scholarly journals Direct Repeats Co-occur with Few Short Dispersed Repeats in Plastid Genome of A Spikemoss, Selaginella vardei (Selaginellaceae, Lycophyta)

2018 ◽  
Author(s):  
Hong-Rui Zhang ◽  
Xian-Chun Zhang ◽  
Qiao-Ping Xiang
Keyword(s):  
Land Plant ◽  
Land Plants ◽  
Late Triassic ◽  
Rrna Gene ◽  
Direct Repeats ◽  
Plastid Genomes ◽  
Ca 50 ◽  
Phylogenetic Framework ◽  
The Stability ◽  
Dispersed Repeats

AbstractBackgroundIt is hypothesized that the highly conserved inverted repeat (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organizations, whereas the mechanism of the occurrence and stability maintenance of the newly reported direct repeats (DR) structure was yet awaiting further exploration. Here we introduced the DR structure of plastome in Selaginella vardei (Selaginellaceae, Lycophyta), trying to elucidate the mechanism of DR occurrence and stability maintenance.ResultsThe plastome of S. vardei is 121,254 bp in length and encodes 76 different genes, of which 62 encode proteins, 10 encode tRNAs and four encode rRNAs. Unexpectedly, the two identical rRNA gene regions (13,893 bp) are arranged into DR, and a ca. 50-kb trnN-trnF inversion spanning one DR copy exists in S. vardei, comparing to the typical IR organization of Isoetes flaccida (Isoetaceae, Lycophyta). We find extremely rare short dispersed repeats (SDRs) in plastome of S. vardei and is confirmed in its closely related species S. indica. The occurrence time of DR in Selaginellaceae is estimated at late Triassic (ca. 215 Ma) based on the phylogenetic framework of land plants.ConclusionsWe propose that the unconventional DR structure, co-occurred with extremely few SDRs, plays key role in maintaining the stability of plastome, and reflects a relic of the environmental upheaval during extinction event. We suggest that the ca. 50-kb inversion resulted in the DR structure, and recombination between DR regions is confirmed to generate multipartite subgenomes and diverse multimers, which shed lights on the diverse structures in plastome of land plants.

Permian–Triassic land-plant diversity in South China: Was there a mass extinction at the Permian/Triassic boundary?

Paleobiology ◽  
2011 ◽  
Vol 37 (1) ◽  
pp. 157-167 ◽  
Author(s):  
Conghui Xiong ◽  
Qi Wang
Keyword(s):  
South China ◽  
Mass Extinction ◽  
Middle Triassic ◽  
Land Plant ◽  
Land Plants ◽  
Late Triassic ◽  
Triassic Boundary ◽  
Permian Triassic Boundary ◽  
Diversity Dynamics ◽  
Early Middle Triassic

Diversity dynamics of the Permian–Triassic land plants in South China are studied by analyzing paleobotanical data. Our results indicate that the total diversity of land-plant megafossil genera and species across the Permian/Triassic boundary (PTB) of South China underwent a progressive decline from the early Late Permian (Wuchiapingian) to the Early-Middle Triassic. In contrast, the diversity of land-plant microfossil genera exhibited only a small fluctuation across the PTB of South China, showing an increase at the PTB. Overall, land plants across the PTB of South China show a greater stability in diversity dynamics than marine faunas. The highest extinction rate (90.91%) and the lowest origination rate (18.18%) of land-plant megafossil genera occurred at the early Early Triassic (Induan), but the temporal duration of the higher genus extinction rates (>60%) in land plants was about 23.4 Myr, from the Wuchiapingian to the early Middle Triassic (Anisian), which is longer than that of the coeval marine faunas (3–11 Myr). Moreover, the change of genus turnover rates in land-plant megafossils steadily fluctuated from the late Early Permian to the Late Triassic. More stable diversity and turnover rate as well as longer extinction duration suggest that land plants near the PTB of South China may have been involved in a gradual floral reorganization and evolutionary replacement rather than a mass extinction like those in the coeval marine faunas.

scholarly journals Regulation of the Poly(A) Status of Mitochondrial mRNA by Poly(A)-Specific Ribonuclease Is Conserved among Land Plants

