scholarly journals Phylogenetic Analysis of the Plant U2 snRNP Auxiliary Factor Large Subunit A Gene Family in Response to Developmental Cues and Environmental Stimuli

2021 ◽  
Vol 12 ◽  
Author(s):  
Shuai Lu ◽  
Cong Gao ◽  
Yongzhou Wang ◽  
Yingying He ◽  
Junrong Du ◽  
...  
Keyword(s):  
Gene Family ◽  
Plant Species ◽  
Plant Biomass ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
High Temperature Stress ◽  
Metal Exposure ◽  
Functional Studies ◽  
Branch Site ◽  
Recognition Motifs

In all organisms, splicing occurs through the formation of spliceosome complexes, and splicing auxiliary factors are essential during splicing. U2AF65 is a crucial splicing cofactor, and the two typical RNA-recognition motifs at its center recognize and bind the polypyrimidine sequence located between the intron branch site and the 3′-splice site. U2AF65A is a member of the U2AF65 gene family, with pivotal roles in diseases in mammals, specifically humans; however, few studies have investigated plant U2AF65A, and its specific functions are poorly understood. Therefore, in the present study, we systematically identified U2AF65A in plant species from algae to angiosperms. Based on 113 putative U2AF65A sequences from 33 plant species, phylogenetic analyses were performed, followed by basic bioinformatics, including the comparisons of gene structure, protein domains, promoter motifs, and gene expression levels. In addition, using rice as the model crop, we demonstrated that the OsU2AF65A protein is localized to the nucleus and cytoplasm, and it is involved in responses to various stresses, such as drought, high salinity, low temperature, and heavy metal exposure (e.g., cadmium). Using Arabidopsis thaliana and rice mutants, we demonstrated that U2AF65A is involved in the accumulation of plant biomass, growth of hypocotyl upon thermal stimulation, and reduction of tolerance of high temperature stress. These findings offer an overview of the U2AF65 gene family and its stress response functions, serving as the reference for further comprehensive functional studies of the essential specific splicing cofactor U2AF65A in the plant kingdom.

scholarly journals Molecular Evolution of the Vacuolar Iron Transporter (VIT) Family Genes in 14 Plant Species

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 144 ◽  
Author(s):  
Jun Cao
Keyword(s):  
Gene Family ◽  
Plant Species ◽  
Tandem Duplication ◽  
Expression Patterns ◽  
Gene Organization ◽  
Development Stages ◽  
Functional Studies ◽  
Iron Transporter ◽  
Group I ◽  
Conserved Gene

The vacuolar iron transporter (VIT) proteins are involved in the storage and transport of iron. However, the evolution of this gene family in plants is unknown. In this study, I first identified 114 VIT genes in 14 plant species and classified these genes into seven groups by phylogenetic analysis. Conserved gene organization and motif distribution implied conserved function in each group. I also found that tandem duplication, segmental duplication and transposition contributed to the expansion of this gene family. Additionally, several positive selection sites were identified. Divergent expression patterns of soybean VIT genes were further investigated in different development stages and under iron stress. Functional network analysis exhibited 211 physical or functional interactions. The results will provide the basis for further functional studies of the VIT genes in plants.

scholarly journals Genome-wide identification, phylogenetic, and expression analysis under abiotic stress conditions of LIM gene family in Medicago sativa L.

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252213
Author(s):  
Lili Nian ◽  
Xuelu Liu ◽  
Yingbo Yang ◽  
Xiaolin Zhu ◽  
Xianfeng Yi ◽  
...  
Keyword(s):  
Gene Family ◽  
Medicago Sativa ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Promoter Sequence ◽  
Regulatory Elements ◽  
Segmental Duplications ◽  
Conserved Motifs ◽  
Functional Studies ◽  
Genome Wide

The LIM (Lin-11, Isl-1 and Mec-3 domains) family is a key transcription factor widely distributed in animals and plants. The LIM proteins in plants are involved in the regulation of a variety of biological processes, including cytoskeletal organization, the development of secondary cell walls, and cell differentiation. It has been identified and analyzed in many species. However, the systematic identification and analysis of the LIM genes family have not yet been reported in alfalfa (Medicago sativa L.). Based on the genome-wide data of alfalfa, a total of 21 LIM genes were identified and named MsLIM01-MsLIM21. Comprehensive analysis of the chromosome location, physicochemical properties of the protein, evolutionary relationship, conserved motifs, and responses to abiotic stresses of the LIM gene family in alfalfa using bioinformatics methods. The results showed that these MsLIM genes were distributed unequally on 21 of the 32 chromosomes in alfalfa. Gene duplication analysis showed that segmental duplications were the major contributors to the expansion of the alfalfa LIM family. Based on phylogenetic analyses, the LIM gene family of alfalfa can be divided into four subfamilies: αLIM subfamily, βLIM subfamily, γLIM subfamily, and δLIM subfamily, and approximately all the LIM genes within the same subfamily shared similar gene structure. The 21 MsLIM genes of alfalfa contain 10 Motifs, of which Motif1 and Motif3 are the conserved motifs shared by these genes. Furthermore, the analysis of cis-regulatory elements indicated that regulatory elements related to transcription, cell cycle, development, hormone, and stress response are abundant in the promoter sequence of MsLIM genes. Real-time quantitative PCR demonstrated that MsLIM gene expression is induced by low temperature and salt. The present study serves as a basic foundation for future functional studies on the alfalfa LIM family.

