A high-quality chromosome-level genome assembly of Ficus hirta.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
22 May 2024
22 May 2024
Historique:
received:
30
11
2023
accepted:
14
05
2024
medline:
23
5
2024
pubmed:
23
5
2024
entrez:
22
5
2024
Statut:
epublish
Résumé
Ficus species (Moraceae) play pivotal roles in tropical and subtropical ecosystems. Thriving across diverse habitats, from rainforests to deserts, they harbor a multitude of mutualistic and antagonistic interactions with insects, nematodes, and pathogens. Despite their ecological significance, knowledge about the genomic background of Ficus remains limited. In this study, we report a chromosome-level reference genome of F. hirta, with a total size of 297.27 Mb, containing 28,625 protein-coding genes and 44.67% repeat sequences. These findings illuminate the genetic basis of Ficus responses to environmental challenges, offering valuable genomic resources for understanding genome size, adaptive evolution, and co-evolution with natural enemies and mutualists within the genus.
Identifiants
pubmed: 38778063
doi: 10.1038/s41597-024-03376-z
pii: 10.1038/s41597-024-03376-z
doi:
Types de publication
Dataset
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
526Informations de copyright
© 2024. The Author(s).
Références
Harrison, R. D. Figs and the diversity of tropical rainforests. Bioscience 55, 1053–1064 (2005).
doi: 10.1641/0006-3568(2005)055[1053:FATDOT]2.0.CO;2
Pierantoni, M. et al. Mineral deposits in Ficus leaves: morphologies and locations in relation to function. Plant Physiol. 176, 1751–1763 (2018).
pubmed: 29242376
doi: 10.1104/pp.17.01516
Shanahan, M., So, S., Compton, S. G. & Corlett, R. Fig-eating by vertebrate frugivores: a global review. Biol. Rev. 76, 529–572 (2001).
pubmed: 11762492
doi: 10.1017/S1464793101005760
Cottee-Jones, H. E. W., Bajpai, O., Chaudhary, L. B. & Whittaker, R. J. The importance of Ficus (Moraceae) trees for tropical forest restoration. Biotropica 48, 413–419 (2016).
doi: 10.1111/btp.12304
Datwyler, S. L. & Weiblen, G. D. On the origin of the fig: phylogenetic relationships of Moraceae from ndhF sequences. Am. J. Bot. 91, 767–777 (2004).
pubmed: 21653431
doi: 10.3732/ajb.91.5.767
Compton, S. G. et al. Ancient fig wasps indicate at least 34 Myr of stasis in their mutualism with fig trees. Biol. lett. 6, 838–842 (2010).
pubmed: 20554563
pmcid: 3001375
doi: 10.1098/rsbl.2010.0389
Gardner, E. M. et al. Echoes of ancient introgression punctuate stable genomic lineages in the evolution of figs. Proc. Natl. Acad. Sci. USA 120, e2222035120 (2023).
pubmed: 37399402
pmcid: 10334730
doi: 10.1073/pnas.2222035120
Zhang, Q., Onstein, R. E., Little, S. A. & Sauquet, H. Estimating divergence times and ancestral breeding systems in Ficus and Moraceae. Ann. Bot. 123, 191–204 (2019).
pubmed: 30202847
doi: 10.1093/aob/mcy159
Condit, I. J. Cytological studies in the genus Ficus. III. Chromosome numbers in sixty-two species. Madrono. 17, 153–155 (1964).
Hans, A. S. Cytomorphology of arborescent Moraceae. J. Arnold. Arbor. 53, 216–225 (1972).
doi: 10.5962/p.185782
Basset, Y. & Novotny, V. Species richness of insect herbivore communities on Ficus in Papua New Guinea. Biol. J. Linn. Soc. Lond. 67, 477–499 (1999).
doi: 10.1111/j.1095-8312.1999.tb01943.x
Elbeaino, T., Digiaro, M. & Martelli, G. P. Complete sequence of fig fleck-associated virus, a novel member of the family Tymoviridae. Virus. Res. 161, 198–202 (2011).
pubmed: 21840352
doi: 10.1016/j.virusres.2011.07.022
Hosomi, A., Miwa, Y., Furukawa, M. & Kawaradani, M. Growth of fig varieties resistant to ceratocystis canker following infection with Ceratocystis fimbriata. J. Jpn. Soc. Hortic.Sci. 81, 159–165 (2012).
doi: 10.2503/jjshs1.81.159
Zhao, C. et al. Ficophagus giblindavisi n. sp (Nematoda: Aphelenchoididae), an associate of Ficus variegata in China. Nematology. 24, 901–914 (2022).
doi: 10.1163/15685411-bja10178
Borges, R. M., Bessière, J. M. & Ranganathan, Y. Diel variation in fig volatiles across syconium development: making sense of scents. J. Chem. Ecol. 39, 630–642 (2013).
pubmed: 23609162
doi: 10.1007/s10886-013-0280-5
Villard, C., Larbat, R., Munakata, R. & Hehn, A. Defence mechanisms of Ficus: pyramiding strategies to cope with pests and pathogens. Planta 249, 617–633 (2019).
pubmed: 30689053
doi: 10.1007/s00425-019-03098-2
Sirisha, N., Sreenivasulu, M., Sangeeta, K. & Chetty, C. M. Antioxidant properties of Ficus species-a review. Int. J. Pharmtech. Res. 2, 2174–2182 (2010).
