The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution (original) (raw)

• Hirase, S. On the spermatozoids of Ginkgo biloba (in Japanese). Bot. Mag. Tokyo 10, 325–328 (1896).
  Article Google Scholar
• Hirase, S. Etudes sur la Fecondation et l’Embryogenie du Ginkgo biloba (second mémoire). J. Coll. Sci. Imp. Univ. Tokyo 12, 103–149 (1898).
  Google Scholar
• Hirase, S. Further studies on fertilisation and embryogeny in Ginkgo biloba (in Japanese). Bot. Mag. Tokyo 32, 83–108 (1918).
  Article Google Scholar
• Ridge, R. W., Hori, T. & Miyamura, S. I. Ginkgo Biloba—A Global Treasure from Biology to Medicine (eds Hori, T. et al.) 99-107 (Springer, 1997).
• Zhao, M. X., Dong, Z. H., Yu, Z. H., Xiao, S. Y. & Li, Y. M. Effects of Ginkgo biloba extract in improving episodic memory of patients with mild cognitive impairment: a randomized controlled trial. J. Chin. Integr. Med. 10, 628–634 (2012).
  Article Google Scholar
• Shimamura, T. J. C. On the spermatozoid of Ginkgo biloba. Cytologia 1, 416–423 (1937).
  Article Google Scholar
• Chanderbali, A. S. et al. Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower. Proc. Natl Acad. Sci. USA 107, 22570–22575 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Guan, R. et al. Draft genome of the living fossil Ginkgo biloba. GigaScience 5, 49 (2016).
  Article PubMed PubMed Central Google Scholar
• Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2020).
• Liu, H., Cao, F., Yin, T. & Chen, Y. A highly dense genetic map for Ginkgo biloba constructed using sequence-based markers. Front. Plant Sci. 8, 1041 (2017).
  Article PubMed PubMed Central Google Scholar
• Simao, 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).
  Article CAS PubMed Google Scholar
• Li, Z. et al. Early genome duplications in conifers and other seed plants. Sci. Adv. 1, e1501084 (2015).
  Article PubMed PubMed Central Google Scholar
• Leebens-Mack, J. H. et al. One Thousand Plant Transcriptomes Initiative. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679–685 (2019).
  Article Google Scholar
• Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011).
  Article CAS PubMed Google Scholar
• Nystedt, B. et al. The Norway spruce genome sequence and conifer genome evolution. Nature 497, 579–584 (2013).
  Article CAS PubMed Google Scholar
• Ruprecht, C. et al. Revisiting ancestral polyploidy in plants. Sci. Adv. 3, e1603195 (2017).
  Article PubMed PubMed Central Google Scholar
• Roodt, D. et al. Evidence for an ancient whole genome duplication in the cycad lineage. PLoS ONE 12, e0184454 (2017).
  Article PubMed PubMed Central Google Scholar
• Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Zwaenepoel, A. & Van de Peer, Y. Inference of ancient whole-genome duplications and the evolution of gene duplication and loss rates. Mol. Biol. Evol. 36, 1384–1404 (2019).
  Article CAS PubMed Google Scholar
• Damon, L. How important are transposons for plant evolution? Nat. Rev. Genet. 14, 49–61 (2013).
  Article Google Scholar
• Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017).
  Article CAS PubMed Google Scholar
• SanMiguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y. & Bennetzen, J. L. The paleontology of intergene retrotransposons of maize. Nat. Genet. 20, 43–45 (1998).
  Article CAS PubMed Google Scholar
• Devos, K. M., Brown, J. K. M. & Bennetzen, J. L. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12, 1075–1079 (2002).
  Article CAS PubMed PubMed Central Google Scholar
• Domansky, A. N. et al. Solitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region. FEBS Lett. 472, 191–195 (2000).
  Article CAS PubMed Google Scholar
• Karp, G. Molekulare Zellbiologie (Springer, 2005).
• Cheng, S., Xian, W., Fu, Y., Marin, B. & Melkonian, M. J. C. Genomes of subaerial Zygnematophyceae provide insights into land plant evolution. Cell 179, 1057–1067 (2019).
  Article CAS PubMed Google Scholar
• Yang, P. et al. Radial spoke proteins of Chlamydomonas flagella. J. Cell Sci. 119, 1165–1174 (2006).
  Article CAS PubMed Google Scholar
• Omoto, C. K. et al. Rotation of the central pair microtubules in eukaryotic flagella. Mol. Biol. Cell 10, 1–4 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Hou, Y. et al. Functional analysis of an individual IFT protein: IFT46 is required for transport of outer dynein arms into flagella. J. Cell Biol. 176, 653–665 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Pazour, G. J., Dickert, B. L. & Witman, G. B. The DHC1b (DHC2) isoform of cytoplasmic dynein is required for flagellar assembly. J. Cell Biol. 144, 473–481 (1999).
  Article CAS PubMed PubMed Central Google Scholar
• Smaczniak, C., Immink, R. G., Angenent, G. C. & Kaufmann, K. Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 139, 3081–3098 (2012).
