Telomerase RNAs in land plants

Abstract To elucidate the molecular nature of evolutionary changes of telomeres in the plant order Asparagales, we aimed to characterize telomerase RNA subunits (TRs) in these plants. The unusually long telomere repeat unit in Allium plants (12 nt) allowed us to identify TRs in transcriptomic data of representative species of the Allium genus. Orthologous TRs were then identified in Asparagales plants harbouring telomere DNA composed of TTAGGG (human type) or TTTAGGG (Arabidopsis-type) repeats. Further, we identified TRs across the land plant phylogeny, including common model plants, crop plants, and plants with unusual telomeres. Several lines of functional testing demonstrate the templating telomerase function of the identified TRs and disprove a functionality of the only previously reported plant telomerase RNA in Arabidopsis thaliana. Importantly, our results change the existing paradigm in plant telomere biology which has been based on the existence of a relatively conserved telomerase reverse transcriptase subunit (TERT) associating with highly divergent TRs even between closely related plant taxa. The finding of a monophyletic origin of genuine TRs across land plants opens the possibility to identify TRs directly in transcriptomic or genomic data and/or predict telomere sequences synthesized according to the respective TR template region.

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Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2000.0615 ◽

2000 ◽

Vol 355 (1398) ◽

pp. 769-793 ◽

Cited By ~ 148

Author(s):

Karen Sue Renzaglia ◽

R. Joel Duff ◽

Daniel L. Nickrent ◽

David J. Garbary

Keyword(s):

Phylogenetic Signal ◽

Phenotypic Variability ◽

Land Plant ◽

Land Plants ◽

Total Evidence ◽

Data Sets ◽

Data Set ◽

Plant Phylogeny ◽

Male Gametes ◽

Early Land

As the oldest extant lineages of land plants, bryophytes provide a living laboratory in which to evaluate morphological adaptations associated with early land existence. In this paper we examine reproductive and structural innovations in the gametophyte and sporophyte generations of hornworts, liverworts, mosses and basal pteridophytes. Reproductive features relating to spermatogenesis and the architecture of motile male gametes are overviewed and evaluated from an evolutionary perspective. Phylogenetic analyses of a data set derived from spermatogenesis and one derived from comprehensive morphogenetic data are compared with a molecular analysis of nuclear and mitochondrial small subunit rDNA sequences. Although relatively small because of a reliance on water for sexual reproduction, gametophytes of bryophytes are the most elaborate of those produced by any land plant. Phenotypic variability in gametophytic habit ranges from leafy to thalloid forms with the greatest diversity exhibited by hepatics. Appendages, including leaves, slime papillae and hairs, predominate in liverworts and mosses, while hornwort gametophytes are strictly thalloid with no organized external structures. Internalization of reproductive and vegetative structures within mucilage–filled spaces is an adaptive strategy exhibited by hornworts. The formative stages of gametangial development are similar in the three bryophyte groups, with the exception that in mosses apical growth is intercalated into early organogenesis, a feature echoed in moss sporophyte ontogeny. A monosporangiate, unbranched sporophyte typifies bryophytes, but developmental and structural innovations suggest the three bryophyte groups diverged prior to elaboration of this generation. Sporophyte morphogenesis in hornworts involves non–synchronized sporogenesis and the continued elongation of the single sporangium, features unique among archegoniates. In hepatics, elongation of the sporophyte seta and archegoniophore is rapid and requires instantaneous wall expandability and hydrostatic support. Unicellular, spiralled elaters and capsule dehiscence through the formation of four regular valves are autapomorphies of liverworts. Sporophytic sophistications in the moss clade include conducting tissue, stomata, an assimilative layer and an elaborate peristome for extended spore dispersal. Characters such as stomata and conducting cells that are shared among sporophytes of mosses, hornworts and pteridophytes are interpreted as parallelisms and not homologies. Our phylogenetic analysis of three different data sets is the most comprehensive to date and points to a single phylogenetic solution for the evolution of basal embryophytes. Hornworts are supported as the earliest divergent embryophyte clade with a moss/liverwort clade sister to tracheophytes. Among pteridophytes, lycophytes are monophyletic and an assemblage containing ferns, Equisetum and psilophytes is sister to seed plants. Congruence between morphological and molecular hypotheses indicates that these data sets are tracking the same phylogenetic signal and reinforces our phylogenetic conclusions. It appears that total evidence approaches are valuable in resolving ancient radiations such as those characterizing the evolution of early embryophytes. More information on land plant phylogeny can be found at: http://www.science.siu.edu/landplants/index.html.