Volf, M. et al. Community structure of insect herbivores is driven by conservatism, escalation and divergence of defensive traits in Ficus. Ecol. Lett. 21, 83–92 (2018).
pubmed: 29143434
doi: 10.1111/ele.12875
Porebski, S., Bailey, L. G. & Baum, B. R. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components. Plant Mol. Biol. Rep. 15, 8–15 (1997).
doi: 10.1007/BF02772108
Xie, T. et al. De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. Mol. Plant 8, 489–492 (2015).
pubmed: 25667002
doi: 10.1016/j.molp.2014.12.015
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
pubmed: 30423086
pmcid: 6129281
doi: 10.1093/bioinformatics/bty560
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
pubmed: 21217122
pmcid: 3051319
doi: 10.1093/bioinformatics/btr011
Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202–2204 (2017).
pubmed: 28369201
pmcid: 5870704
doi: 10.1093/bioinformatics/btx153
Feng, X., Cheng, H., Portik, D. & Li, H. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nat. Methods 19, 671–674 (2022).
pubmed: 35534630
pmcid: 9343089
doi: 10.1038/s41592-022-01478-3
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome biol. 16, 259 (2015).
pubmed: 26619908
pmcid: 4665391
doi: 10.1186/s13059-015-0831-x
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
pubmed: 27467249
pmcid: 5846465
doi: 10.1016/j.cels.2016.07.002
Dudchenko, O. et al. de novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).
pubmed: 28336562
pmcid: 5635820
doi: 10.1126/science.aal3327
Usai, G. et al. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. Plant J. 102, 600–614 (2020).
pubmed: 31808196
doi: 10.1111/tpj.14635
Zhang, X. et al. Genomes of the banyan tree and pollinator wasp provide insights into fig-wasp coevolution. Cell 183, 875–889 (2020).
pubmed: 33035453
doi: 10.1016/j.cell.2020.09.043
Chakraborty, A., Mahajan, S., Bisht, M. S. & Sharma, V. K. Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity. Iscience 25, 105100 (2022).
pubmed: 36164650
pmcid: 9508489
doi: 10.1016/j.isci.2022.105100
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. USA 117, 9451–9457 (2020).
pubmed: 32300014
pmcid: 7196820
doi: 10.1073/pnas.1921046117
Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005).
pubmed: 16093699
doi: 10.1159/000084979
Tarailo-Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 24, 4.10.11–14.10.14 (2009).
Chan, P. P., Lin, B. Y., Mak, A. J. & Lowe, T. M. tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 49, 9077–9096 (2021).
pubmed: 34417604
pmcid: 8450103
doi: 10.1093/nar/gkab688
Cui, X. et al. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. Bioinformatics 32, i332–i340 (2016).
pubmed: 27307635
pmcid: 4908355
doi: 10.1093/bioinformatics/btw271
Gardner, P. P. et al. Rfam: updates to the RNA families database. Nucleic Acids Res. 37, D136–D140 (2009).
pubmed: 18953034
doi: 10.1093/nar/gkn766
Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Genome Res. 14, 988–995 (2004).
pubmed: 15123596
pmcid: 479130
doi: 10.1101/gr.1865504
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. methods 12, 357–360 (2015).
pubmed: 25751142
pmcid: 4655817
doi: 10.1038/nmeth.3317
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).
pubmed: 16845043
pmcid: 1538822
doi: 10.1093/nar/gkl200
Wheeler, D. L. et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 35, D5–D12 (2007).
pubmed: 17170002
doi: 10.1093/nar/gkl1031
Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999. Nucleic Acids Res. 27, 49–54 (1999).
pubmed: 9847139
pmcid: 148094
doi: 10.1093/nar/27.1.49
Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinform. 4, 41 (2003).
doi: 10.1186/1471-2105-4-41
Hernandez-Plaza, A. et al. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Res. 51, D389–D394 (2023).
pubmed: 36399505
doi: 10.1093/nar/gkac1022
Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014).
pubmed: 24288371
doi: 10.1093/nar/gkt1223
Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000).
pubmed: 10802651
pmcid: 3037419
doi: 10.1038/75556
Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27–30 (2000).
pubmed: 10592173
pmcid: 102409
doi: 10.1093/nar/28.1.27
NGDC Genome Sequence Archive https://ngdc.cncb.ac.cn/gsa/browse/CRA012347 (2024).
NCBI GenBank https://identifiers.org/ncbi/insdc.gca:GCA_038430175.1 (2024).
Huang, W. C. A high-quality chromosome-level genome assembly of Ficus hirta. figshare https://doi.org/10.6084/m9.figshare.25246813 (2024).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
pubmed: 19451168
pmcid: 2705234
doi: 10.1093/bioinformatics/btp324
Ou, S., Chen, J. & Jiang, N. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 46, e126–e126 (2018).
pubmed: 30107434
pmcid: 6265445
Simão, F. A. et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
pubmed: 26059717
doi: 10.1093/bioinformatics/btv351