Sugar Transporter Proteins (STPs) in Gramineae Crops: Comparative Analysis, Phylogeny, Evolution, and Expression Profiling

Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.

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Glutathione S-Transferase Gene Family in Gossypium raimondii and G. arboreum: Comparative Genomic Study and their Expression under Salt Stress

Frontiers in Plant Science ◽

10.3389/fpls.2016.00139 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 24

Author(s):

Yating Dong ◽

Cong Li ◽

Yi Zhang ◽

Qiuling He ◽

Muhammad K. Daud ◽

...

Keyword(s):

Salt Stress ◽

Gene Family ◽

Comparative Genomic ◽

Glutathione S Transferase ◽

Transferase Gene ◽

Genomic Study ◽

Gossypium Raimondii ◽

Comparative Genomic Study

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Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica

Biomolecules ◽

10.3390/biom9050188 ◽

2019 ◽

Vol 9 (5) ◽

pp. 188 ◽

Cited By ~ 9

Author(s):

Weilong Kong ◽

Ziyun Gong ◽

Hua Zhong ◽

Yue Zhang ◽

Gangqing Zhao ◽

...

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Plant Cell ◽

Plant Cell Wall ◽

Brachypodium Distachyon ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Oryza Rufipogon ◽

Potential Candidate ◽

Evolutionary Patterns

Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I–IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.

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Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley

Plants ◽

10.3390/plants9111439 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1439

Author(s):

Shazia Rehman ◽

Bodil Jørgensen ◽

Ejaz Aziz ◽

Riffat Batool ◽

Samar Naseer ◽

...

Keyword(s):

Gene Family ◽

Protease Inhibitors ◽

Brachypodium Distachyon ◽

In Silico Analysis ◽

Purifying Selection ◽

Serpin Gene ◽

Bioinformatic Tools ◽

Duplication Events ◽

Genome Level

Serpins (serine protease inhibitors) constitute one of the largest and most widely distributed superfamilies of protease inhibitors and have been identified in nearly all organisms. To gain significant insights, a comprehensive in silico analysis of the serpin gene family was carried out in the model plant for temperate grasses Brachypodium distachyon and barley Hordeum vulgare using bioinformatic tools at the genome level for the first time. We identified a total of 27 BdSRPs and 25 HvSRP genes in Brachypodium and barley, respectively, showing an unexpectedly high gene number in these model plants. Gene structure, conserved motifs and phylogenetic comparisons of serpin genes supported the role of duplication events in the expansion and evolution of serpin gene family. Further, purifying selection pressure was found to be a main driving force in the evolution of serpin genes. Genome synteny analysis indicated that BdSRP genes were present in syntenic regions of barley, rice, sorghum and maize, suggesting that they evolved before the divergence of these species from common ancestor. The distinct expression pattern in specific tissues further suggested a specialization of functions during development and in plant defense. These results suggest that the LR serpins (serpins with Leu-Arg residues at P2–P1′) identified here can be utilized as candidates for exploitation in disease resistance, pest control and preventing stress-induced cell death. Additionally, serpins were identified that could lead to further research aimed at validating and functionally characterizing the role of potential serpin genes from other plants.

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Evolution of the Apicomplexan Sugar Transporter Gene Family Repertoire

International Journal of Genomics ◽

10.1155/2017/1707231 ◽

2017 ◽

Vol 2017 ◽

pp. 1-9 ◽

Cited By ~ 1

Author(s):

Ousman Mahmud ◽

Jessica C. Kissinger

Keyword(s):

Energy Source ◽

Phylogenetic Analysis ◽

Gene Family ◽

Phylogenetic Analyses ◽

Sugar Transporter ◽

Transporter Gene ◽

Transporter Proteins ◽

Sugar Transporters ◽

Subsequent Loss

Apicomplexan protist parasites utilize host sugars transported into the parasite by sugar transporter proteins for use as an energy source. We performed a phylum-wide phylogenetic analysis of the apicomplexan sugar transporter repertoire. Phylogenetic analyses revealed six major subfamilies of apicomplexan sugar transporters. Transporters in one subfamily have undergone expansions in Piroplasma species and Gregarina niphandrodes, while other subfamilies are highly divergent and contain genes found in only one or two species. Analyses of the divergent apicomplexan subfamilies revealed their presence in ciliates, indicating their alveolate ancestry and subsequent loss in chromerids and many apicomplexans.

