All illustrations are specifically created for this study (a high-resolution version is available at https://db.cngb.org/codeplot/datasets/public_dataset?id=PwRftGHfPs5qG3gE). 201916 to Yang Liu, No. Nucleic Acids Res. 7c). (a) Phylogenetic trees of CESA and CSL gene families. We also sequenced transcriptomes of 339 cycad species (Supplementary Tables 2 and 14). The sample extracts were the analysed using the ultra high-performance liquid chromatography system Vanquish (ThermoFisher Scientific) and Q Exactive HF-X (ThermoFisher Scientific). 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. 9, 559 (2008). a, Inference of the number of gene families with duplicated genes surviving after WGD events mapped on a phylogenetic tree depicting the relationships among 16 vascular plants included in this study. Syst. Biol. Xu, Z. 285, 20181012 (2018). Harris, P. J. in Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants (ed. To accomplish quantitative analysis, different concentrations of standard were utilized. No, Cycas are not bryophytes.They are classified under gymnosperms. Embryophyte - Wikipedia For genome sequencing, the genomic DNA was extracted by the QIAGEN Genomic kit followed the manufacturers instructions65. prepared materials. Source data are provided with this paper. Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. 202019 to Shouzhou Zhang and No. The single surviving species of the gingkophytes group is the Gingko biloba. The bryophytes have bifagellated sperm while the ferns have mult- flagellated sperms too. The maximum likelihood tree was generated by RAxML with the PROTCATGTR model and 1,000 bootstrap replicates. In addition, the genome contains almost equal proportions of copia and gypsy long terminal repeat (LTR) elements, in contrast to other gymnosperm genomes, in which gypsy repeats are more frequent14,15 (Supplementary Note 6). Proc. 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. Nat. Our inferences, based on 1,170 low-copy nuclear genes sampled for 339 cycad species and 6 fossil calibrations3 corroborate recent broad analyses of gymnosperms indicating that extant species-rich cycad genera emerged from rapid radiations ranging from 11 to 20Myr ago, which may have been a consequence of dramatic Miocene global temperature changes24,28. 5b). Strong rejection, the clade is not recovered, and the alternative topology is conflict even when poorly supported branches (<85%) are collapsed. 60, 1622 (2021). Ecol. c, Phylogeny of SSPs in some representative species in land plants. Plants People Planet 1, 3237 (2019). The longest gene, CYCAS_013063, encoding a kinesin-like protein KIF3A, covers 2.1Mb in the C. panzhihuaensis genome; the longest intron is approximately 1.5Mb and was detected in CYCAS_030563, a gene that encodes a photosystem II CP43 reaction centre protein. The initial cross-linked long-distance physical interactions were then represented by chimeric fragments, which were processed into paired-end sequencing libraries. Hence, Nostoc in general exhibits a very low host speci city, with no correlation to the taxonomic status of the host. 31, 291307 (2018). 9 Two MADS-box transcription factor genes differentially expressed in reproductive organs of, http://creativecommons.org/licenses/by/4.0/, The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis, Species delimitation in Ceratozamia (Zamiaceae) from Southwestern Mexico, in light of reproductive and climatic diversification, Emerging insights into nitrogen assimilation in gymnosperms, A draft genome of the medicinal plant Cremastra appendiculata (D. Don) provides insights into the colchicine biosynthetic pathway. 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. Nucleic Acids Res. Among these, 106 of the new orthogroups and 55 of the expanded orthogroups are associated with seed development in Arabidopsis37, including the regulation of development during early embryogenesis, seed dormancy and germination, and seed coat formation, as well as in immunity and stress response of the seed (Supplementary Note 6). Gomez, M. D., Ventimilla, D., Sacristan, R. & Perez-Amador, M. A. Gibberellins regulate ovule integument development by interfering with the transcription factor ATS. The cycads are considered to be gymnosperms, because they bear their seeds naked on modified leaves called sporophylls. This work is part of the 10KP project (https://db.cngb.org/10kp/) and was also supported by China National GeneBank (CNGB; https://www.cngb.org/). (c) Transcript expression level is indicated by TPM during seed development. 