scholarly journals Evolution of Methyltransferase-Like (METTL) Proteins in Metazoa: A Complex Gene Family Involved in Epitranscriptomic Regulation and Other Epigenetic Processes

2021 ◽  
Author(s):  
Juliet M Wong ◽  
Jose M Eirin-Lopez
Keyword(s):  
Gene Family ◽  
Purifying Selection ◽  
Functional Differentiation ◽  
Similar Process ◽  
Phenotypic Traits ◽  
Functional Specialization ◽  
Evolutionary Mechanisms ◽  
Binding Domains ◽  
Rates Of Evolution ◽  
Basal Metazoan

Abstract The methyltransferase-like (METTL) proteins constitute a family of seven-beta-strand methyltransferases with S-adenosyl methionine-binding domains that modify DNA, RNA, and proteins. Methylation by METTL proteins contributes to the epigenetic, and in the case of RNA modifications, epitranscriptomic regulation of a variety of biological processes. Despite their functional importance, most investigations of the substrates and functions of METTLs within metazoans have been restricted to model vertebrate taxa. In the present work, we explore the evolutionary mechanisms driving the diversification and functional differentiation of 33 individual METTL proteins across Metazoa. Our results show that METTLs are nearly ubiquitous across the animal kingdom, with most having arisen early in metazoan evolution (i.e., occur in basal metazoan phyla). Individual METTL lineages each originated from single independent ancestors, constituting monophyletic clades, which suggests that each METTL was subject to strong selective constraints driving its structural and/or functional specialization. Interestingly, a similar process did not extend to the differentiation of nucleoside-modifying and protein-modifying METTLs (i.e., each METTL type did not form a unique monophyletic clade). The members of these two types of METTLs also exhibited differences in their rates of evolution. Overall, we provide evidence that the long-term evolution of METTL family members was driven by strong purifying selection, which in combination with adaptive selection episodes, led to the functional specialization of individual METTL lineages. This work contributes useful information regarding the evolution of a gene family that fulfills a variety of epigenetic functions, and can have profound influences on molecular processes and phenotypic traits.

scholarly journals Contrasting Patterns of Gene Duplication, Relocation, and Selection Among Human Taste Genes

2021 ◽  
Vol 17 ◽  
pp. 117693432110351
Author(s):  
Yupeng Wang ◽  
Ying Sun ◽  
Paule Valery Joseph
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Functional Groups ◽  
Purifying Selection ◽  
Comparative Genomic ◽  
Vertebrate Species ◽  
Evolutionary Mechanisms ◽  
Evolutionary Patterns ◽  
Outgroup Species ◽  
Tandem Duplications

In humans, taste genes are responsible for perceiving at least 5 different taste qualities. Human taste genes’ evolutionary mechanisms need to be explored. We compiled a list of 69 human taste-related genes and divided them into 7 functional groups. We carried out comparative genomic and evolutionary analyses for these taste genes based on 8 vertebrate species. We found that relative to other groups of human taste genes, human TAS2R genes have a higher proportion of tandem duplicates, suggesting that tandem duplications have contributed significantly to the expansion of the human TAS2R gene family. Human TAS2R genes tend to have fewer collinear genes in outgroup species and evolve faster, suggesting that human TAS2R genes have experienced more gene relocations. Moreover, human TAS2R genes tend to be under more relaxed purifying selection than other genes. Our study sheds new insights into diverse and contrasting evolutionary patterns among human taste genes.

scholarly journals Global Investigation of TBL Gene Family in Rose (Rosa chinensis) Unveils RcTBL16 Is a Susceptibility Gene in Gray Mold Resistance

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Tian ◽  
Shiya Zhang ◽  
Xintong Liu ◽  
Zhao Zhang
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Susceptibility Gene ◽  
Purifying Selection ◽  
Functional Differentiation ◽  
Gray Mold ◽  
Virus Induced Gene Silencing ◽  
Cell Wall Polysaccharides ◽  
A Genome ◽  
Mold Resistance

The TRICHOME BIREFRINGENCE-LIKE (TBL) family is an important gene family engaged in the O-acetylation of cell wall polysaccharides. There have been a few reports showing that TBL participated in the resistance against phytopathogens in Arabidopsis and rice. However, no relevant studies in rose (Rosa sp.) have been published. In this study, a genome-wide analysis of the TBL gene family in rose was presented, including their phylogenetic relationships, gene structure, chromosomal positioning, and collinearity analysis. The phylogenetic analysis revealed a total of 50 RcTBL genes in the rose genome, and they are unevenly distributed across all seven chromosomes. The occurrence of gene duplication events suggests that both the whole genome duplication and partial duplication may play a role in gene duplication of RcTBLs. The analysis of Ka/Ks showed that the replicated RcTBL genes underwent mainly purifying selection with limited functional differentiation. Gene expression analysis indicated that 12 RcTBLs were down-regulated upon the infection of Botrytis cinerea, the causal agent of the gray mold disease of rose. These RcTBLs may be a sort of candidate genes for regulating the response of rose to B. cinerea. Through virus-induced gene silencing, RcTBL16 was shown to be associated with susceptibility to gray mold in rose. Through this study, meaningful information for further studies on the function of the TBL protein family in rose is provided.