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The mitochondrial phylogeny of land plants shows support for Setaphyta under composition-heterogeneous substitution models

PeerJ ◽

10.7717/peerj.8995 ◽

2020 ◽

Vol 8 ◽

pp. e8995 ◽

Cited By ~ 2

Author(s):

Filipe Sousa ◽

Peter Civáň ◽

João Brazão ◽

Peter G. Foster ◽

Cymon J. Cox

Keyword(s):

Chloroplast Genome ◽

Molecular Phylogenetics ◽

Land Plant ◽

Land Plants ◽

Data Set ◽

Genome Data ◽

Plant Phylogeny ◽

Plant Group ◽

Strong Indicator ◽

Land Plant Phylogeny

Congruence among analyses of plant genomic data partitions (nuclear, chloroplast and mitochondrial) is a strong indicator of accuracy in plant molecular phylogenetics. Recent analyses of both nuclear and chloroplast genome data of land plants (embryophytes) have, controversially, been shown to support monophyly of both bryophytes (mosses, liverworts, and hornworts) and tracheophytes (lycopods, ferns, and seed plants), with mosses and liverworts forming the clade Setaphyta. However, relationships inferred from mitochondria are incongruent with these results, and typically indicate paraphyly of bryophytes with liverworts alone resolved as the earliest-branching land plant group. Here, we reconstruct the mitochondrial land plant phylogeny from a newly compiled data set. When among-lineage composition heterogeneity is accounted for in analyses of codon-degenerate nucleotide and amino acid data, the clade Setaphyta is recovered with high support, and hornworts are supported as the earliest-branching lineage of land plants. These new mitochondrial analyses demonstrate partial congruence with current hypotheses based on nuclear and chloroplast genome data, and provide further incentive for revision of how plants arose on land.

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A Nonflowering Land Plant Phylogeny Inferred from Nucleotide Sequences of Seven Chloroplast, Mitochondrial, and Nuclear Genes

International Journal of Plant Sciences ◽

10.1086/513474 ◽

2007 ◽

Vol 168 (5) ◽

pp. 691-708 ◽

Cited By ~ 139

Author(s):

Yin‐Long Qiu ◽

Libo Li ◽

Bin Wang ◽

Zhiduan Chen ◽

Olena Dombrovska ◽

...

Keyword(s):

Land Plant ◽

Nucleotide Sequences ◽

Nuclear Genes ◽

Plant Phylogeny ◽

Land Plant Phylogeny

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Sequencing of small RNAs of the fern Pleopeltis minima (Polypodiaceae) offers insight into the evolution of the microRNA repertoire in land plants

10.1101/078907 ◽

2016 ◽

Author(s):

Florencia Berruezo ◽

Flavio S. J. de Souza ◽

Pablo I. Picca ◽

Sergio I. Nemirovsky ◽

Leandro Martinez-Tosar ◽

...

Keyword(s):

Small Rna ◽

Land Plant ◽

Land Plants ◽

Phylogenetic Position ◽

Seed Plants ◽

Messenger Rnas ◽

Rna Molecules ◽

Functional Studies ◽

Mirna Genes ◽

Ecological Importance

AbstractMicroRNAs (miRNAs) are short, single stranded RNA molecules that regulate the stability and translation of messenger RNAs in diverse eukaryotic groups. Several miRNA genes are of ancient origin and have been maintained in the genomes of animal and plant taxa for hundreds of millions of years, and functional studies indicate that ancient miRNAs play key roles in development and physiology. In the last decade, genome and small RNA (sRNA) sequencing of several plant species have helped unveil the evolutionary history of land plant miRNAs. Land plants are divided into bryophytes (liverworts, mosses), lycopods (clubmosses and spikemosses), monilophytes (ferns and horsetails), gymnosperms (cycads, conifers and allies) and angiosperms (flowering plants). Among these, the fern group occupies a key phylogenetic position, since it represents the closest extant cousin taxon of seed plants, i.e. gymno- and angiosperms. However, in spite of their evolutionary, economic and ecological importance, no fern genome has been sequenced yet and few genomic resources are available for this group. Here, we sequenced the small RNA fraction of an epiphytic South American fern, Pleopeltis minima (Polypodiaceae), and compared it to plant miRNA databases, allowing for the identification of miRNA families that are shared by all land plants, shared by all vascular plants (tracheophytes) or shared by euphyllophytes (ferns and seed plants) only. Using the recently described transcriptome of another fern, Lygodium japonicum, we also estimated the degree of conservation of fern miRNA targets in relation to other plant groups. Our results pinpoint the origin of several miRNA families in the land plant evolutionary tree with more precision and are a resource for future genomic and functional studies of fern miRNAs.

