scholarly journals Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes in Pyrus

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 490 ◽  
Author(s):  
Yunpeng Cao ◽  
Lan Jiang ◽  
Lihu Wang ◽  
Yongping Cai
Keyword(s):  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Synonymous Substitution ◽  
Evolutionary Rates ◽  
Orthologous Genes ◽  
Protein Coding ◽  
Different Types ◽  
Synonymous Substitution Rates ◽  
Gene Structures

Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In the present study, we investigate the rates of synonymous substitution (Ks) and the rates of non-synonymous substitution (Ka) by comparing the orthologous genes of two sequenced Pyrus species, Pyrus bretschneideri and Pyrus communis. Subsequently, we compared the evolutionary rates, gene structures, and expression profiles during different fruit development between PSGs and NSGs. Compared with the NSGs, the PSGs have fewer exons, shorter gene length, lower synonymous substitution rates and have higher evolutionary rates. Remarkably, gene expression patterns between two Pyrus species fruit indicated functional divergence for most of the orthologous genes derived from a common ancestor, and subfunctionalization for some of them. Overall, the present study shows that PSGs differs from NSGs not only under environmental selective pressure (Ka/Ks), but also in their structural, functional, and evolutionary properties. Additionally, our resulting data provides important insights for the evolution and highlights the diversification of orthologous genes in two Pyrus species.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Enhanced functional divergence of duplicate genes several million years after gene duplication in the Arabidopsis lineage

2016 ◽  
Author(s):  
Kousuke Hanada ◽  
Ayumi Tezuka ◽  
Masafumi Nozawa ◽  
Yutaka Suzuki ◽  
Sumio Sugano ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Orthologous Gene ◽  
Synonymous Substitution ◽  
Duplicate Genes ◽  
Duplicated Genes ◽  
Highly Qualified ◽  
Duplication Events ◽  
Synonymous Substitution Rates

AbstractLineage-specifically duplicated genes likely contribute to the phenotypic divergence in closely related species. However, neither the frequency of duplication events nor the degree of selective pressures immediately after gene duplication is clear in the speciation process. Plants have substantially higher gene duplication rates than most other eukaryotes. Here, using Illumina short reads from Arabidopsis halleri, which has highly qualified plant genomes in close species (Brassica rapa, A. thaliana and A. lyrata), we succeeded in generating orthologous gene groups among B. rapa, A. thaliana, A. lyrata and A. halleri. The frequency of duplication events in the Arabidopsis lineage was approximately 10 times higher than the frequency inferred by comparative genomics of Arabidopsis, poplar, rice and moss. Of the currently retained genes in A. halleri, 11–24% had undergone gene duplication in the Arabidopsis lineage. To examine the degree of selective pressure for duplicated genes, we calculated the ratios of nonsynonymous to synonymous substitution rates (KA/KS) in the A. halleri-lyrata and A. halleri lineages. Using a maximum-likelihood framework, we examined positive (KA/KS > 1) and purifying selection (KA/KS < 1) at a significant level (P < 0.01). Duplicate genes tended to have a higher proportion of positive selection compared with non-duplicated genes. More interestingly, we found that functional divergence of duplicated genes was accelerated several million years after gene duplication at a higher proportion than immediately after gene duplication.

scholarly journals A mini-atlas of gene expression for the domestic goat (Capra hircus) reveals transcriptional differences in immune signatures between sheep and goats

2019 ◽  
Author(s):  
Charity Muriuki ◽  
Stephen J. Bush ◽  
Mazdak Salavati ◽  
Mary E.B. McCulloch ◽  
Zofia M. Lisowski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genome ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Small Ruminants ◽  
Capra Hircus ◽  
Specific Cell ◽  
Domestic Goat ◽  
Protein Coding ◽  
Genomic Resources

