Darwin, C. On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life. (1859).
Wallace, A. R. The Malay Archipelago: The Land of the Orang-utan and the Bird of Paradise; a Narrative of Travel, with Studies of Man and Nature (Courier Corporation, 1962).
Mayr, E. Systematics and the Origin of Species from the Viewpoint of a Zoologist (Columbia Uni. Press, 1942).
Emerson, B. C. Speciation on islands: what are we learning? Biol. J. Linn. Soc. Lond. 95, 47–52 (2008).
Lomolino, M. V., Riddle, B. R., Whittaker, R. J., Brown, J. H. & Lomolino, M. V. Biogeography (Sunderland, Mass: Sinauer Associates, 2017).
Baeckens, S. & Van Damme, R. The island syndrome. Curr. Biol. 30, R338–R339 (2020).
Google Scholar
Burns, K. C. Evolution in Isolation: The Search for an Island Syndrome in Plants (Cambridge University Press, 2019).
Blaschke, J. D. & Sanders, R. W. Preliminary insights into the phylogeny and speciation of scalesia (asteraceae), galápagos islands. J. Bot. Res. Inst. Tex. 3, 177–191 (2009).
Fernández-Mazuecos, M. et al. The radiation of Darwin’s giant daisies in the Galápagos Islands. Curr. Biol. 30, 4989–4998.e7 (2020).
Crawford, D. J. et al. Genetic diversity in Asteraceae endemic to oceanic islands: Baker’s Law and polyploidy. Syst. Evol. Biogeogr. Compos 139, 151 (2009).
Eliasson, U. Studies in Galápagos plants. XIV. The genus Scalesia Arn. Opera Bot. 36, 1–117 (1974).
Itow, S. Phytogeography and ecology of Scalesia (compositae) endemic to the Galapagos islands! Pac. Sci. 49, 17–30 (1995).
Stöcklin, J. Darwin and the plants of the Galápagos-Islands. Bauhinia 21, 33–48 (2009).
Ono, M. Chromosome number of Scalesia (Compositae), an endemic genus of the Galapagos Islands. J. Jpn. Bot. 42, 353–360 (1967).
Eliasson, U. Studies in Galapagos plants. XIV. The genus Scalesia Arn. Opera Bot. 36, 1–117 (1974).
Meudt, H. M. et al. Polyploidy on islands: its emergence and importance for diversification. Front. Plant Sci. 12, 637214 (2021).
Google Scholar
Spring, O., Heil, N. & Vogler, B. Sesquiterpene lactones and flavanones in Scalesia species. Phytochemistry 46, 1369–1373 (1997).
Google Scholar
Schilling, E. E., Panero, J. L. & Eliasson, U. H. Evidence from chloroplast DNA restriction site analysis on the relationships of Scalesia (Asteraceae: Heliantheae). Am. J. Bot. 81, 248–254 (1994).
Peona, V., Weissensteiner, M. H. & Suh, A. How complete are ‘complete’ genome assemblies?-An avian perspective. Mol. Ecol. Resour. 18, 1188–1195 (2018).
Google Scholar
Badouin, H. et al. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature 546, 148–152 (2017).
Google Scholar
Reyes-Chin-Wo, S. et al. Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. Nat. Commun. 8, 14953 (2017).
Google Scholar
Bellinger, M. R., Datlof, E., Selph, K. E., Gallaher, T. J. & Knope, M. L. A genome for Bidens hawaiensis: a member of a hexaploid Hawaiian plant adaptive radiation. J. Hered. https://doi.org/10.1093/jhered/esab077 (2022).
Edger, P. P., McKain, M. R., Bird, K. A. & VanBuren, R. Subgenome assignment in allopolyploids: challenges and future directions. Curr. Opin. Plant Biol. 42, 76–80 (2018).
Google Scholar
Session, A. M. et al. Genome evolution in the allotetraploid frog Xenopus laevis. Nature 538, 336–343 (2016).
Google Scholar
Mitros, T. et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat. Commun. 11, 5442 (2020).
Google Scholar
Funk, V. A. Systematics, Evolution, and Biogeography of Compositae (International Association for Plant Taxonomy, 2009).
