Capella-Gutirrez, S., Silla-Martnez, J. M. & Gabaldn, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Ou, S. & Jiang, N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Both fit and mcf toxins are known for their insecticidal properties, and fit- or mcf-producing bacteria are often used in pest biocontrol62,63,64. These facets include reproductive biology, anatomy, cytology . Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants. Chen, F., Tholl, D., Bohlmann, J. Li, L. et al. The expression of APL is regulated by WOL in the procambium43. 4, 12201231 (2020). Guan, R. et al. Neudecker, P. et al. 7 The Evolution of flagella related genes in embrophyta. 3, Supplementary Fig. Raven, P. H., Evert, R. F. & Eichhorn, S. E. Biology of Plants 7th edn (Macmillan, 2005). How all these gene families related to wood features are regulated in cycads relative to other gymnosperms will be important for understanding the differences in wood density. & Sharma, S. A single Photorhabdus gene, makes caterpillars floppy (mcf), allows Escherichia coli to persist within and kill insects. S.D., Y.G., X.F., A.J.L., Y.Y., X.G., D.L., N.L., H.W. Furthermore, because syntenic information is the most solid evidence for WGD, and the legacy of syntenic blocks may be found if the concentrated gene duplications are indeed derived from WGD events, we also looked into whether such syntenic blocks exist. Dennis Wm. Stevenson New York Botanical Garden 10, 736 (2019). J. Hum. Bioinformatics 25, 19721973 (2009). Yang, J., Lee, S. H., Goddard, M. E. & Visscher, P. M. GCTA: a tool for genome-wide complex trait analysis. The origin of the seed marked one of the most important events of plant evolution10. Article Protoc. Morris, J. L. et al. The protein-coding sequences of 15 completely sequenced genomes and 1 transcriptome, representing seven gymnosperms (C. panzhihuaensis, Encephalatos longifolius, G. biloba, Gnetum montanum, Picea abies, Pinus taeda and Sequoiadendron giganteum), six angiosperms (Arabidopsis thaliana, Amborella trichopoda, Cinnamomum micranthum, Liriodendron chinense, Nymphaea colorata and Oryza sativa) and three other vascular plant outgroups (Azolla filiculoides, Salvinia cucullate and Selaginella moellendorffii), were classified into putative gene families/subfamilies by OrthoFinder82, and then scored for gene duplications across global gene families. For example, genes encoding endochitinases and chitinases as defences against chitin-containing fungal pathogens are expanded as tandem repeats in the C. panzhihuaensis and most gymnosperm genomes compared with other land plants. Plant Biol. 9, R7 (2008). This conflict arising from the mitochondrial data cannot be explained by the presence of extensive RNA editing sites in the mitochondrial data (Fig. PubMed Central 2b, node 1). Rev. Cycads have manoxylic wood, with a large pith, large amounts of parenchyma and relatively few tracheids, in contrast to most other gymnosperms, which have pycnoxylic wood, with small amounts of pith, cortex and parenchyma, and a greater density of tracheids4. Mol. The software KinFin83 was used to select the mostly single-copy genes for phylogenetic reconstruction with default settings. 8), which encodes a GGM13-like MADS-box transcription factor (TF), belonging to a lineage sister to the angiosperm AP3/PI clade that plays crucial roles in floral development. Bioinformatics 5, 4.10.1114.10.14 (2004). Plants People Planet 1, 3237 (2019). The origin of seed plants is marked by the emergence of key traits including the seed, pollen and secondary growth of xylem and phloem36. As in other gymnosperm genomes, a large portion (76.14%) of the C. panzhihuaensis genome consists of ancient repetitive elements (Supplementary Note 4). 85) and ASTRAL86 were used to align the sequences and to infer the species tree for cycads as aforementioned. and L.Y. 2b). Commun. Nei, M. & Gojobori, T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. They swim due to presence of water. PLoS ONE 12, e0184454 (2017). Higashiyama, T. & Takeuchi, H. The mechanism and key molecules involved in pollen tube guidance. Suyama, M., Torrents, D. & Bork, P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. We further confirmed that the relevant assembled regions were free of bacterial contamination. The cellulose synthase superfamily in fully sequenced plants and algae. To identify the co-expressed genes during the seed development, we used the R package WGCNA108 on the basis of the TPM data of the genes whose expression showed a coefficient of variation >0.5 across the four stages. PubMed Single-copy genes as molecular markers for phylogenomic studies in seed plants. The numbers above the branches are bootstrap support values. Y.V.d.P. To maximize the opportunity of identifying transposable elements, a combination of de novo and homology-based approaches was performed following the Repeat Library Construction-Advanced pipeline (http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced). 