| [1] |
Zhang X, Wang G, Zhang S, Chen S, Wang Y, et al. 2020. Genomes of the banyan tree and pollinator wasp provide insights into fig-wasp coevolution. Cell 183:875−889.e17 doi: 10.1016/j.cell.2020.09.043 |
| [2] |
Usai G, Mascagni F, Giordani T, Vangelisti A, Bosi E, et al. 2020. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. The Plant Journal 102:600−14 doi: 10.1111/tpj.14635 |
| [3] |
Yao J, Wang Z, Wang R, Wang Y, Xu J, et al. 2021. Anti-proliferative and anti-inflammatory prenylated isoflavones and coumaronochromones from the fruits of Ficus altissima. Bioorganic Chemistry 113:104996 doi: 10.1016/j.bioorg.2021.104996 |
| [4] |
Zeng J, Yu H. 2022. Integrated metabolomic and transcriptomic analyses to understand the effects of hydrogen water on the roots of Ficus hirta Vahl. Plants 11:602 doi: 10.3390/plants11050602 |
| [5] |
Chakraborty A, Mahajan S, Bisht MS, Sharma VK. 2022. Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity. iScience 25:105100 doi: 10.1016/j.isci.2022.105100 |
| [6] |
Yamauchi T, Tanaka A, Inahashi H, Nishizawa NK, Tsutsumi N, et al. 2019. Fine control of aerenchyma and lateral root development through AUX/IAA- and ARF-dependent auxin signaling. Proceedings of the National Academy of Sciences of the United States of America 116:20770−75 doi: 10.1073/pnas.1907181116 |
| [7] |
Ung KL, Winkler M, Schulz L, Kolb M, Janacek DP, et al. 2022. Structures and mechanism of the plant PIN-FORMED auxin transporter. Nature 609:605−10 doi: 10.1038/s41586-022-04883-y |
| [8] |
Su N, Zhu A, Tao X, Ding ZJ, Chang S, et al. 2022. Structures and mechanisms of the Arabidopsis auxin transporter PIN3. Nature 609:616−21 doi: 10.1038/s41586-022-05142-w |
| [9] |
Larbat R, Kellner S, Specker S, Hehn A, Gontier E, et al. 2007. Molecular cloning and functional characterization of psoralen synthase, the first committed monooxygenase of furanocoumarin biosynthesis. Journal of Biological Chemistry 282:542−54 doi: 10.1074/jbc.M604762200 |
| [10] |
Jamalis J, Yusof FSM, Chander S, Wahab RA, Bhagwat DP, et al. 2020. Psoralen derivatives: recent advances of synthetic strategy and pharmacological properties. Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry 19:222−39 doi: 10.2174/1871523018666190625170802 |
| [11] |
De Coster W, Rademakers R. 2023. NanoPack2: population-scale evaluation of long-read sequencing data. Bioinformatics 39:btad311 doi: 10.1093/bioinformatics/btad311 |
| [12] |
Chen S, Zhou Y, Chen Y, Gu J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884−i890 doi: 10.1093/bioinformatics/bty560 |
| [13] |
Hu J, Wang Z, Sun Z, Hu B, Ayoola AO, et al. 2024. NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads. Genome Biology 25:107 doi: 10.1186/s13059-024-03252-4 |
| [14] |
Hu J, Fan J, Sun Z, Liu S. 2020. NextPolish: a fast and efficient genome polishing tool for long-read assembly. Bioinformatics 36:2253−55 doi: 10.1093/bioinformatics/btz891 |
| [15] |
Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, et al. 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356:92−95 doi: 10.1126/science.aal3327 |
| [16] |
Robinson JT, Turner D, Durand NC, Thorvaldsdóttir H, Mesirov JP, et al. 2018. Juicebox. js provides a cloud-based visualization system for Hi-C data. Cell Systems 6:256−258.e1 doi: 10.1016/j.cels.2018.01.001 |
| [17] |
Manni M, Berkeley MR, Seppey M, Zdobnov EM. 2021. BUSCO: assessing genomic data quality and beyond. Current Protocols 1:e323 doi: 10.1002/cpz1.323 |
| [18] |
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology 37:907−15 doi: 10.1038/s41587-019-0201-4 |
| [19] |
Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923−30 doi: 10.1093/bioinformatics/btt656 |
| [20] |
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 |
| [21] |
Tarailo-Graovac M, Chen N. 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics 25:4.10.1−4.10.14 doi: 10.1002/0471250953.bi0410s25 |
| [22] |
Bao Z, Eddy SR. 2002. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Research 12:1269−76 doi: 10.1101/gr.88502 |
| [23] |
Haas BJ, Salzberg SL, Zhu W, Pertea M, Allen JE, et al. 2008. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biology 9:R7 doi: 10.1186/gb-2008-9-1-r7 |
| [24] |