Julca, I. et al. Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.). BMC Biol 18, 148 (2020).
Google Scholar
te Beest, M. et al. The more the better? The role of polyploidy in facilitating plant invasions. Ann Bot. 109, 19–45 (2012).
Mandel, J. R. et al. A fully resolved backbone phylogeny reveals numerous dispersals and explosive diversifications throughout the history of Asteraceae. Proc. Natl Acad. Sci. USA 116, 14083–14088 (2019).
Google Scholar
Whittaker, R. J., School of Geography Robert J Whittaker & Fernandez-Palacios, J. M. Island Biogeography: Ecology, Evolution, and Conservation (OUP Oxford, 2007).
Diop, S. I. et al. A pseudomolecule-scale genome assembly of the liverwort Marchantia polymorpha. Plant J. 101, 1378–1396 (2020).
Google Scholar
Li, F.-W. et al. Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts. Nat. Plants 6, 259–272 (2020).
Google Scholar
Lang, D. et al. ThePhyscomitrella patenschromosome-scale assembly reveals moss genome structure and evolution. Plant J. 93, 515–533 (2018).
Google Scholar
Bird, K. A., VanBuren, R., Puzey, J. R. & Edger, P. P. The causes and consequences of subgenome dominance in hybrids and recent polyploids. N. Phytol. 220, 87–93 (2018).
Freeling, M., Scanlon, M. J. & Fowler, J. E. Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences. Curr. Opin. Genet. Dev. 35, 110–118 (2015).
Google Scholar
Wolfe, K. H. Yesterday’s polyploids and the mystery of diploidization. Nat. Rev. Genet. 2, 333–341 (2001).
Google Scholar
Bird, K. A. et al. Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. N. Phytol. 230, 354–371 (2021).
Google Scholar
Alger, E. I. & Edger, P. P. One subgenome to rule them all: underlying mechanisms of subgenome dominance. Curr. Opin. Plant Biol. 54, 108–113 (2020).
Google Scholar
Renny-Byfield, S., Gong, L., Gallagher, J. P. & Wendel, J. F. Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution. Mol. Biol. Evol. 32, 1063–1071 (2015).
Google Scholar
Douglas, G. M. et al. Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris. Proc. Natl Acad. Sci. USA 112, 2806–2811 (2015).
Google Scholar
Barrier, M., Baldwin, B. G., Robichaux, R. H. & Purugganan, M. D. Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications. Mol. Biol. Evol. 16, 1105–1113 (1999).
Google Scholar
Catchen, J. M., Conery, J. S. & Postlethwait, J. H. Automated identification of conserved synteny after whole-genome duplication. Genome Res. 19, 1497–1505 (2009).
Google Scholar
Őszi, E. et al. E2FB interacts with RETINOBLASTOMA RELATED and regulates cell proliferation during leaf development. Plant Physiol. 182, 518–533 (2020).
Berckmans, B. et al. Light-dependent regulation of DEL1 is determined by the antagonistic action of E2Fb and E2Fc. Plant Physiol. 157, 1440–1451 (2011).
Google Scholar
Kojima, S. et al. Asymmetric leaves2 and Elongator, a histone acetyltransferase complex, mediate the establishment of polarity in leaves of Arabidopsis thaliana. Plant Cell Physiol. 52, 1259–1273 (2011).
Google Scholar
Husbands, A. Y., Benkovics, A. H., Nogueira, F. T. S., Lodha, M. & Timmermans, M. C. P. The ASYMMETRIC LEAVES complex employs multiple modes of regulation to affect adaxial-abaxial patterning and leaf complexity. Plant Cell 27, 3321–3335 (2016).
Crane, R. A. et al. Negative regulation of age-related developmental leaf senescence by the IAOx pathway, PEN1, and PEN3. Front. Plant Sci. 10, 1202 (2019).
Google Scholar
Fu, M. et al. AtWDS1 negatively regulates age-dependent and dark-induced leaf senescence in Arabidopsis. Plant Sci. 285, 44–54 (2019).
