4), providing evidence that the MRCA of land plants was already equipped with the genetic network for AMF symbiosis. The best-fitting model was chosen as LG+G+I using the FindBestProteinModel function. Hornworts usually grow on damp soils or on rocks in tropical and warm temperate regions. In this scenario, the MRCA of land plants had LCIB. Despite its streamlined nature, some TAPs were only found in hornworts and vascular plants but not in the other two bryophyte genomes, with the most notable example being YABBY (Supplementary Table 8 and Supplementary Note). Front. Rhizoids do not conduct nutrients or water. Two primary classes of liverworts are distinguished by the growth pattern. & Harrison, C. J. All the raw sequences are deposited in the NCBI Sequence Read Archive under the BioProject PRJNA574424 and PRJNA574453, and to European Nucleotide Archive (ENA) under the study accessions PRJEB34763 and PRJEB34743 (Supplementary Tables 2 and 3). From the protonema grows the adult gametophyte, which is the persistent and independent stage in the life cycle. Amongst all the plant associations with cyanobacteria, most of the research has been done on hornworts, using A. punctatus (sequenced here) and the cyanobacterium Nostoc punctiforme as the study system. Bioinformatics 32, 767769 (2016). Curr. The Hornworts: Morphology, evolution and development - PMC Nucleic Acids Res. Hornworts uniquely possess a combination of traits that connect them with both green algae and other land plant lineages9. and F.-W.L. Phylogenetic reconstruction showed that this hornwort subtilase is not orthologous to those involved in other plant symbioses (Supplementary Fig. PC1 and PC2 refer to the first and second axes of principal component analysis on gene expression values. Meeks, J. C. Physiological adaptations in nitrogen-fixing Nostocplant symbiotic associations. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Romera-Branchat, M., Ripoll, J. J., Yanofsky, M. F. & Pelaz, S. The WOX 13 homeobox gene promotes replum formation in the Arabidopsis thaliana fruit. Wherever they are in the world, bryophytes are integral to ecosystem health. Hornworts are the only land plants with a pyrenoid-based CCM. PLoS ONE 6, e21800 (2011). The number and names of genera are a current matter of investigation, and several competing classification schemes have been published since 1988. Once fertilization occurs, the sporophyte begins to develop. PubMed Central 105) and back translated to nucleotides by TranslatorX106. & Dawe, R. K. A molecular view of plant centromeres. The Linked Data Service provides access to commonly found standards and vocabularies promulgated by the Library of Congress. ), This page was last edited on 21 June 2023, at 23:47. The alignments were processed to remove sites with over 50% gaps or Ns and remove sequences shorter than 50% of the alignment length. F.-W.L. [23] Chromosome-scale genome sequencing of three hornwort species corroborate that stomata evolved only once during land plant evolution. The dotted line shows the one-third threshold. We have not succeeded in reconstituting hornwortAMF symbiosis in vitro and hence are unable to test expression of these orthologues in the context of AMF. Curr. However, the most recent phylogenetic evidence leans strongly towards bryophyte monophyly,[26][27][28][29][30][31][24][32][33][excessive citations] and it has been proposed that hornworts are de-ranked to the original class Anthocerotopsida.[28]. The hornwort life cycle, like all plants, is alternation of generations. Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. We also generated a self dot-plot of the A. agrestis Bonn genome to search for regions that are highly similar across scaffolds and are repetitive. Sci. The phylogenetic tree indicates that the hornwort LCIBs form a sister clade to the Klebsormidium nitens homologue (Fig. 1e). 30, 772780 (2013). Whether LCIB also participates in hornwort CCM awaits future functional characterization. 105). Therefore, we hypothesized that dropping scaffolds mainly with non-streptophyte affiliation will effectively remove contaminants from our assembly. Ligrone, R., Duckett, J. G. & Renzaglia, K. S. The origin of the sporophyte shoot in land plants: a bryological perspective. However, their methods of absorbing minerals and water are starkly different from their vascular cousins. 