2019 ◽  
Vol 61 (3) ◽  
pp. 470-480
Author(s):  
Mai Kanazawa ◽  
Yoko Ikeda ◽  
Ryuichi Nishihama ◽  
Shohei Yamaoka ◽  
Nam-Hee Lee ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Regulatory System ◽  
Land Plant ◽  
Molecular Genetic Analysis ◽  
Land Plants ◽  
Marchantia Polymorpha ◽  
Mitochondrial Rna ◽  
Cellular Functions ◽  
The Stability

Abstract Regulation of the stability and the quality of mitochondrial RNA is essential for the maintenance of mitochondrial and cellular functions in eukaryotes. We have previously reported that the eukaryotic poly(A)-specific ribonuclease (PARN) and the prokaryotic poly(A) polymerase encoded by AHG2 and AGS1, respectively, coordinately regulate the poly(A) status and the stability of mitochondrial mRNA in Arabidopsis. Mitochondrial function of PARN has not been reported in any other eukaryotes. To know how much this PARN-based mitochondrial mRNA regulation is conserved among plants, we studied the AHG2 and AGS1 counterparts of the liverwort, Marchantia polymorpha, a member of basal land plant lineage. We found that M. polymorpha has one ortholog each for AHG2 and AGS1, named MpAHG2 and MpAGS1, respectively. Their Citrine-fused proteins were detected in mitochondria of the liverwort. Molecular genetic analysis showed that MpAHG2 is essential and functionally interacts with MpAGS1 as observed in Arabidopsis. A recombinant MpAHG2 protein had a deadenylase activity in vitro. Overexpression of MpAGS1 and the reduced expression of MpAHG2 caused an accumulation of polyadenylated Mpcox1 mRNA. Furthermore, MpAHG2 suppressed Arabidopsis ahg2-1 mutant phenotype. These results suggest that the PARN-based mitochondrial mRNA regulatory system is conserved in land plants.

scholarly journals A Bayesian phylogenetic approach to estimating the stability of linguistic features and the genetic biasing of tone

2010 ◽  
Vol 278 (1704) ◽  
pp. 474-479 ◽  
Author(s):  
Dan Dediu
Keyword(s):  
Cultural Transmission ◽  
Linguistic Diversity ◽  
Large Set ◽  
Linguistic Features ◽  
Major Interest ◽  
Software Implementations ◽  
Phylogenetic Framework ◽  
Linguistic Tone ◽  
The Stability ◽  
Stable Characteristic

Language is a hallmark of our species and understanding linguistic diversity is an area of major interest. Genetic factors influencing the cultural transmission of language provide a powerful and elegant explanation for aspects of the present day linguistic diversity and a window into the emergence and evolution of language. In particular, it has recently been proposed that linguistic tone —the usage of voice pitch to convey lexical and grammatical meaning—is biased by two genes involved in brain growth and development, ASPM and Microcephalin . This hypothesis predicts that tone is a stable characteristic of language because of its ‘genetic anchoring’. The present paper tests this prediction using a Bayesian phylogenetic framework applied to a large set of linguistic features and language families, using multiple software implementations, data codings, stability estimations, linguistic classifications and outgroup choices. The results of these different methods and datasets show a large agreement, suggesting that this approach produces reliable estimates of the stability of linguistic data. Moreover, linguistic tone is found to be stable across methods and datasets, providing suggestive support for the hypothesis of genetic influences on its distribution.

A Geographical Information System (GIS) study of Triassic vertebrate biochronology

2005 ◽  
Vol 142 (4) ◽  
pp. 327-354 ◽  
Author(s):  
E. J. RAYFIELD ◽  
P. M. BARRETT ◽  
R. A. McDONNELL ◽  
K. J. WILLIS
Keyword(s):  
Spatial Data ◽  
Geographical Information Systems ◽  
Western Europe ◽  
Temporal Distribution ◽  
Geographical Information ◽  
Late Triassic ◽  
Spatial And Temporal Scales ◽  
Potential Index ◽  
The Stability ◽  
Land Vertebrate