AbstractGoats (Capra hircus) are an economically important livestock species providing meat and milk across the globe. They are of particular importance in tropical agri-systems contributing to sustainable agriculture, alleviation of poverty, social cohesion and utilisation of marginal grazing. There are excellent genetic and genomic resources available for goats, including a highly contiguous reference genome (ARS1). However, gene expression information is limited in comparison to other ruminants. To support functional annotation of the genome and comparative transcriptomics we created a mini-atlas of gene expression for the domestic goat. RNA-Seq analysis of 22 transcriptionally rich tissues and cell-types detected the majority (90%) of predicted protein-coding transcripts and assigned informative gene names to more than 1000 previously unannotated protein-coding genes in the current reference genome for goat (ARS1). Using network-based cluster analysis we grouped genes according to their expression patterns and assigned those groups of co-expressed genes to specific cell populations or pathways. We describe clusters of genes expressed in the gastro-intestinal tract and provide the expression profiles across tissues of a subset of genes associated with functional traits. Comparative analysis of the goat atlas with the larger sheep gene expression atlas dataset revealed transcriptional differences between the two species in macrophage-associated signatures. The goat transcriptomic resource complements the large gene expression dataset we have generated for sheep and contributes to the available genomic resources for interpretation of the relationship between genotype and phenotype in small ruminants.

scholarly journals Assessment of CircRNA Expression Profiles and Potential Functions in Brown Adipogenesis

2021 ◽  
Vol 12 ◽  
Author(s):  
Pengpeng Zhang ◽  
Mingxuan Sheng ◽  
Chunyu Du ◽  
Zhe Chao ◽  
Haixia Xu ◽  
...  
Keyword(s):  
Binding Sites ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Potential Functions ◽  
Rna Seq ◽  
Specific Expression ◽  
Protein Coding ◽  
Multiple Binding Sites ◽  
Brown Adipose ◽  
Brown Adipogenesis

Brown adipose tissue (BAT) is specialized for energy expenditure, thus a better understanding of the regulators influencing BAT development could provide novel strategies to defense obesity. Many protein-coding genes, miRNAs, and lncRNAs have been investigated in BAT development, however, the expression patterns and functions of circRNA in brown adipogenesis have not been reported yet. This study determined the circRNA expression profiles across brown adipogenesis (proliferation, early differentiated, and fully differentiated stages) by RNA-seq. We identified 3,869 circRNAs and 36.9% of them were novel. We found the biogenesis of circRNA was significantly related to linear mRNA transcription, meanwhile, almost 70% of circRNAs were generated by alternative back-splicing. Next, we examined the cell-specific and differentiation stage-specific expression of circRNAs. Compared to white adipocytes, nearly 30% of them were specifically expressed in brown adipocytes. Further, time-series expression analysis showed circRNAs were dynamically expressed, and 117 differential expression circRNAs (DECs) in brown adipogenesis were identified, with 77 upregulated and 40 downregulated. Experimental validation showed the identified circRNAs could be successfully amplified and the expression levels detected by RNA-seq were reliable. For the potential functions of the circRNAs, GO analysis suggested that the decreased circRNAs were enriched in cell proliferation terms, while the increased circRNAs were enriched in development and thermogenic terms. Bioinformatics predictions showed that DECs contained numerous binding sites of functional miRNAs. More interestingly, most of the circRNAs contained multiple binding sites for the same miRNA, indicating that they may facilitate functions by acting as microRNA sponges. Collectively, we characterized the circRNA expression profiles during brown adipogenesis and provide numerous novel circRNAs candidates for future brown adipogenesis regulating studies.

scholarly journals Characterisation and functional predictions of canine long non-coding RNAs

2018 ◽  
Author(s):  
Céline Le Béguec ◽  
Valentin Wucher ◽  
Lætitia Lagoutte ◽  
Edouard Cadieu ◽  
Nadine Botherel ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Domestic Dog ◽  
Tissue Type ◽  
Protein Coding ◽  
Functional Roles ◽  
Integrative Study ◽  
Non Coding Rnas ◽  
Biological Functionality

AbstractLong non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and humans through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.

scholarly journals Genome-Wide Identification and Expression Profile of OSCA Gene Family Members in Triticum aestivum L.