4 and Supplementary Table 4). 111) to summarize all the 742 gene trees and measured branch supports as local posterior probabilities112. Hornwort DNA was extracted using a CTAB-precipitation method modified from ref. In addition to EPF, an EPF-like gene in the EPFL4-6 clade, was found in hornworts (Supplementary Fig. At the bottom of the sporophyte (closest to the interior of the gametophyte), is a foot. The tendency of an organisms water content to change with its environment is called poikilohydric. In C. reinhardtii, LCIB gene expression is highly induced by CO2 limitation and the encoded proteins localize around pyrenoids to presumably block CO2 leakage59,60. Hornworts (Division Anthocertophyta) The mature sporophytes of a hornwort look like miniature green cattle horns. Gene duplication and evolution in recurring polyploidizationdiploidization cycles in plants. J. Bot. 73) and divided with the total number of reads to calculate percentage mapped. While gene density does fluctuate along the scaffolds, extensive regions with low gene density typical for centromeric regions of vascular plants were missing. PPR genes were identified based on the Orthofinder results (see later). Lab 21 Flashcards | Quizlet Bryophytes (Mosses, Liverworts, and Hornworts) Earth.com While hornworts have a gametophyte-dominant life cycle like other bryophytes, their sporophyte generation (Fig. If a hornwort is dioecious, the life cycle would have antheridia and archegonia produced on separate gametophytes and the sporophyte would grow from the gametophyte producing archegonia. The slides were then pressed with a thumb directly over the coverslip. Natl Acad. Cold Spring Harb. Wickett, N. J. et al. Bainard, J. D. & Villarreal Aguilar, J. C. Genome size increases in recently diverged hornwort clades. Among land plants, hornworts are one of the earliest-diverging lineages of the early land plant ancestors;[24] cladistic analysis implies that the group originated prior to the Devonian, around the same time as the mosses and liverworts. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. We run Tandem Repeats Finder120 to identify tandem repeats with a minimum alignment score of 50 and a maximum period size of 2,000bp. F.-W.L., P.S., K.S., T.N., J.C.V., E.F. and M.W. Biol. The word size was set to 2 and maximum target sequences as 250. 6, 31 (2005). N.P., S.R., M.W., K.S., P.S. CAS [20] However, the same form of columella is also characteristic of basal moss groups, such as the Sphagnopsida and Andreaeopsida, and has been interpreted as a character common to all early land plants with stomata. S.W. PubMed Hornworts have a flattened thalloid gametophyte, out of which grow their long photosynthetic sporophytes (Figure \(\PageIndex{1}\)), composed of a sporangium with a columella and pseudoelaters. be, Anthoceros genomes lack whole genome duplication. Plant J. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Venturini, L., Caim, S., Kaithakottil, G. G., Mapleson, D. L. & Swarbreck, D. Leveraging multiple transcriptome assembly methods for improved gene structure annotation. The detailed summary can be found in Supplementary Table 14. In A. Jonathan Shaw & Bernard Goffinet (Eds. volume6,pages 259272 (2020)Cite this article. & Spalding, M. H. LCIB in the Chlamydomonas CO2-concentrating mechanism. New Phytol. This suggests that hornwort sporophyte identity may not be determined by KNOX2 through interaction with BELL. We used DESeq2 (ref. The libraries were filtered to remove protein-coding genes by blasting against the UniProt plant database. The search parameters were otherwise as default. Some species can also reproduce using brood bodies which are a specialized group of cells that can grow into adult plants. They dont have the structural ability to grow upwards. This third region is the capsule. Metrics Abstract Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes. Greenish-yellow in color, the leaves can often have a slightly translucent appearance. After removal of the coverslip, the slides were air-dried for 10min at room temperature and then extracted with methanol at 20C for 10min. Horizontal transfer of an adaptive chimeric photoreceptor from Google Scholar. The small, threadlike protonema develops into the adult gametophyte stage which is characterized as the more elaborate, leafy stage of the plants life cycle. 