| [1] |
Hardy S, Wilk P, Viola J, Rennie S. 2010. Growing Australian native finger limes. Prime Facts 979: 1−11. www.dpi.nsw.gov.au/__data/assets/pdf_file/0016/320272/growing-australian-native-finger-limes.pdf |
| [2] |
Cai QN, Wang HX, Chen DJ, Ke XR, Zhu ZX, et al. 2022. The complete chloroplast genome sequence of a Citrus australasica cultivar (Rutaceae). Mitochondrial DNA 7(1):54−55 doi: 10.1080/23802359.2021.2008842 |
| [3] |
Wang Y, Chen J, Zhu T, Sun C. 2019. Physicochemical properties, antioxidant capacity and phenolic compounds of Microcitrus australasica. Chinese Society of Horticulture 2019 Annual Academic Conference and 90th Anniversary Conference, Zhengzhou, China. pp. 86 |
| [4] |
Siebert T, Krueger R, Kahn T, Bash J, Vidalakis G. 2010. Descriptions of new varieties recently distributed from the Citrus Clonal Protection Program. Citrograph. pp. 22. https://citrusvariety.ucr.edu/sites/default/files/2022-04/siebert_etal_2010_ccpp_new_varieties_citrographmarchapril2010.pdf |
| [5] |
Xie C, Liu Z, Zhang S, Hu H. 2023. Establishment of in vitro regeneration system of stem segment of finger lemon. Chinese Bulletin of Botany 58(6):926−34 doi: 10.11983/CBB23060 |
| [6] |
Wang Y, Ji S, Zang W, Wang N, Cao J, et al. 2019. Identification of phenolic compounds from a unique citrus species, finger lime (Citrus australasica) and their inhibition of LPS-induced NO-releasing in BV-2 cell line. Food and Chemical Toxicology 129:54−63 doi: 10.1016/j.fct.2019.04.006 |
| [7] |
Zhou Z. 2016. Australia: Finger Lemon Development Gradually Rising. China Fruit Industry Information 33(1):34−35 |
| [8] |
Xiao B, Zhang Q, Wang J, Feng J, Liu J, et al. 2020. Main diseases and pests on Citrus australasica in Hainan Province. Tropical Agricultural Science & Technology 43(4):20−24 doi: 10.16005/j.cnki.tast.2020.04.005 |
| [9] |
Huang Y, He J, Xu Y, Zheng W, Wang S. 2023. Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits. Nature Genetics 55(11):1964−75 doi: 10.1038/s41588-023-01516-6 |
| [10] |
Nakandala U, Furtado A, Masouleh AK, Smith MW, Williams DC, et al. 2024. The genome of Citrus australasica reveals disease resistance and other species specific genes. BMC Plant Biology 24:260 doi: 10.1186/s12870-024-04988-8 |
| [11] |
Ruberto G, Rocco C, Rapisarda P. 2000. Chemical composition of the peel essential oil of Microcitrus australasica var sanguinea (F.M. Bail) swing. Journal of Essential Oil Research 12(3):379−82 doi: 10.1080/10412905.2000.9699540 |
| [12] |
Delort E, Jaquier A, Decorzant E, Chapuis C, Casilli A, et al. 2015. Comparative analysis of three Australian finger lime (Citrus australasica) cultivars: identification of unique citrus chemotypes and new volatile molecules. Phytochemistry 109:111−24 doi: 10.1016/j.phytochem.2014.10.023 |
| [13] |
Xia Z, Zou M, Zhang S, Feng B, Wang W. 2014. AFSM sequencing approach: a simple and rapid method for genome-wide SNP and methylation site discovery and genetic mapping. Scientific Reports 4:7300 doi: 10.1038/srep07300 |
| [14] |
Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34(17):i884−i890 doi: 10.1093/bioinformatics/bty560 |
| [15] |
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 |
| [16] |
Amreen Nisa S, Vinu D, Krupakar P, Govindaraju K, Sharma D, et al. 2021. Jellyfish venom proteins and their pharmacological potentials: A review. International Journal of Biological Macromolecules 176:424−36 doi: 10.1016/j.ijbiomac.2021.02.074 |
| [17] |
Lee S, Nguyen LT, Hayes BJ, Ross EM. 2021. Prowler: a novel trimming algorithm for Oxford Nanopore sequence data. Bioinformatics 37(21):3936−37 doi: 10.1093/bioinformatics/btab630 |
| [18] |
Hu J, Fan J, Sun Z, Liu S. 2020. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36(7):2253−55 doi: 10.1093/bioinformatics/btz891 |
| [19] |
Alonge M, Lebeigle L, Kirsche M, Jenike K, Ou S, et al. 2022. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology 23(1):258 doi: 10.1186/s13059-022-02823-7 |
| [20] |
Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, et al. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Research 18:188−96 doi: 10.1101/gr.6743907 |
