Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Article CAS PubMed Google Scholar
Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. https://doi.org/10.1093/nar/25.17.3389
Article CAS PubMed PubMed Central Google Scholar
Andolfo G, Sánchez CS, Cañizares J, Pico MB, Ercolano MR (2021) Large-scale gene gains and losses molded the NLR defense arsenal during the Cucurbita evolution. Planta 254:1–14. https://doi.org/10.1007/s00425-021-03717-x
Angel VDD, Hjerde E, Sterck L, Capella-Gutierrez S, Notredame C, Pettersson OV, Amselem J, Bouri L, Bocs S, Klopp C, Gibrat J-F, Vlasova A, Leskosek BL, Soler L, Binzer-Panchal M, Lantz H (2018) Ten steps to get started in genome assembly and annotation. F1000Research. https://doi.org/10.12688/f1000research.13598.1
Apablaza H, Solís M, Conejera D, Fonseca A, Cid J, Tarifeño-Saldivia E, Valenzuela S, Emhart V, Fernández M (2022) bHLH transcription factors undergo alternative splicing during cold acclimation in a Eucalyptus hybrid. Plant Mol Biol Rep 40:310–326. https://doi.org/10.1007/s11105-021-01313-7
Bailey TL, Johnson J, Grant CE, Noble WS (2015) The MEME suite. Nucleic Acids Res 43:W39–W49. https://doi.org/10.1093/nar/gkv416
Article CAS PubMed PubMed Central Google Scholar
Bayer PE, Golicz AA, Scheben A, Batley J, Edwards D (2020) Plant pan-genomes are the new reference. Nature Plants 6:914–920. https://doi.org/10.1038/s41477-020-0733-0
Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E (2015) The Arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome. Genesis 53:474–485. https://doi.org/10.1002/dvg.22877
Article CAS PubMed PubMed Central Google Scholar
Birney E, Clamp M, Durbin R (2004) GeneWise and Genomewise. Genome Res 14:988–995. https://doi.org/10.1101/gr.1865504
Article CAS PubMed PubMed Central Google Scholar
Bocsanczy AM, Huguet-Tapia JC, Norman DJ (2017) Comparative genomics of Ralstonia solanacearum identifies candidate genes associated with cool virulence. Front Plant Sci 8:1565–1565. https://doi.org/10.3389/fpls.2017.01565
Article PubMed PubMed Central Google Scholar
Buljan M, Bateman A (2009) The evolution of protein domain families. Biochem Soc Trans 37:751–755. https://doi.org/10.1042/BST0370751
Article CAS PubMed Google Scholar
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinform 10:1–9. https://doi.org/10.1186/1471-2105-10-421
Cao Y-L, Li Y-l, Fan Y-F, Li Z, Yoshida K, Wang J-Y, Ma X-K, Wang N, Mitsuda N, Kotake T, Ishimizu T, Tsai K-C, Niu S-C, Zhang D, Sun W-H, Luo Q, Zhao J-H, Yin Y, Zhang B, Wang J-Y, Qin K, An W, He J, Dai G-L, Wang Y-J, Shi Z-G, Jiao E-N, Wu P-J, Liu X, Liu B, Liao X-Y, Jiang Y-T, Yu X, Hao Y, Xu X-Y, Zou S-Q, Li M-H, Hsiao Y-Y, Lin Y-F, Liang C-K, Chen Y-Y, Wu W-L, Lu H-C, Lan S-R, Wang Z-W, Zhao X, Zhong W-Y, Yeh C-M, Tsai W-C, Van de Peer Y, Liu Z-J (2021) Wolfberry genomes and the evolution of Lycium (Solanaceae). Commun Biol. https://doi.org/10.1038/s42003-021-02152-8
Article PubMed PubMed Central Google Scholar
Chen Z, Vining KJ, Qi X, Yu X, Zheng Y, Liu Z, Fang H, Li L, Bai Y, Liang C, Li W, Lange BM (2021) Genome-wide analysis of terpene synthase gene family in Mentha longifolia and catalytic activity analysis of a single terpene synthase. Genes 12:518. https://doi.org/10.3390/genes12040518
Article CAS PubMed PubMed Central Google Scholar
Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean Irina M, Austine-Orimoloye O, Azov Andrey G, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, Brooks L, Charkhchi M, Cummins C, Da Rin FL, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Martinez Jose G, Guijarro-Clarke C, Gymer A, Hardy M, Hollis Z, Hourlier T, Hunt T, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Marugán JC, Mohanan S, Mushtaq A, Naven M, Ogeh Denye N, Parker A, Parton A, Perry M, Piližota I, Prosovetskaia I, Sakthivel Manoj P, Salam Ahamed Imran A, Schmitt Bianca M, Schuilenburg H, Sheppard D, Pérez-Silva José G, Stark W, Steed E, Sutinen K, Sukumaran R, Sumathipala D, Suner M-M, Szpak M, Thormann A, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh Thomas A, Walts B, Willhoft N, Winterbottom A, Wass E, Chakiachvili M, Flint B, Frankish A, Giorgetti S, Haggerty L, Hunt Sarah E, IIsley Garth R, Loveland Jane E, Martin Fergal J, Moore B, Mudge Jonathan M, Muffato M, Perry E, Ruffier M, Tate J, Thybert D, Trevanion Stephen J, Dyer S, Harrison Peter W, Howe Kevin L, Yates Andrew D, Zerbino Daniel R, Flicek P, (2021) Ensembl 2022. Nucleic Acids Res 50:D988–D995. https://doi.org/10.1093/nar/gkab1049