scholarly journals Comprehensive Analysis of the Chitinase Family Genes in Tomato (Solanum lycopersicum)

Plants ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 52 ◽  
Author(s):  
Jun Cao ◽  
Xiaona Tan
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Functional Divergence ◽  
Functional Studies ◽  
Gene Structures ◽  
Functional Relevance ◽  
Conserved Gene ◽  
Chitinase Genes

Chitinase catalyzes the hydrolysis of chitin β-1,4 linkages. However, plants cannot produce chitin, suggesting that plant chitinases do not have the same function as animals. This study investigated the chitinase gene family in tomato and divided into eight groups via phylogenetic analyses with Arabidopsis and rice members. Conserved gene structures and motif arrangements indicated their functional relevance with each group. These genes were nonrandomly distributed across the tomato chromosomes, and tandem duplication contributed to the expansion of this gene family. Synteny analysis also established orthology relationships and functional linkages between Arabidopsis and tomato chitinase genes. Several positive selection sites were identified, which may contribute to the functional divergence of the protein family in evolution. In addition, differential expression profiles of the tomato chitinase genes were also investigated at some developmental stages, or under different biotic and abiotic stresses. Finally, functional network analysis found 124 physical or functional interactions, implying the diversity of physiological functions of the family proteins. These results provide a foundation for the exploration of the chitinase genes in plants and will offer some insights for further functional studies.

Genome-wide identification and analysis of maize PAL gene family and its expression profile in response to high-temperature stress

2020 ◽  
Vol 52 (5) ◽  
Author(s):  
De-Gong Wu ◽  
Qiu-Wen Zhan ◽  
Hai-Bing Yu ◽  
Bao-Hong Huang ◽  
Xin-Xin Cheng ◽  
...  
Keyword(s):  
High Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Expression Profile ◽  
High Temperature Stress ◽  
Genome Wide

scholarly journals Multilocus phylogenies reveal three new truffle-like taxa and the traces of interspecific hybridization in Octaviania (Boletaceae, Boletales)

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Takamichi Orihara ◽  
Rosanne Healy ◽  
Adriana Corrales ◽  
Matthew E. Smith
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Elongation Factor ◽  
Morphological Observation ◽  
Tree Comparison ◽  
Unknown Species ◽  
The Usa

ABSTRACTAmong many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subg. Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multilocus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri stat. nov. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multilocus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity found within the genus.

scholarly journals Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tao Fan ◽  
Yu-Zhen Zhao ◽  
Jing-Fang Yang ◽  
Qin-Lai Liu ◽  
Yuan Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Splice Site ◽  
Messenger Rna ◽  
Expression Patterns ◽  
Protein Structures ◽  
Single Copy ◽  
Central Component ◽  
Animal Kingdom ◽  
Functional Studies ◽  
U1 Snrnp

AbstractEukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly. The human U1-70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1-70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C-terminal, suggesting the specific role of these U1-70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1-70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.

scholarly journals Deciphering Substrate-Specific Methane Yields of Perennial Herbaceous Wild Plant Species

Agronomy ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 451
Author(s):  
Moritz von Cossel ◽  
Lorena Agra Pereira ◽  
Iris Lewandowski
Keyword(s):  
Plant Species ◽  
Dry Matter ◽  
Plant Biomass ◽  
Cropping Systems ◽  
Wild Plant ◽  
Small Scale ◽  
Social Ecological ◽  
Wild Plant Species ◽  
Global Demand ◽  
Bioenergy Cropping Systems

The global demand for plant biomass to provide bioenergy and heat is continuously increasing because of a growing interest among many industrialized and developing countries towards climate sound and renewable energy supply. The exacerbation of land-use conflicts proliferates social-ecological demands on future bioenergy cropping systems. Perennial herbaceous wild plant mixtures (WPMs) represent an approach to providing social-ecologically more sustainably produced biogas substrate that has gained increasing public and political interest only in recent years. The focus of this study lies on three perennial wild plant species (WPS) that usually dominate the biomass yield performance of WPM cultivation. These WPS were compared with established biogas crops in terms of their substrate-specific methane yield (SMY) and lignocellulosic composition. The plant samples were investigated in a small-scale mesophilic discontinuous biogas batch test for determining the SMY. All WPS were found to have significantly lower SMY (241.5–248.5 lN kgVS−1) than maize (337.5 lN kgVS−1). This was attributed to higher contents of lignin (9.7–12.8% of dry matter) as well as lower contents of hemicellulose (9.9–11.5% of dry matter) in the WPS. Only minor, non-significant differences to cup plant and Virginia mallow were observed. Thus, when planning WPS as a diversification measure in biogas cropping systems, their lower SMY should be considered.