37) and the most differentiated nucleotide diversity () and heterozygosity ratios characterizing the window between 18 and 50Mb on chromosome 8 (Fig. Bot. Next, Hisat76 was used to map the transcriptome to the genome, and then StringTie77 was used to predict transcriptome-based gene models. Genes of fungal or bacterial origin are rare in seed plants61. About 1,010Gb (~100) Nanopore long-read data were used for genome assembly using NextDenovo (https://github.com/Nextomics/NextDenovo) with default parameters (read_cutoff=1k, seed_cutoff=12k, minimap2_options_cns=-x ava-ont -k17 -w17). Proc. Sultana, M., Mukherjee, K. K. & Gangopadhyay, G. in Reproductive Biology of Plants (eds Johri, B. M. & Srivastava, P. S.) 118132 (Springer Science & Business Media, 2014). 33, 511518 (2005). The timescale of early land plant evolution. 91). Soltis, D. et al. The software PHYPARTS87 was used to infer and visualize the gene tree conflicts on the species tree topology with default settings. For instance, those genes encoding egg cell-secreted proteins that prevent attraction of multiple pollen tubes48 originated in the MRCA of living seed plants. ), the National Key R&D Program of China (No. 6 Phylogenetic tree of CESA/CSL gene families. Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. The FUS3/LEC2-like families are unique to gymnosperms, show significant expression after pollination in C. panzhihuaensis (Extended Data Fig. b, Chronogram of seed plants on the basis of the SSCG-NT12 dataset inferred using MCMCTree. Paolillo, D. J. Jr The swimming sperms of land plants. e,f, Morphologies of Plutella xylostella (e) and Helicoverpa armigera (f) after receiving PBS and cytotoxin treatments. PubMed Ginkgo biloba and the cycads are the only extant seed plants with motile sperm cells. Finally, maximum likelihood trees were calculated using RAxML99 with the GTRGAMMA model and bootstrap support was estimated based on 100 replicates. Proc. Brenner, E. D., Stevenson, D. W. & Twigg, R. W. Cycads: evolutionary innovations and the role of plant-derived neurotoxins. 4e). & Mathew, P. M. Cytological studies in the cycads: sex chromosomes in Cycas. Based on BUSCO12 estimation, the gene space completeness of the C. panzhihuaensis genome assembly is 91.6% (Supplementary Note 4). In an RC5 plus centrifuge, the cell lysate was spun at 13,800g for 40min at 4C. & Delevoryas, T. Morphology of Plants and Fungi 5th edn (Harper and Row, 1987). Cycads - Encyclopedia.com | Free Online Encyclopedia De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Bootstrap values (50%) for each major clade (highlighted in colour) and the relationships among them are provided. Bryophytes are a group of plant species that reproduce via spores rather than flowers or seeds. JCYJ20151015162041454 to Huan Liu). (b) Expression of CYCAS_034085 on MSY and CYCAS_010388 on chromosome 2 in male microsporophyll and in the ovule. 1c). Association analyses were performed once with a population of 31 male and 31 female individuals. Sci. Heteromorphic chromosomes have been reported to be associated with sex determination in Cycas54. Phylogeny and Evolution of the Angiosperms: Revised and Updated Edition (Univ. Ovule material was collected from two artificially pollinated individuals, and we divided the development stages into four: unpollinated ovule (before the artificial pollination), early stage of pollinated ovule (21d after the artificial pollination), late stage of pollinated ovule (88d after the artificial pollination) and fertilized ovule or seed (119d after the artificial pollination) (Supplementary Tables 2 and 19). Bootstrap values 50% are shown. The BRL1 and BRL3 genes encode brassinosteroid receptors that play major roles in xylem differentiation and phloem/xylem patterning in angiosperms44. Li, Z. et al. Mhnen, A. P. et al. PubMed The maximum likelihood tree was generated by RAxML with the PROTCATGTR model and 1,000 bootstrap replicates. Nanovesicles are secreted during pollen germination and pollen tube growth: a possible role in fertilization. 