scholarly journals Identification and Expression of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Capsicum annuum and Solanum tuberosum

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1448
Author(s):  
Qinfang Chen ◽  
Linna Wang ◽  
Di Liu ◽  
Sirui Ma ◽  
Yangshuo Dai ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Capsicum Annuum ◽  
Plant Development ◽  
Expression Patterns ◽  
Protein Structures ◽  
Purifying Selection ◽  
Functional Differentiation ◽  
Segmental Duplications ◽  
Toxic Compound

Multidrug and Toxic Compound Extrusion (MATE) proteins are essential transporters that extrude metabolites and participate in plant development and the detoxification of toxins. Little is known about the MATE gene family in the Solanaceae, which includes species that produce a broad range of specialized metabolites. Here, we identified and analyzed the complement of MATE genes in pepper (Capsicum annuum) and potato (Solanum tuberosum). We classified all MATE genes into five groups based on their phylogenetic relationships and their gene and protein structures. Moreover, we discovered that tandem duplication contributed significantly to the expansion of the pepper MATE family, while both tandem and segmental duplications contributed to the expansion of the potato MATE family, indicating that MATEs took distinct evolutionary paths in these two Solanaceous species. Analysis of ω values showed that all potato and pepper MATE genes experienced purifying selection during evolution. In addition, collinearity analysis showed that MATE genes were highly conserved between pepper and potato. Analysis of cis-elements in MATE promoters and MATE expression patterns revealed that MATE proteins likely function in many stages of plant development, especially during fruit ripening, and when exposed to multiple stresses, consistent with the existence of functional differentiation between duplicated MATE genes. Together, our results lay the foundation for further characterization of pepper and potato MATE gene family members.

scholarly journals Why should mitochondria define species?

2018 ◽  
Author(s):  
M.Y. Stoeckle ◽  
D.S. Thaler
Keyword(s):  
Animal Species ◽  
Population Expansion ◽  
Purifying Selection ◽  
Modern Human ◽  
Similar Process ◽  
Lineage Sorting ◽  
Modern Humans ◽  
Evolutionary Mechanisms ◽  
Domain Experts ◽  
Almost All

More than a decade of DNA barcoding encompassing about five million specimens covering 100,000 animal species supports the generalization that mitochondrial DNA clusters largely overlap with species as defined by domain experts. Most barcode clustering reflects synonymous substitutions. What evolutionary mechanisms account for synonymous clusters being largely coincident with species? The answer depends on whether variants are phenotypically neutral. To the degree that variants are selectable, purifying selection limits variation within species and neighboring species may have distinct adaptive peaks. Phenotypically neutral variants are only subject to demographic processes—drift, lineage sorting, genetic hitchhiking, and bottlenecks. The evolution of modern humans has been studied from several disciplines with detail unique among animal species. Mitochondrial barcodes provide a commensurable way to compare modern humans to other animal species. Barcode variation in the modern human population is quantitatively similar to that within other animal species. Several convergent lines of evidence show that mitochondrial diversity in modern humans follows from sequence uniformity followed by the accumulation of largely neutral diversity during a population expansion that began approximately 100,000 years ago. A straightforward hypothesis is that the extant populations of almost all animal species have arrived at a similar result consequent to a similar process of expansion from mitochondrial uniformity within the last one to several hundred thousand years.

scholarly journals Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

2022 ◽  
Vol 23 (2) ◽  
pp. 614
Author(s):  
Weiqi Sun ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Stress Protein ◽  
Purifying Selection ◽  
Cis Acting ◽  
Genome Wide ◽  
Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

scholarly journals Molecular signatures of selection associated with host-plant differences in Pieris butterflies

2019 ◽  
Author(s):  
Yu Okamura ◽  
Ai Sato ◽  
Natsumi Tsuzuki ◽  
Masashi Murakami ◽  
Hanna Heidel-Fischer ◽  
...  
Keyword(s):  
Gene Family ◽  
Host Plant ◽  
Host Plants ◽  
Protein A ◽  
Functional Differentiation ◽  
Major Allergen ◽  
Arms Race ◽  
Defense System ◽  
Evolutionary Forces ◽  
Key Innovation

AbstractAdaptive traits that enable organisms to conquer novel niches and experience subsequent diversification are ecologically and evolutionarily important. The larvae of Pieris butterflies express nitrile-specifier proteins (NSPs), a key innovation for overcoming the glucosinolate (GLS)-myrosinase-based defense system of their Brassicales host-plants. NSPs are a member of the NSP-like gene family, which includes the major allergen (MA) protein, a paralog of NSP with a GLS-disarming function, and a single domain major allergen (SDMA) protein, whose function is unknown. The arms-race between a highly variable host-plant defense system and members of the NSP-like gene family is suggested to mediate diversification in both Pierid butterflies and Brassicales plants. Here, we combined feeding experiments using 25 Brassicaceae plants and five Pieris species with larval transcriptome data to investigate the evolutionary forces acting on NSP-like gene family members associated with patterns of host-plant usage. Although we observed significantly elevated nonsynonymous to synonymous substitution ratios in NSPs, no such pattern was observed in MAs or SDMAs. Furthermore, we found a signature of positive selection of NSP at a phylogenetic branch which reflects different host-plant preferences. Our data indicate that NSPs have evolved in response to shifting preferences for host plants among five Pieris butterflies, whereas MAs and SDMAs appear to have more conserved functions. Our results show that the evolution and functional differentiation of key genes used in host-plant adaptation play a crucial role in the chemical arms-race between Pieris butterflies and their Brassicales host-plants.