| [21] |
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, et al. 2020. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant 13(8):1194−202 doi: 10.1016/j.molp.2020.06.009 |
| [22] |
Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238 doi: 10.1186/s13059-019-1832-y |
| [23] |
Yang Z, Liu Z, Xu H, Li Y, Huang S, et al. 2023. ArecaceaeMDB: a comprehensive multi-omics database for Arecaceae breeding and functional genomics studies. Plant Biotechnology Journal 21:11−13 doi: 10.1111/pbi.13945 |
| [24] |
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 |
| [25] |
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, et al. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology 33(3):290−95 doi: 10.1038/nbt.3122 |
| [26] |
Seppey M, Manni M, Zdobnov EM. 2019. BUSCO: Assessing genome assembly and annotation completeness. Methods in Molecular Biology 1962:227−45 doi: 10.1007/978-1-4939-9173-0_14 |
| [27] |
Ou S, Jiang N. 2018. LTR_retriever: A highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiology 176(2):1410−22 doi: 10.1104/pp.17.01310 |
| [28] |
Su Z, Yang S, Li M, Chen Y, Wang S, et al. 2022. Complete genome sequences of one salt-tolerant and petroleum hydrocarbon-emulsifying Terribacillus saccharophilus strain ZY-1. Frontiers in Microbiology 13:932269 doi: 10.3389/fmicb.2022.932269 |
| [29] |
Cheng X, Gao C, Liu X, Xu D, Pan X, et al. 2022. Characterization of the wheat VQ protein family and expression of candidate genes associated with seed dormancy and germination. BMC Plant Biology 22(1):119 doi: 10.1186/s12870-022-03430-1 |
| [30] |
Zheng K, Pang L, Xue X, Gao P, Zhao H, et al. 2022. Genome-Wide Comprehensive Survey of the Subtilisin-Like Proteases Gene Family Associated With Rice Caryopsis Development. Frontiers in Plant Science 13:943184 doi: 10.3389/fpls.2022.943184 |
| [31] |
Li SF, She HB, Yang LL, Lan LN, Zhang XY, et al. 2022. Impact of LTR-Retrotransposons on Genome Structure, Evolution, and Function in Curcurbitaceae Species. International Journal of Molecular Sciences 23(17):10158 doi: 10.3390/ijms231710158 |
| [32] |
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 |
| [33] |
Sarker B, Khare N, Devignes MD, Aridhi S. 2022. Improving automatic GO annotation with semantic similarity. BMC Bioinformatics 23:433 doi: 10.1186/s12859-022-04958-7 |
| [34] |
Ramos I, Smith G, Ruf-Zamojski F, Martínez-Romero C, Fribourg M, et al. 2019. Innate immune response to influenza virus at single-cell resolution in human epithelial cells revealed paracrine induction of interferon Lambda 1. Journal of Virology 93(20):e00559-19 doi: 10.1128/JVI.00559-19 |
| [35] |
Tang H, Bai Y, Xiong L, Wei Y, Shen L, et al. 2021. Knockdown of CENPF inhibits the progression of lung adenocarcinoma mediated by ERβ2/5 pathway. Aging 13(2):2604−25 doi: 10.18632/aging.202303 |
| [36] |
Cantalapiedra CP, Hernández-Plaza A, Letunic I, Bork P, Huerta-Cepas J. 2021. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Molecular Biology and Evolution 38(12):5825−29 doi: 10.1093/molbev/msab293 |
| [37] |
Cheng Y, Yang P, Zhao LH, Priyadarshani SVGN., Zhou Q, et al. 2019. Studies on genome size estimation, chromosome number, gametophyte development and plant morphology of salt-tolerant halophyte Suaeda salsa. BMC Plant Biology 19:473 doi: 10.1186/s12870-019-2080-8 |
| [38] |
Aguilar-Pontes MV, Brandl J, McDonnell E, Strasser K, Nguyen TTM, et al. 2018. The gold-standard genome of Aspergillus niger NRRL 3 enables a detailed view of the diversity of sugar catabolism in fungi. Studies in Mycology 91:61−78 doi: 10.1016/j.simyco.2018.10.001 |
| [39] |
Jiang S, Xia Z, Zhang C, Zhao L, Bao Y, et al. 2022. Whole Genome Survey Analysis of Canna edulis Ker and Canna indica L. Molecular Plant Breeding 20(03):765−71 |
| [40] |
Ding S, Yuan X, Geng Y, Wang Y, Zhang H, et al. 2023. Genome survey analysis in Altingia Chinensis. Molecular Plant Breeding 00:1−11 |
| [41] |
Tang Q, Ma X, Mo C, Pan L, Wei R, et al. 2015. Genome survey analysis in Siraitia grosvenorii. Guangxi Plant 35(6):786−91 doi: 10.11931/guihaia.gxzw201404041 |