Google Scholar
Zhang, B., Jia, J., Yang, M., Yan, C. & Han, Y. Overexpression of a LAM domain containing RNA-binding protein LARP1c induces precocious leaf senescence in Arabidopsis. Mol. Cells 34, 367–374 (2012).
Google Scholar
Ma, Z., Wu, W., Huang, W. & Huang, J. Down-regulation of specific plastid ribosomal proteins suppresses thf1 leaf variegation, implying a role of THF1 in plastid gene expression. Photosynth. Res. 126, 301–310 (2015).
Google Scholar
Wang, Z. et al. Two chloroplast proteins suppress drought resistance by affecting ROS production in guard cells. Plant Physiol. 172, 2491–2503 (2016).
Google Scholar
Meurer, J. et al. PALE CRESS binds to plastid RNAs and facilitates the biogenesis of the 50S ribosomal subunit. Plant J. 92, 400–413 (2017).
Google Scholar
Holding, D. The chloroplast and leaf developmental mutant, pale cress, exhibits light-conditional severity and symptoms characteristic of its ABA deficiency. Ann. Bot. 86, 953–962 (2000).
Google Scholar
Meurer, J., Grevelding, C., Westhoff, P. & Reiss, B. The PAC protein affects the maturation of specific chloroplast mRNAs in Arabidopsis thaliana. Mol. Gen. Genet. MGG 258, 342–351 (1998).
Google Scholar
Lawesson, J. E. Stand-level dieback and regeneration of forests in the Galápagos Islands. Temporal and Spatial Patterns of Vegetation Dynamics 87–93. https://doi.org/10.1007/978-94-009-2275-4_10 (1988).
Endo, M., Kudo, D., Koto, T., Shimizu, H. & Araki, T. Light-dependent destabilization of PHL in Arabidopsis. Plant Signal. Behav. 9, e28118 (2014).
Google Scholar
Endo, M., Tanigawa, Y., Murakami, T., Araki, T. & Nagatani, A. PHYTOCHROME-DEPENDENT LATE-FLOWERING accelerates flowering through physical interactions with phytochrome B and CONSTANS. Proc. Natl Acad. Sci. USA 110, 18017–18022 (2013).
Google Scholar
Li, G. et al. Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat. Cell Biol. 13, 616–622 (2011).
Google Scholar
Basset, G. J. C. et al. Folate synthesis in plants: the last step of the p-aminobenzoate branch is catalyzed by a plastidial aminodeoxychorismate lyase. Plant J. 40, 453–461 (2004).
Google Scholar
Smeekens, S. Faculty Opinions recommendation of Large-scale analysis of mRNA translation states during sucrose starvation in arabidopsis cells identifies cell proliferation and chromatin structure as targets of translational control. Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature. https://doi.org/10.3410/f.1032260.373846 (2006).
Oravecz, A. et al. CONSTITUTIVELY PHOTOMORPHOGENIC1 is required for the UV-B response in Arabidopsis. Plant Cell 18, 1975–1990 (2006).
Google Scholar
Dal Bosco, C. et al. Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana. J. Biol. Chem. 279, 1060–1069 (2004).
Google Scholar
Tan, Y.-F., O’Toole, N., Taylor, N. L. & Millar, A. H. Divalent metal ions in plant mitochondria and their role in interactions with proteins and oxidative stress-induced damage to respiratory function. Plant Physiol. 152, 747–761 (2010).
Google Scholar
Kim, J. Y. et al. Functional characterization of a glycine-rich RNA-binding protein 2 in Arabidopsis thaliana under abiotic stress conditions. Plant J. 50, 439–451 (2007).
Google Scholar
ten Hove, C. A. et al. Probing the roles of LRR RLK genes in Arabidopsis thaliana roots using a custom T-DNA insertion set. Plant Mol. Biol. 76, 69–83 (2011).
Google Scholar
Jakoby, M. J. et al. Transcriptional profiling of mature Arabidopsis trichomes reveals that NOECK encodes the MIXTA-like transcriptional regulator MYB106. Plant Physiol. 148, 1583–1602 (2008).
Google Scholar
Fox, A. R. et al. Plasma membrane aquaporins interact with the endoplasmic reticulum resident VAP27 proteins at ER-PM contact sites and endocytic structures. N. Phytol. 228, 973–988 (2020).