21, 18131819 (2004). PLoS Genet. This is partly because both the bryophytes that have published genomes to date (P. patens and M. polymorpha) are incapable of AMF symbiosis and may have secondarily lost the symbiosis genes, as exemplified in some angiosperms45. Why is it so popular? PubMed 5) and thus is consistent with the organisms tree with many losses in various lineages. To infer gene trees, we used both the amino acid and nucleotide matrices, and employed the maximum likelihood method implemented in IQ-Tree v.1.6.12 (ref. Libraries were sequenced at the FGCZ on a HiSeq4000 machine. This species is common of moist soil throughout North America. Evolution of the YABBY gene family in seed plants. i-ADHoRe 3.0fast and sensitive detection of genomic homology in extremely large data sets. The hornworts, formally known as Anthocerotae, are a monophyletic group comprising a third extant lineage of nonvascular land plants. 15, 550 (2014). These are the sporophyte and gametophyte generations. The asterisk indicates that the M. paleacea transcriptome was searched instead of M. polymorpha genome because the latter secondarily lost AMF. 85) to carry out differential gene expression analysis, with false-discovery rate set to 0.005 and log2-fold-change threshold set to 1. B. Supplementary Table 13 shows the origin and specimen voucher for each of the three strains. Transcriptomes were assembled for each species/strain separately. We explored whether hornwort genomes have genes that are known to be required for pyrenoid-based CCM in C. reinhardtii. f, P. patens, on the other hand, shows a clear 1:1 and some 1:2 syntenic relationship, suggesting paleopolyploidy. conducted RNA-seq experiment on developmental stages. Meiosis occurs within the sporangium (also called a capsule), producing haploid spores that are dispersed aerially. (1) We trained Augustus with only the RNA-seq evidence and predicted gene models by taking into account RNA-seq, protein, Mikado and PASA assembled transcripts. Plant J. Ou, S. & Jiang, N. LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons. conducted analysis on salicylic acid signalling. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. The Pfam protein families database in 2019. Marchler-Bauer, A. et al. For each extensively analysed gene family, we directly searched the raw genomic sequence using bryophyte or vascular plant homologues as query sequences to find additional gene models that might have been missed by our gene prediction pipeline. 5). It is possible that such differences may contribute to the unique developmental pattern of hornwort sporophytes. Meeks, J. C. Symbiosis between nitrogen-fixing cyanobacteria and plants. Accessibility StatementFor more information contact us atinfo@libretexts.org. found: LC data base, 2/7/91 (hornworts, anthocerotes) found: PREMARC, 2/7/91 (Anthocerotaceae) LC Classification. Camacho, C. et al. AagrOXF_evm.model.utg000018l.552.1 was used as a query to BLASTp search at NCBI on 9 October 2019. Commun. Whether LCIB homologues have a similar function and localization in hornworts remains to be experimentally tested. 45, D200D203 (2017). On the exterior of the thallus, simple pores allow for gas exchange. WOX13-like genes are required for reprogramming of leaf and protoplast cells into stem cells in the moss Physcomitrella patens. We used the D-GENIES dot-plot tool114 with the default options to visually assess collinearity of the three genome assemblies. Sequences identical in the included region were treated as a single operational taxonomic unit (OTU) during the phylogenetic analysis. The Illumina libraries were prepared by BGI and sequenced on HiSeq4000. Sci. Here, we report the draft genome sequence of the. Notably, hornwort sporophytes are photosynthetic and capable of transferring photosynthates to the gametophyte. Hornworts, as the earliest diverging lineage in bryophytes, are crucial to infer character evolution and reveal the nature of the MRCA of bryophytes and that of land plants. Zimin, A. V. et al. J. Exp. The number of species is uncertain. Figure 5.1. To investigate the phylogenetic position of hornworts, we compiled 742 mostly single-copy genes from 21 genomes spanning major lineages of land plants and streptophyte algae. 