The emergence, evolution, and diversification of the miR390-TAS3-ARF pathway in land plants

AbstractIn plants, miR390 directs the production of tasiRNAs from TRANS-ACTING SIRNA 3 (TAS3) transcripts to regulate AUXIN RESPONSIVE FACTOR (ARF) genes, transcription factors critical for auxin signaling; these tasiRNAs are known as tasiARFs. This pathway is highly conserved, with the TAS3 as the only one noncoding gene present almost ubiquitously in land plants. To understand the evolution of this miR390-TAS3-ARF pathway, we characterized homologs of these three genes from thousands of plant species, from bryophytes to angiosperms. Both miR390 and TAS3 are present and functional in liverworts, confirming their ancestral role to regulate ARFs in land plants. We found the lower-stem region of MIR390 genes, critical for accurate DCL1 (DICER-LIKE 1) processing, is conserved in sequence in seed plants. We propose a model for the transition of functional tasiRNA sequences in TAS3 genes occurred at the emergence of vascular plants, in which the two miR390 target sites of TAS3 genes showed distinct pairing patterns in different plant lineages. Based on the cleavability of miR390 target sites and the distance between target site and tasiARF we inferred a potential bidirectional processing mechanism exists for some TAS3 genes. We also demonstrated a tight mutual selection between tasiARF and its target genes, and characterized unusual aspects and diversity of regulatory components of this pathway. Taken together, these data illuminate the evolutionary path of the miR390-TAS3-ARF pathway in land plants, and demonstrate the significant variation that occurs in the production of phasiRNAs in plants, even in the functionally important and archetypal miR390-TAS3-ARF regulatory circuit.

Download Full-text

Counting counts: revised estimates of numbers of accepted species of flowering plants, seed plants, vascular plants and land plants with a review of other recent estimates

Phytotaxa ◽

10.11646/phytotaxa.272.1.5 ◽

2016 ◽

Vol 272 (1) ◽

pp. 82 ◽

Cited By ~ 52

Author(s):

EIMEAR NIC LUGHADHA ◽

RAFAËL GOVAERTS ◽

IRINA BELYAEVA ◽

NICHOLAS BLACK ◽

HEATHER LINDON ◽

...

Keyword(s):

Vascular Plants ◽

Flowering Plants ◽

Land Plants ◽

Seed Plants ◽

Seed Plant ◽

Plant Names ◽

The World ◽

Alternative Approaches ◽

Plant Families ◽

International Plant

We present revised estimates of the numbers of accepted species of flowering plants (369,434), seed plants (370,492), vascular plants (383,671) and land plants (403,911) based on a recently de-duplicated version of the International Plant Names Index and rates of synonymy calculated from the seed plant families published in the World checklist of selected plant families. Alternative approaches to estimating or calculating the number of accepted plant species are discussed and differences between results are highlighted and interpreted.

Download Full-text

Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein–protein interaction network

Scientific Reports ◽

10.1038/s41598-021-93661-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Suthanthiram Backiyarani ◽

Rajendran Sasikala ◽

Simeon Sharmiladevi ◽

Subbaraya Uma

Keyword(s):

Candidate Genes ◽

Protein Interaction ◽

Target Genes ◽

Interaction Network ◽

Enrichment Analysis ◽

Auxin Signaling ◽

Pathway Enrichment Analysis ◽

Ppi Network ◽

Protein Protein Interaction ◽

The Difference

AbstractBanana, one of the most important staple fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein–protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By further validating these candidate genes in seeded and seedless accession of Musa spp. we put forward MaAGL8, MaMADS16, MaGH3.8, MaMADS29, MaRGA1, MaEXPA1, MaGID1C, MaHK2 and MaBAM1 as possible target genes in the study of natural parthenocarpy. In contrary, expression profile of MaACLB-2 and MaZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. By exploring the PPI of validated genes from the network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLAVATA(CLV)–WUSHEL(WUS) signaling pathway in addition to gibberellin mediated auxin signaling in parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through PPI network.

Download Full-text

Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

Frontiers in Genetics ◽

10.3389/fgene.2021.741858 ◽

2021 ◽

Vol 12 ◽

Author(s):

Pengfei Xu ◽

Yantao Zhu ◽

Yanfeng Zhang ◽

Jianxia Jiang ◽

Liyong Yang ◽

...

Keyword(s):

Mirna Target ◽

Target Genes ◽

Rare Variants ◽

Agronomic Traits ◽

Global Analysis ◽

Variant Calling ◽

Genetic Variations ◽

Nucleotide Polymorphisms ◽

A Genome ◽

Target Sites

MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.

Download Full-text

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.