Geographical Information Systems (GIS) have been applied extensively to analyse spatial data relating to varied environmental issues, but have not so far been used to address biostratigraphical or macroevolutionary questions over extended spatial and temporal scales. Here, we use GIS techniques to test the stability, validity and utility of proposed Middle and Late Triassic ‘Land Vertebrate Faunachrons’ (LVFs), a global biostratigraphical framework based upon terrestrial/freshwater tetrapod occurrences. A database of tetrapod and megafloral localities was constructed for North America and Western Europe that also incorporated information on relevant palaeoenvironmental variables. This database was subjected to various spatial analysis techniques. Our GIS analysis found support at a global level for Eocyclotosaurus as an Anisian index taxon and probably Aetosaurus as a Norian indicator. Other tetrapod taxa are useful biostratigraphical/biochronological markers on a regional basis, such as Longosuchus and Doswellia for Late Carnian time. Other potential index fossils are hampered, however, by taxonomic instability (Mastodonsaurus, Metoposaurus, Typothorax, Paleorhinus, Pseudopalatus, Redondasaurus, Redondasuchus) and/or are not clearly restricted in temporal distribution (Paleorhinus, Angistorhinus, Stagonolepis, Metoposaurus and Rutiodon). This leads to instability in LVF diagnosis. We found only in the western Northern Hemisphere is there some evidence for an Anisian–Ladinian biochronological unit amalgamating the Perovkan and Berdyankian LVFs, and a possible late Carnian unit integrating the Otischalkian and Adamanian.Megaplants are generally not useful for biostratigraphical correlation in the Middle and Upper Triassic of the study area, but there is some evidence for a Carnian-age floral assemblage that corresponds to the combined Otischalkian and Adamanian LVFs. Environmental biases do not appear to strongly affect the spatial distribution of either the tetrapods or megaplants that have been proposed as index taxa in biostratigraphical schemes, though several examples of apparent environmental bias were detected by the analysis. Consequently, we argue that further revision and refinement of Middle and Late Triassic LVFs is needed before they can be used to support global or multi-regional biostratigraphical correlations. Caution should therefore be exercised when using the current scheme as a platform for macroevolutionary or palaeoecological hypotheses. Finally, this study demonstrates the potential of GIS as a powerful tool for tackling palaeontological questions over extended timescales.

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

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.

scholarly journals Evaluation of Anti-biofilm Potential of Biosurfactant Extracted from Nocardia Species

Folia Medica ◽  
2021 ◽  
Vol 63 (3) ◽  
pp. 392-399
Author(s):  
Ali Javadi ◽  
Mohamad Reza Pourmand ◽  
Javad Hamedi ◽  
Fatemeh Gharebaghi ◽  
Zohre Baseri ◽  
...  
Keyword(s):  
Agar Plate ◽  
Compositional Analysis ◽  
16S Rrna Gene Sequencing ◽  
Hydrocarbon Chain ◽  
Laboratory Method ◽  
Rrna Gene ◽  
Surface Active Agents ◽  
Rrna Gene Sequencing ◽  
The Stability ◽  
Spreading Test

Introduction: Bacterial natural products such as biosurfactants and surface-active agents are important compounds which exhibit many applications in the fields of medicine.Aim: The aim of the present study was to isolate and identify Nocardia strains with high biosurfactant production and antibiofilm ability.Materials and methods: In the present study, a biosurfactant producing Nocardia species was isolated and identified by a laboratory method. Nocardia species were initially screened and then tested for their ability to produce biosurfactant. The oil spreading test and the surface tension measurements showed that one strain was a biosurfactant producer. The strain with the best surface activity results was selected for further studies and identified by 16S rRNA gene sequencing method. Fourier transform infrared spectroscopy (FTIR) and compositional analysis proved a biosurfactant structure.Results: Oil spreading test and blue agar plate test confirmed biosurfactants and extracellular anionic glycolipids. E24% assay using olive oil revealed strong emulsifying characteristic of the extracted biosurfactant with 100% emulsifying strength. FTIR spectrum indicated the presence of aliphatic hydrocarbon chain (lipid) along with the polysaccharide portion, confirming the glycolipid nature of the biosurfactant. The stability of the biosurfactant produced in different conditions was significant. Increasing concentration of BS significantly inhibited Pseudomonas aeruginosa biofilm.Conclusions: N. coubleae can be a representative of the genus Nocardia for the production of biosurfactants with beneficial physicochemical properties.