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The Chloroplast Land Plant Phylogeny: Analyses Employing Better-Fitting Tree- and Site-Heterogeneous Composition Models

Frontiers in Plant Science ◽

10.3389/fpls.2020.01062 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 2

Author(s):

Filipe Sousa ◽

Peter Civáň ◽

Peter G. Foster ◽

Cymon J. Cox

Keyword(s):

Land Plant ◽

Plant Phylogeny ◽

Land Plant Phylogeny

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Desiccation tolerance in streptophyte algae and the algae to land plant transition: evolution of LEA and MIP protein families within the Viridiplantae

Journal of Experimental Botany ◽

10.1093/jxb/eraa105 ◽

2020 ◽

Vol 71 (11) ◽

pp. 3270-3278 ◽

Cited By ~ 1

Author(s):

Burkhard Becker ◽

Xuehuan Feng ◽

Yanbin Yin ◽

Andreas Holzinger

Keyword(s):

Desiccation Tolerance ◽

Experimental Studies ◽

Sister Group ◽

Land Plant ◽

Late Embryogenesis Abundant ◽

Land Plants ◽

Desiccation Stress ◽

Protein Families ◽

Intrinsic Protein ◽

Late Embryogenesis

Abstract The present review summarizes the effects of desiccation in streptophyte green algae, as numerous experimental studies have been performed over the past decade particularly in the early branching streptophyte Klebsormidium sp. and the late branching Zygnema circumcarinatum. The latter genus gives its name to the Zygenmatophyceae, the sister group to land plants. For both organisms, transcriptomic investigations of desiccation stress are available, and illustrate a high variability in the stress response depending on the conditions and the strains used. However, overall, the responses of both organisms to desiccation stress are very similar to that of land plants. We highlight the evolution of two highly regulated protein families, the late embryogenesis abundant (LEA) proteins and the major intrinsic protein (MIP) family. Chlorophytes and streptophytes encode LEA4 and LEA5, while LEA2 have so far only been found in streptophyte algae, indicating an evolutionary origin in this group. Within the MIP family, a high transcriptomic regulation of a tonoplast intrinsic protein (TIP) has been found for the first time outside the embryophytes in Z. circumcarinatum. The MIP family became more complex on the way to terrestrialization but simplified afterwards. These observations suggest a key role for water transport proteins in desiccation tolerance of streptophytes.

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Age of the Cedarberg Formation, South Africa and early land plant evolution

Geological Magazine ◽

10.1017/s0016756800033537 ◽

1986 ◽

Vol 123 (4) ◽

pp. 445-454 ◽

Cited By ~ 26

Author(s):

J. Gray ◽

J. N. Theron ◽

A. J. Boucot

Keyword(s):