2021 ◽  
Vol 23 (1) ◽  
pp. 469
Author(s):  
Kai Tong ◽  
Xinyang Wu ◽  
Long He ◽  
Shiyou Qiu ◽  
Shuang Liu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Expression Profiles ◽  
Stomatal Closure ◽  
Expression Patterns ◽  
Family Members ◽  
Triticum Aestivum L ◽  
Free Calcium ◽  
Cis Acting ◽  
Gene Structures

Hyperosmolality and various other stimuli can trigger an increase in cytoplasmic-free calcium concentration ([Ca2+]cyt). Members of the Arabidopsis thaliana (L.) reduced hyperosmolality-gated calcium-permeable channels (OSCA) gene family are reported to be involved in sensing extracellular changes to trigger hyperosmolality-induced [Ca2+]cyt increases and controlling stomatal closure during immune signaling. Wheat (Triticum aestivum L.) is a very important food crop, but there are few studies of its OSCA gene family members. In this study, 42 OSCA members were identified in the wheat genome, and phylogenetic analysis can divide them into four clades. The members of each clade have similar gene structures, conserved motifs, and domains. TaOSCA genes were predicted to be regulated by cis-acting elements such as STRE, MBS, DRE1, ABRE, etc. Quantitative PCR results showed that they have different expression patterns in different tissues. The expression profiles of 15 selected TaOSCAs were examined after PEG (polyethylene glycol), NaCl, and ABA (abscisic acid) treatment. All 15 TaOSCA members responded to PEG treatment, while TaOSCA12/-39 responded simultaneously to PEG and ABA. This study informs research into the biological function and evolution of TaOSCA and lays the foundation for the breeding and genetic improvement of wheat.

Evolution of Acyl-CoA-binding protein gene family in plants provides insights into potential functions of grapevine (Vitis vinifera L.)

2020 ◽  
Vol 10 (4) ◽  
pp. 677-696
Author(s):  
Zhi-Gang Dong ◽  
Hui Liu ◽  
Xiao-Long Wang ◽  
Jun Tang ◽  
Kai-Kai Zhu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gene Family ◽  
Microarray Data ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Potential Functions ◽  
Physiological Data ◽  
Structural Annotation ◽  
Qrt Pcr

BACKGROUND: Grapevine was one of the most important perennial fruit crops worldwide. Acyl-CoA-binding proteins (ACBPs) in eudicots and monocots show conservation in an acyl-CoA-binding domain (ACB domain) which binds acyl-CoA esters. OBJECTIVE: The information and data provided in the present study contributes to understand the evolutionary processes and potential functions of this gene family in grapevine growth and development, and responses to abiotic stress. METHODS: Using the complete grapevine genome sequences, we investigated the number grapevine ACBP genes, the exon-intron structure, phylogenetic relationships and synteny with the Arabidopsis ACBP gene family. Furthermore, the expression profiles of VvACBP genes based on public microarray data in different tissues, and the expression patterns responding to different exogenous hormones as well as abiotic and biotic stresses were presented. The qRT-PCR was used to verify the microarray data under drought stress treatments. Finally, the leaf relative water content (RWC), leaf chlorophyll content, and enzymatic activities were measured to further examine the tolerance to drought stress in grapevine. RESULTS: The six grapevine ACBPs were identified. Their distribution into various groups differed from Arabidopsis and rice. Synteny analysis demonstrated that several VvACBP genes were found in corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of the respective lineages. Sequence alignment and structural annotation provided an overview of variations that might contribute to functional divergence from Arabidopsis ACBPs. Expressional analyses suggested that both conserved and variant biological functions exist in ACBPs across different species. The expression pattern of these genes were similar in the microarray and qRT-PCR analyses. Gene structure organization and expression characteristics of VvACBPs resembled those of their Arabidopsis orthologous, although species-specific differences also exist. Differential regulation of genes suggested functional diversification among isoforms. The biochemical and physiological data showed the tolerance to drought stress of grapevine. CONCLUSIONS: These findings provided insight into evolution of ACBP gene family in plants and a solid foundation for a deeper understanding of the complex molecular responses of grapevine to stress.