7a,b). CAS Answer: C 53) Chapter Section: 22.3. seedless vascular plants . Plants 7, 10151025 (2021). a, Phylogenetic analysis of the TcdA/TcdB pore-forming domain containing proteins shows that the genes encoding four cytotoxin proteins of Cycas were likely acquired from fungi through an ancient horizontal gene transfer event. Cycad - Wikipedia Annu. Variance component model to account for sample structure in genome-wide association studies. The abbreviated name given before the protein ID represents species name: CYCAS: Cycas panzhihuaensis, Gb: Ginkgo biloba, ELO: Encephalartos longifolius, SEGI: Sequoiadendron giganteum, GMON: Gnetum montanum, PICABI: Picea abies, PITA: Pinus taeda. and X.L. Genome Res. The CSLE/G from gymnosperm are the ancestral form of the angiosperm CSLE and CSLG. Phylogenetic tree analysis was used to verify the majority of TFs and transcriptional regulators. Extended Data Fig. See Supplementary Note 5 for details on organellar phylogenetic reconstruction, evaluation of the impact of RNA editing and investigation of cyto-nuclear incongruences. 14, 29382943 (2000). CNLs are expanded widely in both gymnosperms and angiosperms, whereas the TNL family tends to have been more expanded in gymnosperms than in most angiosperms, indicating different evolutionary patterns of plant resistance (R) genes in these two lineages. Natl Acad. Cycads living today have large, heavy seeds that suggests they rely on. We also performed additional BLAST searches against the OneKP database and many other available genomes. The RNL family plays a critical role in downstream resistance signal transduction in angiosperms, and the broad occurrence of the RNL family in gymnosperms suggests that this signalling pathway may have been established no later than the origin of seed plants. 9, 11301147 (2017). Genome Biol. Nucleic Acids Res. In Which Plant Sporophyte Is Dependent On Gametophyte? 33, 290295 (2015). 1c). 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). Vanneste, K., Van de Peer, Y. Protoc. Description: Cycad fossils have been found on every continent, including Antarctica, and some of the larger islands of the world. Cycads exhibit other special features, . Pertea, M. et al. Are Cycas bryophytes? Learn Answers to this Question and More 10, 736 (2019). Nagalingum, N. S. et al. Evol. Biol. The software KinFin83 was used to select single-copy gene families for phylogenetic reconstruction with default parameters. Internet Explorer). Ginkgos are classified as a angiosperms b bryophytes - Course Hero The tree was constructed using the maximum likelihood method with 500 bootstrap replicates. Non-Vascular Plant - an overview | ScienceDirect Topics and Yang Liu conceived the study. & Jiao, Y. GWAS analysis of sex differentiation was performed on the linkage disequilibrium-pruned SNP set using the EMMAX program103 (beta-07Mar2010 version). 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]. 4c and Supplementary Fig. Distmat from the EMBOSS (v.6.5.7.0) package was then used to calculate the K value of the retrotransposons 5- and 3-LTR sequences. 46, 152164 (2019). Nat. 67, 940964 (2018). Extended Data Fig. The most highly expressed gene in the MSY and also the most differentially regulated gene between the two sexes is CYCAS_034085 (Fig. Neudecker, P. et al. 14.2: Seedless Plants - Biology LibreTexts Rev. Nat. Answer: D Chapter Section: 22.3 Learning Outcome: 22.4 55) Roses are classified as A) angiosperms. 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). Front. & Pawowski, T. A. DNA synthesis pattern, proteome, and ABA and GA signalling in developing seeds of Norway maple (Acer platanoides). Evol. Conifers, in the division Pinophyta or Coniferophyta, are the most numerous of the gymnosperms; woody and with vascular tissue, these are cone bearing trees and shrubs.. Conifers can be found growing in all parts of . In addition, the NeiGojobori method101 as implemented in the PAML packages yn00 program91 was used to estimate synonymous substitutions per synonymous site (KS) for pairwise comparisons of paralogous genes located on syntenic blocks. Phylogeny and Evolution of the Angiosperms: Revised and Updated Edition (Univ. Gene families encoding resistance-related proteins are greatly expanded in C. panzhihuaensis and other gymnosperm genomes compared with non-seed plants (Supplementary Note 14). *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. De novo plant genome assembly based on chromatin interactions: a case study of Arabidopsis thaliana. Evidence for an ancient whole genome duplication in the cycad lineage. E. the zygote formed in ferns from the union of two gametes. Genet. & Xu, Y. The Cycas genome contains four homologues of the fitD gene family that were likely acquired via horizontal gene transfer from fungi, and these genes confer herbivore resistance in cycads. Bar, 1cm. 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. Sprunck, S. et al. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Niu, S. et al. The sperms swim to the female part for fertilization to take place. Conifers, cycads, ginkgo, and gnetophytes are collectively called: a 42, 348354 (2010). 