  Article CAS PubMed Google Scholar
• Theißen, G. Development of floral organ identity: stories from the MADS house. Curr. Opin. Plant Biol. 4, 75–85 (2001).
  Article PubMed Google Scholar
• Krizek, B. A. & Fletcher, J. C. J. N. R. G. Molecular mechanisms of flower development: an armchair guide. Nat. Rev. Genet. 6, 688–698 (2005).
  Article CAS PubMed Google Scholar
• Matsumoto, S. & Fukui, H. J. A. H. ABCDE model for wild rose (Rosa rugosa Thunb. ex Murray) floral development. Acta Hortic. 751, 369–373 (2007).
  Article Google Scholar
• McConnell, J. R. et al. Role of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots. Nature 411, 709–713 (2001).
  Article CAS PubMed Google Scholar
• Kidner, C. A. & Timmermans, M. C. Mixing and matching pathways in leaf polarity. Curr. Opin. Plant Biol. 10, 13–20 (2007).
  Article PubMed Google Scholar
• Singh, A. et al. Plant small RNAs: advancement in the understanding of biogenesis and role in plant development. Planta 248, 545–558 (2018).
  Article CAS PubMed Google Scholar
• Townsley, B. T. & Sinha, N. R. A new development: evolving concepts in leaf ontogeny. Annu. Rev. Plant Biol. 63, 535–562 (2012).
  Article CAS PubMed Google Scholar
• Xia, R., Xu, J. & Meyers, B. C. The emergence, evolution, and diversification of the miR390-TAS3-ARF pathway in land plants. Plant Cell 29, 1232–1247 (2017).
  Article CAS PubMed PubMed Central Google Scholar
• Zhu, W. et al. Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid. Genome Biol. 18, 157 (2017).
  Article PubMed PubMed Central Google Scholar
• Wang, C. M. et al. Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res. 25, 246–256 (2015).
  Article PubMed PubMed Central Google Scholar
• Chin, C. S., Alexander, D. H., Marks, P., Klammer, A. A. & Korlach, J. J. N. M. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).
  Article Google Scholar
• Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
  Article PubMed PubMed Central Google Scholar
• Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
  Article PubMed PubMed Central Google Scholar
• Akdemir, K. C. & Chin, L. HiCPlotter integrates genomic data with interaction matrices. Genome Biol. 16, 198 (2015).
  Article PubMed PubMed Central Google Scholar
• Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 (2013).
  Article CAS PubMed Google Scholar
• Kent, W. J. J. G. R. BLAT—the BLAST-like alignment tool. Genome Res. 12, 656–664 (2002).
  CAS PubMed PubMed Central Google Scholar
• Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005).
  Article CAS PubMed Google Scholar
• Price, A. L., Jones, N. C. & Pevzner, P. A. De novo identification of repeat families in large genomes. Bioinformatics 21, i351–i358 (2005).
  Article CAS PubMed Google Scholar
• Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007).
  Article PubMed PubMed Central Google Scholar
• Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. Nucleic Acids Res. 32, 1792–1797 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Stanke, M., Steinkamp, R., Waack, S. & Morgenstern, B. AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res. 32, W309–W312 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinform. 10, 421 (2009).
  Article Google Scholar
• She, R., Chu, J. S.-C., Wang, K., Pei, J. & Chen, N. J. G. R. GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res. 19, 143–149 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Birney, E., Clamp, M. & Durbin, R. Gene wise and genomewise. Genome Res. 14, 988–995 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
  Article PubMed PubMed Central Google Scholar
• Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).
  Article CAS PubMed PubMed Central Google Scholar
• Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008).
• Wan, T. et al. A genome for gnetophytes and early evolution of seed plants. Nat. Plants 4, 82–89 (2018).
  Article CAS PubMed Google Scholar
• Scott, A. D. et al. A reference genome sequence for Giant Sequoia. G3 (Bethesda) 10, 3907–3919 (2020).
  Article CAS Google Scholar
• Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 (2000).
  Article CAS PubMed PubMed Central Google Scholar
• Zdobnov, E. M. & Apweiler, R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17, 847–848 (2001).
  Article CAS PubMed Google Scholar
• Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
  Article CAS PubMed PubMed Central Google Scholar
• Felsenstein, J. P. J. C. PHYLIP (Phylogeny Inference Package) v.3.6 (Univ. of Washington, 2005).
• Bie, T. D., Cristianini, N., Demuth, J. P. & Hahn, Bioinformatics, M. W. J. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22, 1269–1271 (2006).
  Article PubMed Google Scholar
• Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
  Article CAS PubMed Google Scholar
• Potter, S. C. et al. HMMER web server: 2018 update. Nucleic Acids Res. 46, W200–W204 (2018).
  Article CAS PubMed PubMed Central Google Scholar
• Zhang, Z. et al. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 4, 259–263 (2006).
  Article CAS PubMed Google Scholar
• UniProt Consortium. The universal protein resource (UniProt). Nucleic Acids Res. 36, D190–D195 (2008).
  Article Google Scholar