 28−29 May 2020. pp. 74−83. DOI: 10.20380/GI2020.09 |