scholarly journals Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to abscisic acid treatment

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhiwei Chen ◽  
Longhua Zhou ◽  
Panpan Jiang ◽  
Ruiju Lu ◽  
Nigel G. Halford ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Gene Family ◽  
Stress Responses ◽  
Phylogenetic Analyses ◽  
Regulatory Elements ◽  
Gene Promoters ◽  
Related Protein ◽  
Rna Seq ◽  
Response Elements ◽  
Genome Data

Abstract Background Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study, we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environments. Results The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis showed that many of the HvSnRK genes responded to ABA, some positively, some negatively and some with complex time-dependent responses. Conclusions The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and HvSnRK3 (34 members), showing differential positive and negative responses to ABA.

scholarly journals Relationships between resource availability and elevation vary between metrics creating gradients of nutritional complexity

Oecologia ◽  
2021 ◽  
Vol 195 (1) ◽  
pp. 213-223
Author(s):  
Mark A. Lee ◽  
Grace Burger ◽  
Emma R. Green ◽  
Pepijn W. Kooij
Keyword(s):  
Species Richness ◽  
Plant Species ◽  
Resource Availability ◽  
Plant Biomass ◽  
Plant Species Richness ◽  
Mineral Contents ◽  
Nutritive Values ◽  
Animal Community ◽  
Nutritional Chemistry ◽  
The Relationship

AbstractPlant and animal community composition changes at higher elevations on mountains. Plant and animal species richness generally declines with elevation, but the shape of the relationship differs between taxa. There are several proposed mechanisms, including the productivity hypotheses; that declines in available plant biomass confers fewer resources to consumers, thus supporting fewer species. We investigated resource availability as we ascended three aspects of Helvellyn mountain, UK, measuring several plant nutritive metrics, plant species richness and biomass. We observed a linear decline in plant species richness as we ascended the mountain but there was a unimodal relationship between plant biomass and elevation. Generally, the highest biomass values at mid-elevations were associated with the lowest nutritive values, except mineral contents which declined with elevation. Intra-specific and inter-specific increases in nutritive values nearer the top and bottom of the mountain indicated that physiological, phenological and compositional mechanisms may have played a role. The shape of the relationship between resource availability and elevation was different depending on the metric. Many consumers actively select or avoid plants based on their nutritive values and the abundances of consumer taxa vary in their relationships with elevation. Consideration of multiple nutritive metrics and of the nutritional requirements of the consumer may provide a greater understanding of changes to plant and animal communities at higher elevations. We propose a novel hypothesis for explaining elevational diversity gradients, which warrants further study; the ‘nutritional complexity hypothesis’, where consumer species coexist due to greater variation in the nutritional chemistry of plants.

scholarly journals Molecular evolution of the plant R regulatory gene family.

Genetics ◽  
1994 ◽  
Vol 138 (3) ◽  
pp. 849-854
Author(s):  
M D Purugganan ◽  
S R Wessler
Keyword(s):  
Molecular Evolution ◽  
Gene Family ◽  
Plant Species ◽  
Regulatory Gene ◽  
Nonsynonymous Substitution ◽  
R Genes ◽  
Nucleotide Substitutions ◽  
Variable Regions ◽  
Helix Loop Helix ◽  
Regulatory Loci

Abstract Anthocyanin pigmentation patterns in different plant species are controlled in part by members of the myc-like R regulatory gene family. We have examined the molecular evolution of this gene family in seven plant species. Three regions of the R protein show sequence conservation between monocot and dicot R genes. These regions encode the basic helix-loop-helix domain, as well as conserved N-terminal and C-terminal domains; mean replacement rates for these conserved regions are 1.02 x 10(-9) nonsynonymous nucleotide substitutions per site per year. More than one-half of the protein, however, is diverging rapidly, with nonsynonymous substitution rates of 4.08 x 10(-9) substitutions per site per year. Detailed analysis of R homologs within the grasses (Poaceae) confirm that these variable regions are indeed evolving faster than the flanking conserved domains. Both nucleotide substitutions and small insertion/deletions contribute to the diversification of the variable regions within these regulatory genes. These results demonstrate that large tracts of sequence in these regulatory loci are evolving at a fairly rapid rate.

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