Stanke M, Diekhans M, Baertsch R, Haussler D. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics 24:637−44 doi: 10.1093/bioinformatics/btn013 |
| [25] |
Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, et al. 2017. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Molecular Biology and Evolution 34:2115−22 doi: 10.1093/molbev/msx148 |
| [26] |
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Research 19:1639−45 doi: 10.1101/gr.092759.109 |
| [27] |
Emms DM, Kelly S. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biology 20:238 doi: 10.1186/s13059-019-1832-y |
| [28] |
Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C. 2014. jvenn: an interactive Venn diagram viewer. BMC Bioinformatics 15:293 doi: 10.1186/1471-2105-15-293 |
| [29] |
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. 2019. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453−55 doi: 10.1093/bioinformatics/btz305 |
| [30] |
Wang Y, Dong W, Liang Y, Lin W, Chen J, et al. 2024. PhyloForge: unifying micro- and macroevolution with comprehensive genomic signals. Molecular Ecology Resources 25:e14050 doi: 10.1111/1755-0998.14050 |
| [31] |
Kumar S, Suleski M, Craig JM, Kasprowicz AE, Sanderford M, et al. 2022. TimeTree 5: an expanded resource for species divergence times. Molecular Biology and Evolution 39:msac174 doi: 10.1093/molbev/msac174 |
| [32] |
Puttick MN. 2019. MCMCtreeR: functions to prepare MCMCtree analyses and visualize posterior ages on trees. Bioinformatics 35:5321−22 doi: 10.1093/bioinformatics/btz554 |
| [33] |
Mendes FK, Vanderpool D, Fulton B, Hahn MW. 2021. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36:5516−18 doi: 10.1093/bioinformatics/btaa1022 |
| [34] |
Letunic I, Bork P. 2024. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Research 52:W78−W82 doi: 10.1093/nar/gkae268 |
| [35] |
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:e49 doi: 10.1093/nar/gkr1293 |
| [36] |
Tang H, Krishnakumar V, Zeng X, Xu Z, Taranto A, et al. 2024. JCVI: a versatile toolkit for comparative genomics analysis. iMeta 3:e211 doi: 10.1002/imt2.211 |
| [37] |
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, et al. 2021. Pfam: the protein families database in 2021. Nucleic Acids Research 49:D412−D419 doi: 10.1093/nar/gkaa913 |
| [38] |
Al-Fatlawi A, Menzel M, Schroeder M. 2023. Is protein BLAST a thing of the past? Nature Communications 14:8195 doi: 10.1038/s41467-023-44082-5 |
| [39] |
Bailey TL, Johnson J, Grant CE, Noble WS. 2015. The MEME suite. Nucleic Acids Research 43:W39−W49 doi: 10.1093/nar/gkv416 |
| [40] |
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, et al. 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research 30:325−27 doi: 10.1093/nar/30.1.325 |
| [41] |
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 13:1194−202 doi: 10.1016/j.molp.2020.06.009 |
| [42] |
Rhie A, Walenz BP, Koren S, Phillippy AM. 2020. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology 21:245 doi: 10.1186/s13059-020-02134-9 |
| [43] |
Tian Y, Liang T, Peng H, Wang Q, Luo X, et al. 2024. Chromosome-scale genome assembly provides insights into the evolution and color synthesis of finger lemon (Citrus australasica). Tropical Plants 3:e015 doi: 10.48130/tp-0024-0021 |
| [44] |
Liao Z, Zhang T, Lei W, Wang Y, Yu J, et al. 2024. A telomere-to-telomere reference genome of ficus (Ficus hispida) provides new insights into sex determination. Horticulture Research 11:uhad257 doi: 10.1093/hr/uhad257 |
| [45] |
Li BJ, Bao RX, Shi YN, Grierson D, Chen KS. 2024. Auxin response factors: important keys for understanding regulatory mechanisms of fleshy fruit development and ripening. Horticulture Research 11:uhae209 doi: 10.1093/hr/uhae209 |
| [46] |
Xuan Y, Liu S, Xie L, Pan J. 2023. Establishment of Amaranthus spp. calluses and cell suspension culture, and the effect of plant growth regulators on total flavonoid content. Tropical Plants 2:15 doi: 10.48130/TP-2023-0015 |
| [47] |
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 |
| [48] |
Lv M, Zhang L, Wang Y, Ma L, Yang Y, et al. 2024. Floral volatile benzenoids/phenylpropanoids: biosynthetic pathway, regulation and ecological value. Horticulture Research 11:uhae220 doi: 10.1093/hr/uhae220 |