2019YFC1711000 to Huan Liu), the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (No. Our understanding of biotic evolution relies heavily on phylogenetic and dating reconstructions that provide insight into the periods of major diversification [].In the last decade, the advent of molecular dating approaches has fostered an explosion of studies constructing time-calibrated trees for diverse plant clades like bryophytes [], ferns [3,4], gymnosperms [5-8] and angiosperms [9-11]. The Nat | Cycads Nat. Plant Divers. The asterisk indicates a significant difference (two-sided Students t-test, P<0.05, n=3 biologically independent experiments), whereas the error bar represents the standard error. Are Cycads Vascular Or Nonvascular? - Quick Answers to Your Questions 4g and Supplementary Fig. Genet. Extended Data Fig. S.Z., H.L. Biol. Most bryophytes are found in damp environments and consist of three types of non-vascular land plants: the mosses, hornworts, and liverworts. 37, 15301534 (2020). Plant Reprod. Bryophytes are a group of land plants, sometimes treated as a taxonomic division, that contains three groups of non-vascular land plants (embryophytes): the liverworts, hornworts and mosses. *Cycadophyta (*cycads*)* A division of gymnosperms [1] comprising plants with leaves and habit similar to those of palm trees, although some species are quite small. 1a)6. In contrast to CYCAS_034085, CYCAS_010388 was much more highly expressed in the ovule than in the microsporophyll (Fig. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Using an horseradish peroxidase-conjugated monoclonal antibody and a western blot assay, the purified His-tagged protein was identified (HRP-66005). Raw gels figure for Supplementary Fig. led and managed the project. To obtain Bryophyte - Wikipedia 2012, 205049 (2012). Cycads are ancient seed-bearing plants that appeared before the age of dinosaurs, during the Permian period, almost 280 million years ago. Nat. Condamine, F. L., Nagalingum, N. S., Marshall, C. R. & Morlon, H. Origin and diversification of living cycads: a cautionary tale on the impact of the branching process prior in Bayesian molecular dating. (a) Sketch of the Cycas sperm. Nature 574, 679685 (2019). 62, 485514 (2011). The modules are enriched in seed nutrition metabolic processes (M2, M6 and M8), membrane biosynthesis (M9, which may relate to the development of the integument) and genes synthesizing callose, a major component of the pollen tube (M4) (Supplementary Note 10). The authors declare no competing interests. Learn the answer to this question and many more only on BYJU'S NEET and Y.L. 6). BMC Evol. The plant tissues were collected and stored in liquid nitrogen, then transferred to freezer at 80C. Fertilized ovules accumulated a high level of abscisic acid and expressed the genes related to cell wall organization and biogenesis, indicating their activity in embryo development, seed coat formation, and seed maturation and dormancy40 (Supplementary Note 10.110.5). Sayyari, E., Whitfield, J. The raw genomic, transcriptomic and Hi-C data generated in this study were deposited in the NCBI Sequence Read Archive (SRA, BioProject PRJNA734434) and the CNGB data center (https://db.cngb.org/) under project number CNP0001756. Article Gibberellin, which is reported to regulate integument development in the ovules of flowering plants39, accumulated in the late stage of the pollinated ovule in Cycas. All authors read and approved the manuscript. BMC Plant Biol. Vanneste, K., Van de Peer, Y. Solution structure, dynamics, and hydrodynamics of the calcium-bound cross-reactive birch pollen allergen Bet v 4 reveal a canonical monomeric two EF-hand assembly with a regulatory function. Mol. To further enhance assembly contiguity, about 456Gb of Hi-C data were used to execute Hi-C chromosome conformation in conjunction with 3D-dna algorithm67. For protein evidence, Genewise75 was used to predict gene models based on Cycas proteins downloaded from the UniProt protein database and other proteins collected from representative plant species. The bootstrap values 50% are shown in the central branches. Nucleic Acids Res. This problem has been solved! Science 338, 10931097 (2012). a, Heatmap showing relative expression of genes in 11 co-expression modules by WGCNA across 4 developmental stages of the seed: S1, unpollinated ovule; S2, early stage of pollinated ovule; S3, late stage of pollinated ovule; and S4, fertilized ovule. A. Phylogenetic analyses and morphological innovations in land plants. Answer: D Chapter Section: 22.3 Learning Outcome: 22.4 55) Roses are classified as A) angiosperms. Katoh, K., Kuma, K.