Article CAS PubMed Central Google Scholar
de Boissier P, Habermann BH (2020) A practical guide to orthology resources. Evolutionary Biology—A Transdisciplinary Approach. Springer, Cham, pp 41–77
Delaux PM, Varala K, Edger PP, Coruzzi GM, Pires JC, Ané JM (2014) Comparative phylogenomics uncovers the impact of symbiotic associations on host genome evolution. PLoS Genet. https://doi.org/10.1371/journal.pgen.1004487
Article PubMed PubMed Central Google Scholar
Dohmen E, Kremer LPM, Bornberg-Bauer E, Kemena C (2016) DOGMA: Domain-based transcriptome and proteome quality assessment. Bioinformatics 32:2577–2581. https://doi.org/10.1093/bioinformatics/btw231
Article CAS PubMed Google Scholar
Dong S, Liu M, Liu Y, Chen F, Yang T, Chen L, Zhang X, Guo X, Fang D, Li L, Deng T, Yao Z, Lang X, Gong Y, Wu E, Wang Y, Shen Y, Gong X, Liu H, Zhang S (2021) The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids. Horticulture Res. https://doi.org/10.1038/s41438-021-00471-9
Eddy SR (1998) Profile hidden markov models. Bioinformatics 14:755–763. https://doi.org/10.1093/bioinformatics/14.9.755
Article CAS PubMed Google Scholar
Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7:1002195–1002195. https://doi.org/10.1371/journal.pcbi.1002195
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Article CAS PubMed PubMed Central Google Scholar
El-Metwally S, Hamza T, Zakaria M, Helmy M (2013) Next-generation sequence assembly: four stages of data processing and computational challenges. PLoS Comput Biol 9:e1003345–e1003345. https://doi.org/10.1371/journal.pcbi.1003345
Article CAS PubMed PubMed Central Google Scholar
Emms DM, Kelly S (2019) OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20:1–14. https://doi.org/10.1186/S13059-019-1832-Y
Favre P, Bapaume L, Bossolini E, Delorenzi M, Falquet L, Reinhardt D (2014) A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants. BMC Plant Biol 14:333–333. https://doi.org/10.1186/s12870-014-0333-0
Article CAS PubMed PubMed Central Google Scholar
Feng S, Liu Z, Cheng J, Li Z, Tian L, Liu M, Yang T, Liu Y, Liu Y, Dai H, Yang Z, Zhang Q, Wang G, Zhang J, Jiang H, Wei A (2021) Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. Horticulture Res. https://doi.org/10.1038/s41438-021-00665-1
Fernandez CGT, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D (2022a) Pangenomes as a resource to accelerate breeding of under-utilised crop species. Int J Mol Sci 23:2671. https://doi.org/10.3390/ijms23052671
Fernandez CGT, Nestor BJ, Danilevicz MF, Marsh JI, Petereit J, Bayer PE, Batley J, Edwards D (2022b) Expanding gene-editing potential in crop improvement with pangenomes. Int J Mol Sci. https://doi.org/10.3390/IJMS23042276
Article PubMed PubMed Central Google Scholar
Fernandez-Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Mittelsten Scheid O, Theißen G, Schranz ME, Leubner-Metzger G, Rensing SA (2021) Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. Plant J 106:275–293. https://doi.org/10.1111/tpj.15161
Article CAS PubMed PubMed Central Google Scholar
Fitch WM (1970) Distinguishing homologous from analogous proteins. Syst Zool 19:99–99. https://doi.org/10.2307/2412448
Article CAS PubMed Google Scholar
Forslund K, Pekkari I, Sonnhammer ELL (2011) Domain architecture conservation in orthologs. BMC Bioinform 12:326–326. https://doi.org/10.1186/1471-2105-12-326
Fu L, Niu B, Zhu Z, Wu S, Li W (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150–3152. https://doi.org/10.1093/bioinformatics/bts565
Comments (0)