8 and Supplementary Tables 8 and 9). F.-W.L., P.S., K.S. The Anthoceros genomes also have a single FLORICAULA/LEAFY (FLO/LFY) gene (Supplementary Fig. Simo, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. All bryophytes have two things in common they are terrestrial and nonvascular. Sequencing reads were mapped to the respective genomes by HiSat2 (ref. RNA interference knockdown of a subtilase (SBTM1) in the legume Lotus japonicus resulted in a decreased arbuscule formation52. Methods and results of the pan genome construction as well as gene set comparison can be found in the Supplementary notes. 10, e1004487 (2014). and P.S. Natl Acad. The thallus is lobed with toothed edges. BMC Bioinf. Jin, S. et al. The three genomes are highly collinear with a greater collinearity found between the two A. agrestis strains (Supplementary Fig. Hornwort, also called rigid hornwort, coontail, and coon's tail, is an underwater, free-floating aquatic plant that can be found in bodies of water on every continent except Antarctica. https://doi.org/10.1038/s41477-020-0618-2, DOI: https://doi.org/10.1038/s41477-020-0618-2. We found that some of the small scaffolds were classified as of non-streptophyte origin with high confidence; these scaffolds were then removed from the assembly. 130) and 149 well-conserved sites of 51 sequences were included. A distinctive long, thin, needle-like sporangium looks like a horn. Delaux, P.-M. et al. assembled the genomes. We then used single-linkage clustering to construct gene families and estimate KS divergence using phylogenetic analysis by maximum likelihood (PAML)123 with the F3X4 model for each node in the gene family phylogenies. Svistoonoff, S. et al. 9, R7 (2008). Hornwort is a type of algae that can be found in freshwater or saltwater environments. The hornwort genomes presented here offer a unique window into the biology of land plant MRCA. Our Ks plots on the annotated Anthoceros genes similarly show no sign of WGD (Supplementary Fig. 6, e4958 (2018). 103) with the Viridiplantae set to assess the completeness of our genomes and annotations. Plant Cell 7, 785794 (1995). Within bryophytes, no collinear segment conserved across all three lineages was found, although there were genomic regions exclusively collinear between each of two bryophyte genomes (Supplementary Fig. Throughout their lifecycles, they play an important role in soil formation, maintaining soil moisture, and recycling nutrients. In addition to EPF, an EPF-like gene in the EPFL4-6 clade, was found in hornworts (Supplementary Fig. Bioinformatics 30, 21142120 (2014). For the EPF and EPF-like gene family, we used the matrix compiled by Takata et al.136 and added the Anthoceros and M. polymorpha homologues. Although they lack true veins, many species of mosses have long narrow cells in their stems, the midribs of their leaves, and their rhizoids (root-like plant Almost 40 percent of the species belong to a single family . All other . 3 shows that our genomes have similar (if not better) BUSCO scores compared to many published non-flowering plant genomes. For each genome, we used the DupPipe pipeline to construct gene families and estimate the age of gene duplications121. 13). F1000Res. Dendroceros and Megaceros are mainly tropical genera. The total assembly length varied between 117 and 133Mb, which is consistent with the size estimates based on k-mer analysis (Table 1) but slightly larger than those from flow cytometry17,18. Genome Biol. Methods 14, 417419 (2017). The fertilized zygote will then develop into the diploid sporophyte. 3d), suggesting that they may have similar roles in stomatal patterning in hornworts. After deriving the consensus gene models, we used PASA and the PASA assembled transcripts to correct erroneous gene models, add UTRs (untranslated regions), and predict alternative splice variants in two rounds. Bioinformatics 27, 764770 (2011). Cell 171, 287299 (2017). To obtain protein homology information, we retrieved the 19 proteomes (only primary transcripts; Supplementary Table 15) and aligned them to the genome assemblies using exonerate98. [6] This particular feature is very unusual in land plants, unique to hornworts, but is common among algae.