-i, Toh, H. & Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Draft genome of the living fossil Ginkgo biloba. c,d, Mortalities of Plutella xylostella (c) and Helicoverpa armigera (d) after treatment with phosphate buffered saline (PBS) and cytotoxin. Why? Dumont, M. et al. Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. 2a), supporting recent findings based on transcriptome data24. S.D., Yang Liu, Y.G., J.L., Y.Y. CAS Based on the following criteria, all candidate genes were screened: first, candidate gene sequences were detected by BLAST searches with an e value cut-off of 1105to the collected query gene sequences gathered from previous studies or public databases; and second, features of candidate genes should be similar to the online functional annotation or UniProt functional annotation as the query genes. Google Scholar. 5a). Methods 12, 357360 (2015). Quartet support for six internal branches I, II, III, IV, V, VI were indicated on the left panel as barcharts. SNPs were filtered using the following criteria: (1) SNPs were filtered by GATK VariantFiltrations with QD<2.0 || FS>60.0 || MQ<40.0 || SOR>3.0 || MQRankSum<12.5 || ReadPosRankSum<8.0, and indels with QD<2.0 || FS>200.0 || SOR>10.0 || MQRankSum<12.5 || ReadPosRankSum<8.0; (2) total depth <80 or >1,300; (3) variants with more than two alleles; (4) variants with a missing rate >10% or minor allele frequencies <0.1 were removed; and (5) a linkage disequilibrium pruning with PLINK (v.1.9) using a window size of 10kb with a step size of one SNP and r2 threshold of 0.5, resulting a 4.65-million pruned SNP set for association analysis of sex differentiation. Cycads: Ancient Plants With Bacteria Living in Their Roots Frontiers Cycads exhibit other special features, such as the accumulation of toxins that deter herbivores8 in seeds and vegetative tissues. For genome sequencing, the genomic DNA was extracted by the QIAGEN Genomic kit followed the manufacturers instructions65. 104, 13991409 (2020). We firstly used an e value (<11020) as a cut-off to filter candidates and then filtered the candidates with functional annotation. Identifying genomic features uniquely shared by cycads and other extant seed plants, but not non-seed-producing plants, may shed light on the origin of key innovations, as well as the early diversification of seed plants. 202105 to Y.G. In addition, we identified a novel TPS subfamily in Cycas, with three copies in C. panzhihuaensis and eight copies in Cycas debaoensis (Extended Data Fig. PubMed My major research interests in the past few years have focused upon the evolution and classification of the Cycadales (cycads) and their placement in seed plant phylogeny. The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. & Pichersky, E. The family of terpene synthases in plants: a mid-size family of genes for specialized metabolism that is highly diversified throughout the kingdom. Science 334, 796799 (2011). & Sanmartn, I. IQ-TREE 2 (ref. Biology - Chapter Sixteen Flashcards | Chegg.com 39b). The abbreviated name given before the protein ID represents species name: CYCAS: Cycas panzhihuaensis, Gb: Ginkgo biloba, SEGI: Sequoiadendron giganteum, GMON: Gnetum montanum, PICABI: Picea abies, PITA: Pinus taeda, ATH, Arabidopsis thaliana, DEBAO: Cycas debaoensis, AMTR: Amborella trichopoda, OS: Oryza sativa, AFILI: Azolla filiculoides, SACU: Salvinia cucullata, SELMO: Selaginella moellendorffii, PPATEH: Physcomitrella patens, MARPO: Marchantia polymorpha. b, Evolutionary analyses and phylogenetic profiles depicting the gains (light green), losses (light red), expansions (light yellow) and contractions (light blue) of orthogroups, according to the reconstruction of the ancestral gene content at key nodes and the dynamic changes of the lineage-specific gene characteristics. To accomplish quantitative analysis, different concentrations of standard were utilized. and Z.L. Profile. Plants 4, 8289 (2018). 9b) reveal that many TPS genes are mainly expressed in the root (especially primary root and coralloid root), microsporophyll and pollen sac, late stage of the pollinated ovule and fertilized ovule. Proc.
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