Genome-wide Analysis of the Rice Mate Gene Family: Identification, Genomic Organization and Expression Profiles in Response to Abiotic Stresses

2020 ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Chemical Properties ◽  
Motif Analysis ◽  
Functional Homology ◽  
Exogenous Compounds

Abstract Background: Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice.Results: In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. In addition, physical and chemical properties of the encoded proteins, subcellular localization, chromosome localization, stress-related cis-elements in abiotic stresses were determined, and a phylogenetic analysis and conserved motif analysis were performed. The rice MATE family can be divided into four subfamilies. It is speculated that members of the rice MATE family have many potential functions, such as the transport and accumulation of flavonoids and alkaloids, the extrusion of plant or exogenous compounds, the regulation of disease resistance and the response to abiotic stress, based on the proteins and cis-acting elements with known functions in the same subfamily. Analysis of gene expression showed that most of the genes were constitutively expressed. Furthermore, eight MATE genes were chosen for qRT-PCR-based analysis and showed differential expression patterns in response to salt and drought stress. Conclusions: Phylogenetic analysis, element prediction, expression data and homology with other species provided strong evidence for functional homology of MATE gene in rice. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Genome-Wide Analysis of the β-Amylase Gene Family in Brassica L. Crops and Expression Profiles of BnaBAM Genes in Response to Abiotic Stresses

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1855
Author(s):  
Dan Luo ◽  
Ziqi Jia ◽  
Yong Cheng ◽  
Xiling Zou ◽  
Yan Lv
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Chromosomal Distribution ◽  
Brassica Napus L ◽  
Oil Crops ◽  
Genome Wide ◽  
Gene Structures

The β-amylase (BAM) gene family, known for their property of catalytic ability to hydrolyze starch to maltose units, has been recognized to play critical roles in metabolism and gene regulation. To date, BAM genes have not been characterized in oil crops. In this study, the genome-wide survey revealed the identification of 30 BnaBAM genes in Brassica napus L. (B. napus L.), 11 BraBAM genes in Brassica rapa L. (B. rapa L.), and 20 BoBAM genes in Brassica oleracea L. (B. oleracea L.), which were divided into four subfamilies according to the sequence similarity and phylogenetic relationships. All the BAM genes identified in the allotetraploid genome of B. napus, as well as two parental-related species (B. rapa and B. oleracea), were analyzed for the gene structures, chromosomal distribution and collinearity. The sequence alignment of the core glucosyl-hydrolase domains was further applied, demonstrating six candidate β-amylase (BnaBAM1, BnaBAM3.1-3.4 and BnaBAM5) and 25 β-amylase-like proteins. The current results also showed that 30 BnaBAMs, 11 BraBAMs and 17 BoBAMs exhibited uneven distribution on chromosomes of Brassica L. crops. The similar structural compositions of BAM genes in the same subfamily suggested that they were relatively conserved. Abiotic stresses pose one of the significant constraints to plant growth and productivity worldwide. Thus, the responsiveness of BnaBAM genes under abiotic stresses was analyzed in B. napus. The expression patterns revealed a stress-responsive behaviour of all members, of which BnaBAM3s were more prominent. These differential expression patterns suggested an intricate regulation of BnaBAMs elicited by environmental stimuli. Altogether, the present study provides first insights into the BAM gene family of Brassica crops, which lays the foundation for investigating the roles of stress-responsive BnaBAM candidates in B. napus.

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