Evolution of coastal forests based on a full set of mangrove genomes
Tóm tắt
Từ khóa
Tài liệu tham khảo
He, Z. et al. Speciation with gene flow via cycles of isolation and migration: insights from multiple mangrove taxa. Natl Sci. Rev. 6, 275–288 (2019).
Zhou, R. et al. Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves. Mol. Biol. Evol. 24, 2746–2754 (2007).
Xu, S. et al. Genome-wide convergence during evolution of mangroves from woody plants. Mol. Biol. Evol. 34, 1008–1015 (2017).
He, Z. et al. Convergent adaptation of the genomes of woody plants at the land–sea interface. Natl Sci. Rev. 7, 978–993 (2020).
Lyu, H., He, Z., Wu, C.-I. & Shi, S. Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes. New Phytol. 217, 428–438 (2018).
Xu, S. et al. The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing. Natl Sci. Rev. 4, 721–734 (2017).
Feng, X. et al. Molecular adaptation to salinity fluctuation in tropical intertidal environments of a mangrove tree Sonneratia alba. BMC Plant Biol. 20, 178 (2020).
Feng, X. et al. Genomic insights into molecular adaptation to intertidal environments in the mangrove Aegiceras corniculatum. New Phytol. 231, 2346–2358 (2021).
Angelini, C. et al. A keystone mutualism underpins resilience of a coastal ecosystem to drought. Nat. Commun. 7, 12473 (2016).
Atwood, T. B. et al. Global patterns in mangrove soil carbon stocks and losses. Nat. Clim. Change 7, 523–528 (2017).
Barbier, E. B. et al. Coastal ecosystem-based management with nonlinear ecological functions and values. Science 319, 321–323 (2008).
Barbier, E. B. et al. The value of estuarine and coastal ecosystem services. Ecol. Monogr. 81, 169–193 (2011).
Hensel, M. J. S. & Silliman, B. R. Consumer diversity across kingdoms supports multiple functions in a coastal ecosystem. Proc. Natl Acad. Sci. USA 110, 20621–20626 (2013).
Rovai, A. S. et al. Global controls on carbon storage in mangrove soils. Nat. Clim. Change 8, 534–538 (2018).
Guo, Z. et al. Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses. Glob. Change Biol. 24, 1741–1748 (2018).
Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493–496 (2011).
Sollars, E. S. A. et al. Genome sequence and genetic diversity of European ash trees. Nature 541, 212–216 (2017).
Zhao, S. et al. Whole-genome sequencing of giant pandas provides insights into demographic history and local adaptation. Nat. Genet. 45, 67–71 (2013).
Duke, N. C. in Mangrove Ecosystems: A Global Biogeographic Perspective (eds Rivera-Monroy, V. H. et al.) 17–53 (Springer, 2017).
Ellison, A. M., Farnsworth, E. J. & Merkt, R. E. Origins of mangrove ecosystems and the mangrove biodiversity anomaly. Glob. Ecol. Biogeogr. 8, 95–115 (1999).
Gee, C. T. The mangrove palm Nypa in the geologic past of the new world. Wetl. Ecol. Manag. 9, 181–203 (2001).
Germeraad, J. H., Hopping, C. A. & Muller, J. Palynology of tertiary sediments from tropical areas. Rev. Palaeobot. Palynol. 6, 189–348 (1968).
Graham, A. Paleobotanical evidence and molecular data in reconstructing the historical phytogeography of Rhizophoraceae. Ann. Missouri Bot. Gard. 93, 325–334 (2006).
Mazer, S. J. & Tiffney, B. H. Fruits of Wetherellia and Palaeowetherellia (?Euphorbiaceae) from Eocene sediments in Virginia and Maryland. Brittonia 34, 300–333 (1982).
Srivastava, J. & Prasad, V. Evolution and paleobiogeography of mangroves. Mar. Ecol. 40, e12571 (2019).
Hu, M.-J. et al. Chromosome-scale assembly of the Kandelia obovata genome. Hortic. Res. 7, 75 (2020).
Jin, Y. & Qian, H. V.PhyloMaker: an R package that can generate very large phylogenies for vascular plants. Ecography 42, 1353–1359 (2019).
Zachos, J. C., Dickens, G. R. & Zeebe, R. E. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. Nature 451, 279–283 (2008).
Handley, L., Crouch, E. M. & Pancost, R. D. A New Zealand record of sea level rise and environmental change during the Paleocene–Eocene Thermal Maximum. Palaeogeogr. Palaeoclimatol. Palaeoecol. 305, 185–200 (2011).
Louca, S. & Pennell, M. W. Extant timetrees are consistent with a myriad of diversification histories. Nature 580, 502–505 (2020).
Saintilan, N. et al. Thresholds of mangrove survival under rapid sea level rise. Science 368, 1118–1121 (2020).
Lu, J. & Wu, C.-I. Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc. Natl Acad. Sci. USA 102, 4063–4067 (2005).
Ohta, T. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23, 263–286 (1992).
Liu, X. & Fu, Y. X. Exploring population size changes using SNP frequency spectra. Nat. Genet. 47, 555–559 (2015).
Liu, X. & Fu, Y.-X. Stairway Plot 2: demographic history inference with folded SNP frequency spectra. Genome Biol. 21, 280 (2020).