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Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica

Plants ◽

10.3390/plants8020030 ◽

2019 ◽

Vol 8 (2) ◽

pp. 30 ◽

Cited By ~ 14

Author(s):

Weilong Kong ◽

Hua Zhong ◽

Xiaoxiao Deng ◽

Mayank Gautam ◽

Ziyun Gong ◽

...

Keyword(s):

Oryza Sativa ◽

Gene Family ◽

Salinity Stress ◽

Common Ancestor ◽

Oryza Rufipogon ◽

Oryza Species ◽

Evolutionary Analysis ◽

Wild Rice Species ◽

Oryza Punctata ◽

Duplication Events

Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.

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LARGE-SCALE GENOME SAMPLING REVEALS UNIQUE IMMUNITY AND METABOLIC ADAPTATIONS IN BATS

10.22541/au.160977727.76870866/v3 ◽

2021 ◽

Author(s):

Diana Moreno Santillan ◽

Tanya Lama ◽

Yocelyn Gutiérrez Guerrero ◽

Alexis Brown ◽

Paul Donat ◽

...

Keyword(s):

Immune System ◽

Gene Family ◽

Molecular Mechanisms ◽

Small Body ◽

Gene Family Evolution ◽

Comparative Genomic ◽

Metabolic Genes ◽

Pathway Gene ◽

Genomic Study ◽

Molecular Patterns

Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.

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LARGE-SCALE GENOME SAMPLING REVEALS UNIQUE IMMUNITY AND METABOLIC ADAPTATIONS IN BATS

10.22541/au.160977727.76870866/v2 ◽

2021 ◽

Author(s):

Diana Moreno Santillan ◽

Tanya Lama ◽

Yocelyn Gutiérrez Guerrero ◽

Alexis Brown ◽

Paul Donat ◽

...

Keyword(s):

Immune System ◽

Gene Family ◽

Molecular Mechanisms ◽

Small Body ◽

Gene Family Evolution ◽

Comparative Genomic ◽

Metabolic Genes ◽

Pathway Gene ◽

Genomic Study ◽

Molecular Patterns

Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.

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Origin and Evolutionary Dynamics of the miR2119 and ADH1 Regulatory Module in Legumes

Genome Biology and Evolution ◽

10.1093/gbe/evaa205 ◽

2020 ◽

Vol 12 (12) ◽

pp. 2355-2369

Author(s):

Carlos De la Rosa ◽

Luis Lozano ◽

Santiago Castillo-Ramírez ◽

Alejandra A Covarrubias ◽

José L Reyes

Keyword(s):

Gene Family ◽

Evolutionary Dynamics ◽

Single Gene ◽

Human Consumption ◽

Mirna Regulation ◽

Mirna Genes ◽

Adh1 Gene ◽

Recent Emergence ◽

Duplication Events ◽

Single Transcript

Abstract MicroRNAs are important regulators of gene expression in eukaryotes. Previously, we reported that in Phaseolus vulgaris, the precursor for miR2119 is located in the same gene as miR398a, conceiving a dicistronic MIR gene. Both miRNA precursors are transcribed and processed from a single transcript resulting in two mature microRNAs that regulate the mRNAs encoding ALCOHOL DEHYDROGENASE 1 (ADH1) and COPPER-ZINC SUPEROXIDE DISMUTASE 1 (CSD1). Genes for miR398 are distributed throughout the spermatophytes; however, miR2119 is only found in Leguminosae species, indicating its recent emergence. Here, we used public databases to explore the presence of the miR2119 sequence in several plant species. We found that miR2119 is present only in specific clades within the Papilionoideae subfamily, including important crops used for human consumption and forage. Within this subfamily, MIR2119 and MIR398a are found together as a single gene in the genomes of the Millettioids and Hologalegina. In contrast, in the Dalbergioids MIR2119 is located in a different locus from MIR398a, suggesting this as the ancestral genomic organization. To our knowledge, this is a unique example where two separate MIRNA genes have merged to generate a single polycistronic gene. Phylogenetic analysis of ADH1 gene sequences in the Papilionoideae subfamily revealed duplication events resulting in up to four ADH1 genes in certain species. Notably, the presence of MIR2119 correlates with the conservation of target sites in particular ADH1 genes in each clade. Our results suggest that post-transcriptional regulation of ADH1 genes by miR2119 has contributed to shaping the expansion and divergence of this gene family in the Papilionoideae. Future experimental work on ADH1 regulation by miR2119 in more legume species will help to further understand the evolutionary history of the ADH1 gene family and the relevance of miRNA regulation in this process.

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