Download Full-text

O-methylated N-glycans Distinguish Mosses from Vascular Plants

Biomolecules ◽

10.3390/biom12010136 ◽

2022 ◽

Vol 12 (1) ◽

pp. 136

Author(s):

David Stenitzer ◽

Réka Mócsai ◽

Harald Zechmeister ◽

Ralf Reski ◽

Eva L. Decker ◽

...

Keyword(s):

Green Algae ◽

Vascular Plants ◽

Land Plants ◽

Phylogenetic Relation ◽

Complex Type ◽

Animal Kingdom ◽

Moss Species ◽

First Finding ◽

The Common ◽

Terminal Mannose

In the animal kingdom, a stunning variety of N-glycan structures have emerged with phylogenetic specificities of various kinds. In the plant kingdom, however, N-glycosylation appears to be strictly conservative and uniform. From mosses to all kinds of gymno- and angiosperms, land plants mainly express structures with the common pentasaccharide core substituted with xylose, core α1,3-fucose, maybe terminal GlcNAc residues and Lewis A determinants. In contrast, green algae biosynthesise unique and unusual N-glycan structures with uncommon monosaccharides, a plethora of different structures and various kinds of O-methylation. Mosses, a group of plants that are separated by at least 400 million years of evolution from vascular plants, have hitherto been seen as harbouring an N-glycosylation machinery identical to that of vascular plants. To challenge this view, we analysed the N-glycomes of several moss species using MALDI-TOF/TOF, PGC-MS/MS and GC-MS. While all species contained the plant-typical heptasaccharide with no, one or two terminal GlcNAc residues (MMXF, MGnXF and GnGnXF, respectively), many species exhibited MS signals with 14.02 Da increments as characteristic for O-methylation. Throughout all analysed moss N-glycans, the level of methylation differed strongly even within the same family. In some species, methylated glycans dominated, while others had no methylation at all. GC-MS revealed the main glycan from Funaria hygrometrica to contain 2,6-O-methylated terminal mannose. Some mosses additionally presented very large, likewise methylated complex-type N-glycans. This first finding of the methylation of N-glycans in land plants mirrors the presumable phylogenetic relation of mosses to green algae, where the O-methylation of mannose and many other monosaccharides is a common trait.

Download Full-text

Allosteric deregulation of phenylalanine biosynthesis evolved with the emergence of vascular plants

10.1101/834747 ◽

2019 ◽

Author(s):

Jorge El-Azaz ◽

Francisco M. Cánovas ◽

Belén Barcelona ◽

Concepción Ávila ◽

Fernando de la Torre

Keyword(s):

Vascular Plants ◽

Seed Plants ◽

Type I ◽

Type Ii ◽

Adjacent Region ◽

In Planta ◽

Secondary Products ◽

Rate Limiting Step ◽

Limiting Step ◽

Rate Limiting

AbstractPhenylalanine (Phe) is the precursor of essential secondary products in plants. Here we show that a key, rate-limiting step in Phe biosynthesis, which is catalyzed by arogenate dehydratase (ADT), experienced allosteric de-regulation during evolution. Enzymes from microorganisms and type-I ADTs from plants are strongly feedback-inhibited by Phe, while type-II isoforms remain active at high levels of Phe. We have found that type-II ADTs are widespread across seed plants and their overproduction resulted in a dramatic accumulation of Phe in planta, up to 40-times higher than those observed following the expression of type-I enzymes. Punctual changes in the allosteric binding site of Phe and adjacent region are responsible for the observed relaxed regulation. The phylogeny of plant ADTs evidences that the emergence of type-II isoforms with relaxed regulation occurred at some point in the transition between non-vascular plants and tracheophytes enabling the massive production of Phe-derived compounds, primarily lignin, which are attributes of vascular plants.

Download Full-text

Simultaneous parsimony jackknife analysis of 2538rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants

Plant Systematics and Evolution ◽

10.1007/bf00985205 ◽

1998 ◽

Vol 213 (3-4) ◽

pp. 259-287 ◽

Cited By ~ 136

Author(s):

Mari K�llersj� ◽

James S. Farris ◽

Mark W. Chase ◽

Birgitta Bremer ◽

Michael F. Fay ◽

...