Google Scholar
Wang, P. et al. Plant AtEH/Pan1 proteins drive autophagosome formation at ER-PM contact sites with actin and endocytic machinery. Nat. Commun. 10, 5132 (2019).
Google Scholar
Bittner, A., Hause, B. & Baier, M. Cold-priming causes oxylipin dampening during the early cold and light response of Arabidopsis thaliana. J. Exp. Bot. https://doi.org/10.1093/jxb/erab314 (2021).
Kuki, Y., Ohno, R., Yoshida, K. & Takumi, S. Heterologous expression of wheat WRKY transcription factor genes transcriptionally activated in hybrid necrosis strains alters abiotic and biotic stress tolerance in transgenic Arabidopsis. Plant Physiol. Biochem. 150, 71–79 (2020).
Google Scholar
Czarnocka, W. et al. FMO1 is involved in excess light stress-induced signal transduction and cell death signaling. Cells 9, 2163 (2020).
Kleine, T., Kindgren, P., Benedict, C., Hendrickson, L. & Strand, A. Genome-wide gene expression analysis reveals a critical role for CRYPTOCHROME1 in the response of Arabidopsis to high irradiance. Plant Physiol. 144, 1391–1406 (2007).
Google Scholar
Castells, E. et al. The conserved factor DE-ETIOLATED 1 cooperates with CUL4-DDB1DDB2 to maintain genome integrity upon UV stress. EMBO J. 30, 1162–1172 (2011).
Google Scholar
Lahari, T., Lazaro, J., Marcus, J. M. & Schroeder, D. F. RAD7 homologues contribute to Arabidopsis UV tolerance. Plant Sci. 277, 267–277 (2018).
Google Scholar
Kim, A. et al. Non-intrinsic ATP-binding cassette proteins ABCI19, ABCI20 and ABCI21 modulate cytokinin response at the endoplasmic reticulum in Arabidopsis thaliana. Plant Cell Rep. 39, 473–487 (2020).
Google Scholar
Chen, D., Molitor, A., Liu, C. & Shen, W.-H. The Arabidopsis PRC1-like ring-finger proteins are necessary for repression of embryonic traits during vegetative growth. Cell Res. 20, 1332–1344 (2010).
Google Scholar
Shen, L. et al. The putative PRC1 RING-finger protein AtRING1A regulates flowering through repressing MADS AFFECTING FLOWERING genes in Arabidopsis. Development 141, 1303–1312 (2014).
Google Scholar
Li, J., Wang, Z., Hu, Y., Cao, Y. & Ma, L. Polycomb group proteins RING1A and RING1B regulate the vegetative phase transition in Arabidopsis. Front. Plant Sci. 8, 867 (2017).
Google Scholar
An, Z. et al. The histone methylation readers MRG1/MRG2 and the histone chaperones NRP1/NRP2 associate in fine-tuning Arabidopsis flowering time. Plant J. 103, 1010–1024 (2020).
Google Scholar
Gómez-Zambrano, Á. et al. Arabidopsis SWC4 binds DNA and recruits the SWR1 complex to modulate histone H2A.Z deposition at key regulatory genes. Mol. Plant 11, 815–832 (2018).
Glass, M., Barkwill, S., Unda, F. & Mansfield, S. D. Endo-β−1,4-glucanases impact plant cell wall development by influencing cellulose crystallization. J. Integr. Plant Biol. 57, 396–410 (2015).
Google Scholar
Markakis, M. N. et al. Identification of genes involved in the ACC-mediated control of root cell elongation in Arabidopsis thaliana. BMC Plant Biol. 12, 1–11 (2012).
Noutoshi, Y. et al. Loss of necrotic spotted lesions 1 associates with cell death and defense responses in Arabidopsis thaliana. Plant Mol. Biol. 62, 29–42 (2006).
Google Scholar
Fukunaga, S. et al. Dysfunction of Arabidopsis MACPF domain protein activates programmed cell death via tryptophan metabolism in MAMP-triggered immunity. Plant J. 89, 381–393 (2017).