Krauss, K. W. et al. How mangrove forests adjust to rising sea level. New Phytol. 202, 19–34 (2014).
Lovelock, C. E. et al. The vulnerability of Indo-Pacific mangrove forests to sea-level rise. Nature 526, 559–563 (2015).
Frederiksen, N. O. Review of Early Tertiary Sporomorph Paleoecology (American Association of Stratigraphic Palynologists Foundation, 1985).
Smith, D. E., Harrison, S., Firth, C. R. & Jordan, J. T. The early Holocene sea level rise. Quat. Sci. Rev. 30, 1846–1860 (2011).
Bouillon, S. et al. Mangrove production and carbon sinks: a revision of global budget estimates. Glob. Biogeochem. Cycles 22, GB2013 (2008).
Donato, D. C. et al. Mangroves among the most carbon-rich forests in the tropics. Nat. Geosci. 4, 293–297 (2011).
Hamilton, S. E. & Friess, D. A. Global carbon stocks and potential emissions due to mangrove deforestation from 2000 to 2012. Nat. Clim. Change 8, 240–244 (2018).
Hutchison, J., Manica, A., Swetnam, R., Balmford, A. & Spalding, M. Predicting global patterns in mangrove forest biomass. Conserv. Lett. 7, 233–240 (2014).
Ouyang, X. & Lee, S. Y. Improved estimates on global carbon stock and carbon pools in tidal wetlands. Nat. Commun. 11, 317 (2020).
Richards, D. R., Thompson, B. S. & Wijedasa, L. Quantifying net loss of global mangrove carbon stocks from 20 years of land cover change. Nat. Commun. 11, 4260 (2020).
Sanders, C. J. et al. Are global mangrove carbon stocks driven by rainfall? J. Geophys. Res. Biogeosci. 121, 2600–2609 (2016).
Alongi, D. M. Carbon cycling and storage in mangrove forests. Ann. Rev. Mar. Sci. 6, 195–219 (2014).
Valiela, I., Bowen, J. L. & York, J. K. Mangrove forests: one of the world’s threatened major tropical environments. Bioscience 51, 807–815 (2001).
Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
Yang, G., Zhou, R., Tang, T. & Shi, S. Simple and efficient isolation of high-quality total RNA from Hibiscus tiliaceus, a mangrove associate and its relatives. Prep. Biochem. Biotechnol. 38, 257–264 (2008).
Wang, O. et al. Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Res. 29, 798–808 (2019).
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
Liu, B. et al. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Preprint at https://arxiv.org/abs/1308.2012v2 (2013).
Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202–2204 (2017).
Chin, C.-S. et al. Phased diploid genome assembly with single-molecule real-time sequencing. Nat. Methods 13, 1050–1054 (2016).
Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2020).
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
Xiao, C.-L. et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat. Methods 14, 1072–1074 (2017).
Chin, C.-S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563–569 (2013).
Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Weisenfeld, N. I., Kumar, V., Shah, P., Church, D. M. & Jaffe, D. B. Direct determination of diploid genome sequences. Genome Res. 27, 757–767 (2017).
Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 4, 30 (2015).
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99–101 (2016).
Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).
Bao, W., Kojima, K. K. & Kohany, O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob. DNA 6, 11 (2015).
Tarailo‐Graovac, M. & Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics 25, 4.10.1–4.10.14 (2009).
Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl Acad. Sci. USA 117, 9451–9457 (2020).
Xu, Z. & Wang, H. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 35, W265–W268 (2007).
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).
Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997).
Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004).
Kent, W. J. BLAT—The BLAST-Like Alignment Tool. Genome Res. 12, 656–664 (2002).
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. 7, 562–578 (2012).
Cantarel, B. L. et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18, 188–196 (2007).
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. 9, R7 (2008).
Seppey, M., Manni, M. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness. Methods Mol. Biol. 1962, 227–245 (2019).
Katoh, K. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34, W609–W612 (2006).
Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).
Yang, Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
Reis, M. Dos & Yang, Z. Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times. Mol. Biol. Evol. 28, 2161–2172 (2011).
Yu, G., Smith, D. K., Zhu, H., Guan, Y. & Lam, T. T. GGTREE: an package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol. Evol. 8, 28–36 (2017).
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).
Smith, S. A. & Brown, J. W. Constructing a broadly inclusive seed plant phylogeny. Am. J. Bot. 105, 302–314 (2018).
Zanne, A. E. et al. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89–92 (2014).
Louca, S. & Doebeli, M. Efficient comparative phylogenetics on large trees. Bioinformatics 34, 1053–1055 (2018).
Liang, Y. et al. Chromosome level genome assembly of Andrographis paniculata. Front. Genet. 11, 701 (2020).
Zhang, L. et al. The water lily genome and the early evolution of flowering plants. Nature 577, 79–84 (2020).
Huang, X. et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42, 961–967 (2010).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
McKenna, A. et al. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Miller, K. G. et al. The Phanerozoic record of global sea-level change. Science 310, 1293–1298 (2005).
Marçais, G. et al. MUMmer4: a fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).
Narasimhan, V. et al. BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. Bioinformatics 32, 1749–1751 (2016).
Cingolani, P. et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6, 80–92 (2012).