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). b, The expression level of four cytotoxin proteins in different tissues of C. panzhihuaensis. Bot. Fresh megagametophytes of Cycas panzhihuaensis, cultivated in the garden of the Kunming Institute of Botany, Chinese Academy of Sciences, were collected for genome sequencing. PubMed Press, 1997). and L.Y. Stanke, M. et al. Proc. B. Question: Cycads are Multiple Choice ferns. bryophytes - Rent Textbooks The most divergent 32-Mb region (between the 18 and 50Mb locations) between the X and Y chromosomes probably represents an ancient evolutionary segment in the Cycas sex chromosomes. The study was supported by the National Cycad Conservation Center at Fairy Lake Botanical Garden. The origin of the seed marked one of the most important events of plant evolution10. Plant Biol. 3, Supplementary Fig. Its closest homologue, CYCAS_010388, was identified on autosomal chromosome 2. Such expansion also includes polcalcin, which is involved in calcium signalling to guide pollen tube growth50 (Supplementary Note 11). The plant was originally transplanted from the Pudu River, Luquan county, Yunnan, China (25 57 35.2584 N, 102 43 41.5848 E) and the voucher specimen (collection number: PZHF03) has been deposited in the Herbarium of the Kunming Institute of Botany (KUN). (a) Phylogenetic tree of the TPS gene family. 1a)6. Parts of genes were then filtered if they were not the homologues according to their functional annotation of SwissProt (<1105). 1c), which in some cases has been reported to bias phylogenetic inferences25,26, and instead may be best explained by incomplete lineage sorting, which is supported by our PhyloNet27 and coalescent analyses of nuclear genes (Supplementary Note 5). Our phylogenetic analyses of separate nuclear (Fig. 4g and Supplementary Fig. Mol. 46, 107671 (2020). Plants) 29,30,31). The shift from swimming to non-motile sperm is a major innovation in land plant evolution, and C. panzhihuaensis and G. biloba exhibit an ancestral gene content that is part of the shift from producing flagellate to non-flagellate sperm cells. Baucher, M., El Jaziri, M. & Vandeputte, O. PDF Lab 10:NONVASCULAR PLANTS: (Bryophytes) - Portland Community College We found that many genes regulating pollen and pollen tube development (pollen maturation, pollen tube growth, pollen tube perception and prevention of multiple-pollen tube attraction) were gained (or the respective gene family expanded) in the MRCA of extant seed plants (Fig. Biol. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. On the basis of molecular phylogenetic analyses, extant gymnosperms are resolved as a monophyletic group, but the branching order among their major lineages has remained controversial19,20,21,22,23. 195205 (Springer, 2002). Pink boxes in ac represent the most differentiated regions between the sex chromosomes. b, Chronogram of seed plants on the basis of the SSCG-NT12 dataset inferred using MCMCTree. Sentieon DNASeq variant calling workflow demonstrates strong computational performance and accuracy. The red colors in the tree represent the cycas genes. 24, 15861591 (2007). Sign up for the Nature Briefing newsletter what matters in science, free to your inbox daily. 88, 7682 (2011). Dong, S., Li, H., Goffinet, B. Lab 7.docx - 1. a. Based on your knowledge of reproduction trees that produce large cones. The Biology of the Cycads (Cornell Univ. Biol. 2a), surpassing those of Ginkgo14. The variant call format and VCFtools. The Chinese pine genome and methylome unveil key features of conifer evolution. 176, 14101422 (2018). As in other gymnosperm genomes, a large portion (76.14%) of the C. panzhihuaensis genome consists of ancient repetitive elements (Supplementary Note 4). S.D., Y.G., X.F., A.J.L., Y.Y., X.G., D.L., N.L., H.W. In contrast, the evolutionarily more recent angiosperms (flowering plants) bear their seeds inside of ovaries. The reduced size of MSY compared with the X chromosome indicates that the Y chromosome of Cycas, unlike that reported for some angiosperms55, underwent severe degeneration and gene loss. Article Genetic contribution of paleopolyploidy to adaptive evolution in angiosperms. Yang, D.-Q. Evol. 5). Plant Biol. The transcriptome sequencing reads from 339 cycad species were generated in the current study. To identify the sex-differentiation region in the Cycas genome, a GWAS approach was adopted on sequence variations from 31 male and 31 female individuals with sex treated as a binary phenotype. Biol. FUS3 and LEC2 are shared by all living seed plants; the Cycas and other gymnosperm genomes contain genes composing a new clade of B3 domain proteins, that is, the FUS3/LEC2-like clade, which is sister to the clade of FUS3 and LEC2 (Extended Data Fig. 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. 23, 352354 (1985). bryophytes. Synonymous substitutions per synonymous site (KS) analysis of duplicate genes33 revealed a clear peak at similar KS values (~0.85, range 0.51.2) for both Cycas and Ginkgo, suggestive of an ancient WGD possibly shared by these two lineages (Supplementary Note 7)34. Natl Acad. Evol. STAG (https://github.com/davidemms/STAG) was also used to construct the species tree with default settings using low-copy genes (one to four copies). (c) The phylogenetic tree of CSLE and CSLG genes. Bootstrap values are shown on the braches. 15, 150 (2015). Pchy-Tarr, M. et al. Cycads are long-lived woody plants that, unlike other extant gymnosperms, bear frond-like leaves clustered at the tip of the stem4.