| [42] |
Wu Y, Xiao F, Xu H, Zhang T, Jiang X. 2014. Genome survey in Cinnamomum camphora L. Journal of Plant Genetic Resources 15(1):149−52 doi: 10.13430/j.cnki.jpgr.2014.01.020 |
| [43] |
Xu Q, Chen LL, Ruan X, Chen D, Zhu A, et al. 2013. The draft genome of sweet orange (Citrus sinensis). Nature Genetics 45:59−66 doi: 10.1038/ng.2472 |
| [44] |
Yu H, Zhang C, Lu C, Wang Y, Ge C, et al. 2024. The lemon genome and DNA methylome unveil epigenetic regulation of citric acid biosynthesis during fruit development. Horticulture Research 11(3):uhae005 doi: 10.1093/hr/uhae005 |
| [45] |
Sabir IA, Manzoor MA, Shah IH, Liu X, Jiu S, et al. 2022. Identification and comprehensive genome-wide analysis of glutathione s-transferase gene family in sweet cherry (Prunus avium) and their expression profiling reveals a likely role in anthocyanin accumulation. Frontiers in Plant Science 13:938800 doi: 10.3389/fpls.2022.938800 |
| [46] |
Tu M, Fang J, Zhao R, Liu X, Yin W, et al. 2022. CRISPR/Cas9-mediated mutagenesis of VvbZIP36 promotes anthocyanin accumulation in grapevine (Vitis vinifera). Horticulture Research 9:uhac022 doi: 10.1093/hr/uhac022 |
| [47] |
Li X, Li Y, Zhao M, Hu Y, Meng F, et al. 2021. Molecular and metabolic insights into anthocyanin biosynthesis for leaf color change in chokecherry (Padus virginiana). International Journal of Molecular Sciences 22(19):10697 doi: 10.3390/ijms221910697 |
| [48] |
Xia X, Gong R, Zhang C. 2022. Integrative analysis of transcriptome and metabolome reveals flavonoid biosynthesis regulation in Rhododendron pulchrum petals. BMC Plant Biology 22(1):401 doi: 10.1186/s12870-022-03762-y |
| [49] |
Lv YQ, Li D, Wu LY, Zhu YM, Ye Y, et al. 2022. Sugar signal mediates flavonoid biosynthesis in tea leaves. Horticulture Research 9:uhac049 doi: 10.1093/hr/uhac049 |
| [50] |
Bian XH, Li W, Niu CF, Wei W, Hu Y, et al. 2020. A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis. New Phytologist 225(1):268−83 doi: 10.1111/nph.16104 |
| [51] |
Zhang Q, Wang L, Liu Z, Zhao Z, Zhao J, et al. 2020. Transcriptome and metabolome profiling unveil the mechanisms of Ziziphus jujuba Mill. peel coloration. Food Chemistry 312:125903 doi: 10.1016/j.foodchem.2019.125903 |
| [52] |
Wang J, Li G, Li C, Zhang C, Cui L, et al. 2021. NF-Y plays essential roles in flavonoid biosynthesis by modulating histone modifications in tomato. New Phytologist 229(6):3237−52 doi: 10.1111/nph.17112 |
| [53] |
Sun J, Zan J, Zang X. 2022. Research of fluridone's effects on growth and pigment accumulation of Haematococcus pluvialis based on transcriptome sequencing. International Journal of Molecular Sciences 23(6):3122 doi: 10.3390/ijms23063122 |
| [54] |
Ding C, Shao Z, Yan Y, Zhang G, Zeng D, et al. 2024. Carotenoid isomerase regulates rice tillering and grain productivity by its biosynthesis pathway. Journal of Integrative Plant Biology 66(2):172−75 doi: 10.1111/jipb.13617 |
| [55] |
Song J, Sun B, Chen C, Ning Z, Zhang S, et al. 2023. An R-R-type MYB transcription factor promotes non-climacteric pepper fruit carotenoid pigment biosynthesis. The Plant Journal 115(3):724−41 doi: 10.1111/tpj.16257 |
| [56] |
Yan H, Sun M, Zhang Z, Jin Y, Zhang A, et al. 2023. Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet. Nature Genetics 55:507−18 doi: 10.1038/s41588-023-01302-4 |
| [57] |
Zhang HB. 2024. Gene-based Breeding (GBB), a novel discipline of biological science and technology for plant and animal breeding. Tropical Plants 3:e005 doi: 10.48130/tp-0024-0005 |
| [58] |
Zhang P. 2022. Tropical crops enter the era of genome editing. Tropical Plants 1:10 doi: 10.48130/tp-2022-0010 |
| [59] |
Zou M, Xia Z. 2022. Hyper-seq: A novel, effective, and flexible marker-assisted selection and genotyping approach. Innovation 3(4):100254 doi: 10.1016/j.xinn.2022.100254 |
| [60] |
He S, Dong W, Chen J, Zhang J, Lin W, et al. 2024. DataColor: unveiling biological data relationships through distinctive color mapping. Horticulture Research 11:uhad273 doi: 10.1093/hr/uhad273 |