Google Scholar
Singh, S., Kailasam, S., Lo, J. & Yeh, K. Histone H3 lysine4 trimethylation‐regulated GRF11 expression is essential for the iron‐deficiency response in Arabidopsis thaliana. N. Phytologist 230, 244–258 (2021).
Google Scholar
Fal, K. et al. Phyllotactic regularity requires the Paf1 complex in Arabidopsis. Development https://doi.org/10.1242/dev.154369 (2017).
He, Y. PAF1-complex-mediated histone methylation of FLOWERING LOCUS C chromatin is required for the vernalization-responsive, winter-annual habit in Arabidopsis. Genes Dev. 18, 2774–2784 (2004).
Google Scholar
Hoson, T. et al. Growth stimulation in inflorescences of an Arabidopsis tubulin mutant under microgravity conditions in space. Plant Biol. 16, 91–96 (2014).
Xiong, X., Xu, D., Yang, Z., Huang, H. & Cui, X. A single amino-acid substitution at lysine 40 of an Arabidopsis thaliana α-tubulin causes extensive cell proliferation and expansion defects. J. Integr. Plant Biol. 55, 209–220 (2013).
Google Scholar
Whitewoods, C. D. et al. CLAVATA was a genetic novelty for the morphological innovation of 3D growth in land plants. Curr. Biol. 30, 2645–2648 (2020).
Google Scholar
Galbraith, D. W. et al. Rapid flow cytometric analysis of the cell cycle in intact plant tissues. Science 220, 1049–1051 (1983).
Google Scholar
Dolezel, J., Sgorbati, S. & Lucretti, S. Comparison of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants. Physiologia Plant. 85, 625–631 (1992).
Google Scholar
Loureiro, J., Rodriguez, E., Dolezel, J. & Santos, C. Two new nuclear isolation buffers for plant DNA flow cytometry: a test with 37 species. Ann. Bot. 100, 875–888 (2007).
Google Scholar
Suda, J. et al. Genome size variation and species relationships in Hieracium sub-genus Pilosella (Asteraceae) as inferred by flow cytometry. Ann. Bot. 100, 1323–1335 (2007).
Google Scholar
Greilhuber, J., Dolezel, J., Lysák, M. A. & Bennett, M. D. The origin, evolution and proposed stabilization of the terms ‘genome size’ and ‘C-value’ to describe nuclear DNA contents. Ann. Bot. 95, 255–260 (2005).
Google Scholar
Dolezel, J., Bartos, J., Voglmayr, H. & Greilhuber, J. Nuclear DNA content and genome size of trout and human. Cytom. Part A: J. Int. Soc. Anal. Cytol. 51, 127–128 (2003).
Google Scholar
Putnam, N. H. et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res. 26, 342–350 (2016).
Google Scholar
Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2020).
Google Scholar
Laetsch, D. R. & Blaxter, M. L. BlobTools: Interrogation of genome assemblies. F1000Res. 6, 1287 (2017).
Guan, D. et al. Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics 36, 2896–2898 (2020).
Google Scholar
Bradnam, K. R. et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2, 10 (2013).
Google Scholar
Smit, A., Hubley, R. & Green, P. RepeatMasker 4.0 (Institute for Systems Biology, 2013).
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451–9457 (2020).
Google Scholar
Tardaguila, M. et al. Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. Genome Res. 28, 1096 (2018).
Google Scholar
Holt, C. & Yandell, M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinforma. 12, 491 (2011).
Moore, B., Holt, C., Alvarado, A. S. & Yandell, M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome 18, 188–196 (2008).
Parra, G., Bradnam, K. & Korf, I. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23, 1061–1067 (2007).
Google Scholar
Korf, I. Gene finding in novel genomes. BMC Bioinforma. 5, 59 (2004).
Keller, O., Kollmar, M., Stanke, M. & Waack, S. A novel hybrid gene prediction method employing protein multiple sequence alignments. Bioinformatics 27, 757–763 (2011).
Google Scholar
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35, 543–548 (2018).
Google Scholar
Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness. Methods Mol. Biol. 1962, 227–245 (2019).