Keyword(s):

Dna Sequences ◽

Flowering Plants ◽

Land Plants ◽

Seed Plants ◽

Green Plants ◽

Jackknife Analysis

Download Full-text

Comparative profile analysis reveals differentially expressed microRNAs regulate anther and pollen development in kenaf cytoplasmic male sterility line

Genome ◽

10.1139/gen-2018-0207 ◽

2019 ◽

Vol 62 (7) ◽

pp. 455-466

Author(s):

Peng Chen ◽

Qiqi Shi ◽

Zhichen Liang ◽

Hai Lu ◽

Ru Li

Keyword(s):

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Regulatory Network ◽

Pollen Development ◽

Protein Modification ◽

Target Genes ◽

Profile Analysis ◽

Differentially Expressed ◽

Auxin Signaling ◽

Mirna Regulation

Cytoplasmic male sterility (CMS) is advantageous in extensive crop breeding and represents a perfect model for understanding anther and pollen development research. MicroRNAs (miRNAs) play key roles in regulating various biological processes. However, the miRNA-mediated regulatory network in kenaf CMS occurrence remains largely unknown. In the present study, a comparative deep sequencing approach was used to investigate the miRNAs and their roles in regulating anther and pollen development during CMS occurrence. We identified 283 known and 46 new candidate miRNAs in kenaf anther. A total of 67 differentially expressed miRNAs (DEMs) were discovered between CMS and its maintainer line. Among them, 40 and 27 miRNAs were up- and downregulated, respectively. These 67 DEMs were predicted to target 189 genes. Validation of DEMs and putative target genes were confirmed by using real-time quantitative PCR. In addition, a potential miRNA-mediated regulatory network, which mainly involves the auxin signaling pathway, signal transduction, glycolysis and energy metabolism, gene expression, transmembrane transport, protein modification and metabolism, and floral development, that mediates anther development during CMS occurrence was proposed. Taken together, our findings provide a better understanding of the molecular mechanism of miRNA regulation in pollen development and CMS occurrence in kenaf.

Download Full-text

A fern WUSCHEL-RELATED HOMEOBOX gene functions in both gametophyte and sporophyte generations

BMC Plant Biology ◽

10.1186/s12870-019-1991-8 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Christopher E. Youngstrom ◽

Lander F. Geadelmann ◽

Erin E. Irish ◽

Chi-Lien Cheng

Keyword(s):

Stem Cells ◽

Lateral Roots ◽

Homeobox Gene ◽

Genetic Networks ◽

Land Plants ◽

Seed Plants ◽

Wild Type ◽

Cell Fates ◽

Cell Divisions ◽

Gene Functions

Abstract Background Post-embryonic growth of land plants originates from meristems. Genetic networks in meristems maintain the stem cells and direct acquisition of cell fates. WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors involved in meristem networks have only been functionally characterized in two evolutionarily distant taxa, mosses and seed plants. This report characterizes a WOX gene in a fern, which is located phylogenetically between the two taxa. Results CrWOXB transcripts were detected in proliferating tissues, including gametophyte and sporophyte meristems of Ceratopteris richardii. In addition, CrWOXB is expressed in archegonia but not the antheridia of gametophytes. Suppression of CrWOXB expression in wild-type RN3 plants by RNAi produced abnormal morphologies of gametophytes and sporophytes. The gametophytes of RNAi lines produced fewer cells, and fewer female gametes compared to wild-type. In the sporophyte generation, RNAi lines produced fewer leaves, pinnae, roots and lateral roots compared to wild-type sporophytes. Conclusions Our results suggest that CrWOXB functions to promote cell divisions and organ development in the gametophyte and sporophyte generations, respectively. CrWOXB is the first intermediate-clade WOX gene shown to function in both generations in land plants.

Download Full-text

Diversity of Sperm Cell Architecture in Ferns

Microscopy and Microanalysis ◽

10.1017/s1431927600028336 ◽

2001 ◽

Vol 7 (S2) ◽

pp. 452-453

Author(s):

Thomas H. Johnson ◽

Steven J. Schmitt ◽

Karen S. Renzaglia

Keyword(s):

Phosphate Buffer ◽

Vascular Plants ◽

Sperm Cell ◽

Electron Microscope Study ◽

Osmium Tetroxide ◽

Land Plants ◽

Scanning Electron Microscope Study ◽

Leptosporangiate Fern ◽

Male Gametes ◽

Cell Architecture

Among land plants, lower vascular plants produce the most elaborate of all male gametes. in order to characterize the degree of variability in sperm cell architecture among ferns, this scanning electron microscope study was undertaken on three highly disparate genera: Ceratopteris(a derived leptosporangiate fern) Angiopteris(a derived eusporangiate fern) and Psilotum(a putatively basal eusporangiate fern).Mature gametophytes were placed in 0.01M phosphate buffer (pH ca. 7.2) or distilled water until spermatozoids were released. Gametophyte portions were removed and the spermatozoid suspension fixed with 2% glutaraldehyde in 0.05M phosphate buffer. Post-fixation utilized 1% aqueous osmium tetroxide for lhr, followed by rinsing and dehydration in ethanol (10 min @ 25, 50, 75 and 100%). The dehydrated pellet was suspended in 100% hexamethyldisilazane, immediately centrifuged and the pellet deposited onto clean glass coverslips. Specimens were dried at 60°C, sputtered with ca. 350 A of palladium/gold and imaged in a Hitachi S570 SEM.

Download Full-text