scholarly journals The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

2021 ◽  
Vol 9 ◽  
Author(s):  
Abdullah ◽  
Sahar Faraji ◽  
Parviz Heidari ◽  
Péter Poczai
Keyword(s):  
Gene Family ◽  
Theobroma Cacao ◽  
Critical Role ◽  
Divergence Time ◽  
Purifying Selection ◽  
Plant Metabolites ◽  
Corchorus Capsularis ◽  
Cell Stability ◽  
Duplication Events ◽  
And Function

The benzyl alcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase, and deacetylvindoline 4-O-acetyltransferase (BAHD) enzymes play a critical role in regulating plant metabolites and affecting cell stability. In the present study, members of the BAHD gene family were recognized in the genome of Theobroma cacao and characterized using various bioinformatics tools. We found 27 non-redundant putative tcBAHD genes in cacao for the first time. Our findings indicate that tcBAHD genes are diverse based on sequence structure, physiochemical properties, and function. When analyzed with BAHDs of Gossypium raimondii and Corchorus capsularis clustered into four main groups. According to phylogenetic analysis, BAHD genes probably evolved drastically after their divergence. The divergence time of duplication events with purifying selection pressure was predicted to range from 1.82 to 15.50 MYA. Pocket analysis revealed that serine amino acid is more common in the binding site than other residuals, reflecting its key role in regulating the activity of tcBAHDs. Furthermore, cis-acting elements related to the responsiveness of stress and hormone, particularly ABA and MeJA, were frequently observed in the promoter region of tcBAHD genes. RNA-seq analysis further illustrated that tcBAHD13 and tcBAHD26 are involved in response to Phytophthora megakarya fungi. In conclusion, it is likely that evolutionary processes, such as duplication events, have caused high diversity in the structure and function of tcBAHD genes.

scholarly journals Evolution, functional differentiation, and co-expression of the RLK gene family revealed in Jilin ginseng, Panax ginseng C.A. Meyer

2018 ◽  
Vol 293 (4) ◽  
pp. 845-859 ◽  
Author(s):  
Yanping Lin ◽  
Kangyu Wang ◽  
Xiangyu Li ◽  
Chunyu Sun ◽  
Rui Yin ◽  
...  
Keyword(s):  
Gene Family ◽  
Panax Ginseng ◽  
Functional Differentiation

Adaptive evolution of interferon induced protein with tetratricopeptide repeats 5(IFIT5) in birds

2020 ◽  
Author(s):  
Bei Zhang ◽  
Chuansheng Zhang ◽  
Jie Meng ◽  
Yifan Ren ◽  
Jing Gong ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Purifying Selection ◽  
Functional Domain ◽  
Immune Mechanism ◽  
Tetratricopeptide Repeats ◽  
Host Interaction ◽  
Domestic Bird ◽  
Episodic Selection ◽  
Joint Influence

Abstract Background : Previous studies have revealed that wild birds are reservoirs and mobile vectors of viruses, many of which cause illness and mortality in domestic bird and humans. In birds, the invasion of viruses will quickly trigger the innate immune mechanism induced by interferon (IFN). As IFN-stimulated genes (ISGs), the IFIT gene family plays an important role in innate immunity. However, only IFIT5 of the IFIT gene family exists in birds, and the direction and strength of selection acting on IFIT5 are largely unknown. Results : Here, we studied the selection on IFIT5 based on the coding sequence (CDS) data of 20 birds. We identified 12 persistent positive selection sites (PSS), other sites suffered purifying selection and neutral selection; probably due to functional constraints. We also found humans have only 3PSS (189,197and 295), likely due to having more IFIT gene family member that can cooperate to resist virus invasion. The 12 PSS located in the closed clamp structure of the IFIT5 protein, except for position 45. In particular, 3 PSS (335, 342 and 367) were located in the TPR domain, which implied their important roles in virus recognition. We only found 2 episodic PSS (30,332) in Passeriformes, indicating episodic selection pressure in Passeriformes lineage. The positive selection of IFIT5 might provide a theoretical basis for the pathogen-host interaction in birds. Conclusions : We found that the diversity of IFIT5 domains in birds, and that the PSS of IFIT5 is the joint influence of functional domain conservation and the pressure of virus evolution.We speculated that persistent PSS may affect the antiviral function of IFIT5, especially in the region of closed clamp structure. These results lay a theoretical foundation for the further study of the antiviral immune mechanism of IFIT5 in birds.

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