Google Scholar
Andrews, S. FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (2010).
Schubert, M., Lindgreen, S. & Orlando, L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes 9, 88 (2016).
Google Scholar
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011).
Google Scholar
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Mandel, J. R. et al. A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae. Appl. Plant Sci. 2, 1300085 (2014).
Faircloth, B. C. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32, 786–788 (2016).
Google Scholar
Faircloth, B. C. et al. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Syst. Biol. 61, 717–726 (2012).
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
Google Scholar
Delcher, A. L. et al. Alignment of whole genomes. Nucleic Acids Res. 27, 2369–2376 (1999).
Google Scholar
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).
Google Scholar
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).
Google Scholar
Allen, M., Poggiali, D., Whitaker, K., Marshall, T. R. & Kievit, R. A. Raincloud plots: a multi-platform tool for robust data visualization. Wellcome Open Res. 4, 63 (2019).
Google Scholar
Hao, Z. et al. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Comput Sci. 6, e251 (2020).
Google Scholar
Laforest, M. et al. A chromosome-scale draft sequence of the Canada fleabane genome. Pest Manag. Sci. 76, 2158–2169 (2020).
Google Scholar
Liu, B. et al. Mikania micrantha genome provides insights into the molecular mechanism of rapid growth. Nat. Commun. 11, 340 (2020).
Google Scholar
Emms, D. M. & Kelly, S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 16, 157 (2015).
Google Scholar
Cerca, J. et al. The Tetragnatha kauaiensis genome sheds light on the origins of genomic novelty in spiders. Genome Biol. Evol. 13, evab262 (2021).
Laetsch, D. R. & Blaxter, M. L. KinFin: software for taxon-aware analysis of clustered protein sequences. G3 7, 3349–3357 (2017).
Google Scholar
Conway, J. R., Lex, A. & Gehlenborg, N. UpSetR: an R package for the visualization of intersecting sets and their properties. Bioinformatics 33, 2938–2940 (2017).
Google Scholar
Sanderson, M. J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19, 301–302 (2003).
Google Scholar
Lovell, J. T. et al. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature 590, 438–444 (2021).
Google Scholar
Ellinghaus, D., Kurtz, S. & Willhoeft, U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinforma. 9, 18 (2008).
Steinbiss, S., Willhoeft, U., Gremme, G. & Kurtz, S. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Res. 37, 7002–7013 (2009).
Google Scholar
Eddy, S. HMMER user’s guide. Dep. Genet., Wash. Univ. Sch. Med. 2, 13 (1992).
Llorens, C. et al. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0. Nucleic Acids Res. 39, D70–D74 (2011).
Google Scholar
Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).
Google Scholar
Talavera, G. & Castresana, J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56, 564–577 (2007).
Google Scholar
De Bie, T., Cristianini, N., Demuth, J. P. & Hahn, M. W. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22, 1269–1271 (2006).
Mendes, F. K., Vanderpool, D., Fulton, B. & Hahn, M. W. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics https://doi.org/10.1093/bioinformatics/btaa1022 (2020).
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
Google Scholar
Alexa, A. & Rahnenfuhrer, J. topGO: enrichment analysis for gene ontology. R. Package Version 2, 2010 (2010).
Alexa, A. & Rahnenführer, J. Gene set enrichment analysis with topGO. Bioconductor Improv 27, 1–26 (2009).
Supek, F., Bošnjak, M., Škunca, N. & Šmuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6, e21800 (2011).
Google Scholar
Löytynoja, A. Phylogeny-aware alignment with PRANK. Methods Mol. Biol. 1079, 155–170 (2014).
Wu, M., Chatterji, S. & Eisen, J. A. Accounting for alignment uncertainty in phylogenomics. PLoS ONE 7, e30288 (2012).
Google Scholar
Smith, M. D. et al. Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection. Mol. Biol. Evol. 32, 1342–1353 (2015).
Google Scholar
Pond, S. L. K., Frost, S. D. W. & Muse, S. V. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21, 676–679 (2005).
Google Scholar
Szklarczyk, D. et al. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43, D447–D452 (2015).
Google Scholar
Source: Ecology - nature.com