Molecular data provide new insights into the phylogeny of Cladonotinae (Orthoptera: Tetrigoidea) from China with the description of a new genus and species

Zootaxa ◽  
2020 ◽  
Vol 4809 (3) ◽  
pp. 547-559
Author(s):  
RONG-JIAO ZHANG ◽  
CONG-LIN ZHAO ◽  
FEI-PENG WU ◽  
WEI-AN DENG
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
New Genus ◽  
Molecular Data ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Close Relationship ◽  
Phylogenetic Framework ◽  
Mitochondrial Cytochrome Oxidase

Considerable effort has been devoted to elucidating the phylogenetic relationships of tetrigides. However, there is still no commonly accepted phylogenetic hypothesis. Therefore, the phylogenetic relationships among some subfamilies remain unclear; e.g., Cladonotinae is a controversial group, in which the phylogenetic relationships between genera and the boundaries of some of the included genera are unclear, causing some of the taxa to be difficult to identify. Therefore, an in-depth phylogenetic analysis of Cladonotinae is urgently needed. In this study, a robust phylogenetic framework for the tetrigides was reconstructed based on the combined mitochondrial cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and nuclear 18S ribosomal RNA (18S rRNA) gene sequences of 25 species belonging to 16 genera of Tetrigoidea from China, which included 13 species from 8 genera of Cladonotinae. Phylogenetic inferences were performed using the combined dataset and Bayesian inference (BI) and Maximum Parsimony (MP) methods, and the phylogenetic tree of Cladonotinae was reconstructed. All inferences based on the results of the present study supported the Cladonotinae subfamily as a polyphyletic group; within the Cladonotinae subfamily, Tetradinodula, and Tuberfemurus were closely related to Tetriginae, while Austrohancockia and Gibbotettix showed a close relationship to the Scelimenidae subfamily. Additionally, a new genus and new species of the Cladonotinae subfamily are described and illustrated: Hainantettix Deng, gen. nov. and Hainantettix strictivertex Deng, sp. nov. 

scholarly journals Age-Related Colonic Mucosal Microbiome Community Shifts in Monkeys

2020 ◽  
Author(s):  
Ravichandra Vemuri ◽  
Chrissy Sherrill ◽  
Matthew A Davis ◽  
Kylie Kavanagh
Keyword(s):  
Microbial Community ◽  
Systemic Inflammation ◽  
16S Rrna Gene Sequencing ◽  
Microbial Interactions ◽  
Rrna Gene ◽  
Vervet Monkeys ◽  
Fecal Samples ◽  
Age Related ◽  
Rrna Gene Sequencing ◽  
The Stability

Abstract Age-related changes in gut microbiome impact host health. The interactive relationship between the microbiome and physiological systems in an aged body system remains to be clearly defined, particularly in the context of inflammation. Therefore, we aimed to evaluate systemic inflammation, microbial translocation (MT), and differences between fecal and mucosal microbiomes. Ascending colon mucosal biopsies, fecal samples, and blood samples from healthy young and old female vervet monkeys were collected for 16S rRNA gene sequencing, MT, and cytokine analyses, respectively. To demonstrate microbial co-occurrence patterns, we used Kendall’s tau correlation measure of interactions between microbes. We found elevated levels of plasma LBP-1, MCP-1, and CRP in old monkeys, indicative of higher MT and systemic inflammation. Microbiome analysis revealed significant differences specific to age. At the phylum level, abundances of pathobionts such as Proteobacteria were increased in the mucosa of old monkeys. At the family level, Helicobacteriaceae was highly abundant in mucosal samples (old); in contrast, Ruminococcaceae were higher in the fecal samples of old monkeys. We found significantly lower Firmicutes:Bacteroidetes ratio and lower abundance of butyrate-producing microbes in old monkeys, consistent with less healthy profiles. Microbial community co-occurrence analysis on mucosal samples revealed 13 nodes and 41 associations in the young monkeys, but only 12 nodes and 21 associations in the old monkeys. Our findings provide novel insights into systemic inflammation and gut microbial interactions, highlight the importance of the mucosal niche, and facilitate further understanding of the decline in the stability of the microbial community with aging.

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

2020 ◽  
Vol 71 (11) ◽  
pp. 3270-3278 ◽  
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.

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

1986 ◽  
Vol 123 (4) ◽  
pp. 445-454 ◽  
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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