South Africa ◽

Land Plant ◽

Plant Evolution ◽

Marine Phytoplankton ◽

Land Plants ◽

Table Mountain ◽

Plant Remains ◽

First Occurrence ◽

Land Plant Evolution ◽

Early Land

AbstractThe first occurrence of Early Paleozoic land plants is reported from South Africa. The plant remains are small, compact tetrahedral spore tetrads. They occur abundantly in the Soom Shale Member of the Cedarberg Formation, Table Mountain Group. Marine? phytoplankton (sphaeromorphs or leiospheres) occur with the spore tetrads in all samples. Rare chitinozoans are found in half the samples. Together with similar spore tetrads from the Paraná Basin (Gray et al. 1985) these are the first well-documented records of Ashgill and/or earlier Llandovery land plants from the Malvinokaffric Realm, and from the African continent south of Libya. These spore tetrads have botanical, evolutionary, and biogeographic significance. Their size in comparison with spore tetrads from stratigraphic sections throughout eastern North America, suggests that an earliest Llandovery age is more probable for the Soom Shale Member, although a latest Ordovician age cannot be discounted. The age of the brachiopods in the overlying Disa Siltstone Member has been in contention for over a decade. Both Ashgillian and Early Llandovery ages have been proposed. The age of the underlying Soom Shale Member based on plant spores and trilobites (earliest Llandovery or latest Ashgillian) suggests that the Disa Siltstone Member is also likely to be of Early Llandovery age, although the distance between the Soom Shale Member spore-bearing locality and rocks to the south yielding abundant invertebrate body fossils at one locality is great enough to permit diachroneity.

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Molecular Basis for Telomere Repeat Divergence in Budding Yeast

Molecular and Cellular Biology ◽

10.1128/mcb.21.21.7277-7286.2001 ◽

2001 ◽

Vol 21 (21) ◽

pp. 7277-7286 ◽

Cited By ~ 49

Author(s):

Klaus Förstemann ◽

Joachim Lingner

Keyword(s):

Reverse Transcription ◽

Budding Yeast ◽

Repetitive Sequences ◽

Telomerase Rna ◽

Wild Type ◽

Telomere Repeat ◽

Telomere Binding Protein ◽

Linear Chromosomes ◽

Substrate Annealing

ABSTRACT Telomerase is a ribonucleoprotein enzyme that adds repetitive sequences to the ends of linear chromosomes, thereby counteracting nucleotide loss due to incomplete replication. A short region of the telomerase RNA subunit serves as template for nucleotide addition onto the telomere 3′ end. Although Saccharomyces cerevisiaecontains only one telomerase RNA gene, telomere repeat sequences are degenerate in this organism. Based on a detailed analysis of the telomere sequences specified by wild-type and mutant RNA templates in vivo, we show that the divergence of telomere repeats is due to abortive reverse transcription in the 3′ and 5′ regions of the template and due to the alignment of telomeres in multiple registers within the RNA template. Through the interpretation of wild-type telomere sequences, we identify nucleotides in the template that are not accessible for base pairing during substrate annealing. Rather, these positions become available as templates for reverse transcription only after alignment with adjacent nucleotides has occurred, indicating that a conformational change takes place upon substrate binding. We also infer that the central part of the template region is reverse transcribed processively. The inaccessibility of certain template positions for alignment and the processive polymerization of the central template portion may serve to reduce the possible repeat diversification and enhance the incorporation of binding sites for Rap1p, the telomere binding protein of budding yeast.

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Laurussian land-plant diversity during the Silurian and Devonian: mass extinction, sampling bias, or both?

Paleobiology ◽

10.1017/s0094837300013087 ◽

1995 ◽

Vol 21 (1) ◽

pp. 74-91 ◽

Cited By ~ 53

Author(s):

Anne Raymond ◽

Cheryl Metz

Keyword(s):

Plant Diversity ◽

Mass Extinction ◽

Sampling Bias ◽

Land Plant ◽

Land Plants ◽

Data Sets ◽

Data Set ◽

Extinction Event ◽

Genus Richness ◽

Total Diversity

In phytogeographic data sets, the number of assemblages or floras from each interval may provide a test of the influence of sampling intensity on land-plant diversity. Using a data set of Silurian and Devonian compression-impression plant genera from Laurussia and the Acadian terrain, regression of five measures of land-plant diversity (total diversity, mean genus richness of floras, median assemblage diversity, most diverse assemblage, and standing diversity at interval boundaries) against the number assemblages or floras from thirteen intervals suggests that sampling bias influences all of the diversity measures to some extent, including within-habitat measures. The standing diversity of land plants at interval boundaries, the measure least influenced by sampling (r = 0.65, p = 0.05), increased steadily from the Middle Silurian to the late Givetian/early–middle Frasnian boundary, fell sharply in the early–middle Frasnian and remained low throughout the late Frasnian–middle Famennian. Standing diversity rose dramatically in the late Famennian and Strunian (latest Devonian): the Frasnian–Famennian extinction event may have affected land plants. The standing diversity of Silurian and Devonian microspore genera at interval boundaries mirrors that of compression-impression genera: neither record supports a land-plant diversity equilibrium during the Devonian.

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