[7][8]. Sakakibara, K. et al. [19] The tip of the germ tube divides to form an octant (solid geometry) of cells, and the first rhizoid grows as an extension of the original germ cell. This implication is supported by the fact that only exogenous glucose, fructose or sucrose sustained dark nitrogen fixation in the A. punctatusN. The sporophyte grows from a basal meristem, with the oldest tissues at the apex. Internet Explorer). Examples of tracheophytes include trees, ferns, grasses, and flowering plants. Lab. ; JSPS grant nos KAKENHI 25113001, 26650143, 18H04843 and 18K06367 to K.S. The evolution of land plants is underlined by the rise of morphological, molecular and physiological innovations. And Why Do Farmers Do It? Hornworts look fairly similar to liverworts in the gametophyte stage, and they are generally blue-green in color. The spores are polar, usually with a distinctive Y-shaped tri-radiate ridge on the proximal surface, and with a distal surface ornamented with bumps or spines. Plants were grown on agar plates containing BCD medium67 at 22C. 4), other than the putative telomeric regions. Anthoceros agrestis Paton is emerging as the model system for the study of hornwort biology (Szvnyi et al., 2015). Maddison, W. P. & Maddison, D. R. Mesquite: A Modular System for Evolutionary Analysis v.3.04 (Mesquite, accessed 5 July 2016); http://mesquiteproject.org. Bot. The genetics behind hornwort pyrenoids, however, has remained completely unknown. Home > Plant encyclopedia > Bryophytes (Mosses, Liverworts, and Hornworts). The search parameters were otherwise set as the default. [2], Like all bryophytes, the dominant life phase of a hornwort is the haploid gametophyte. PubMed Orthofinder was run using the default setting, except that the msa option was used. 17, 70 (2019). Lee, L. R. & Bergmann, D. C. The plant stomatal lineage at a glance. Liverworts have two primary growth patterns: leafy and thalloid. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. The best-fitting model was chosen as JTTDCMUTF with ProteinModelSelection8.pl. F.-W.L. F.-W.L., P.S., K.S., T.N., D.H., S.C. and G.K.-S.W. These long stems are covered in a feathery whorl of thin, green leaves that more . For A. punctatus, Illumina genomic libraries were prepared by BGI and sequenced on HiSeq4000. Such pyrenoid-based CCM has been extensively studied in the model green alga Chlamydomonas reinhardtii with the hope of installing a CCM in crop plants57. These are released from the capsule when it splits lengthwise from the tip. 4, 150 (2013). a, Orthologues of AMF symbiosis pathway genes can be found in hornworts, indicating their presence in the common ancestor of land plants. 105). All the hornwort LCIB sequences have the conserved amino acid residues at the active sites that are shared with other algal LCIBs61 (Fig. Current Biology 29, 27432750 (2019). El-Gebali, S. et al. Thallophytes were the first plants. For example, the presence of a basal sporophytic meristem and asynchronous meiosis are unique to hornworts14. One Thousand Plant Transcriptomes Initiative. The name Anthocerotophyta means 'horn flower plant'. The hornwort genome and early land plant evolution - Nature Bryologist 68, 227231 (1965). Monogr. Bootstrap samples (1,000 replicates) were generated with seqboot from PHYLIP package v.3.697 (ref. Anthocerotophyta (Hornworts) The Biology Primer On the other end of the spectrum, there are thallophytes, which, while also nonvascular, require a fully aquatic life to survive. K.n., K. nitens; C.r., C. reinhardtii; O.l., Ostreococcus lucimarinus. Resulting alignments were subjected to ML tree inference using IQ-TREE v.1.6.1 (ref. As in mosses and liverworts, hornworts have a gametophyte-dominant life cycle, in which cells of the plant carry only a single set of genetic information; the flattened, green plant body of a hornwort is the gametophyte stage of the plant. Hornworts are a group of non-vascular Embryophytes (land plants) constituting the division Anthocerotophyta (/nosrtft, -tfat/). Wheeler, T. J. ; funding from Foundation of German Business (sdw), Georges and Antoine Claraz Foundation and URPP Evolution in Action to A.N. & Briones-Moreno, A. [17][18] In most species, there is a single cell inside the spore, and a slender extension of this cell called the germ tube germinates from the proximal side of the spore.

725 Chestnut St, Newton, Ma, Articles W