Stronger purifying selection against gene conversions in a pathogenicSaccharomyces cerevisiaestrain

Genome ◽  
2012 ◽  
Vol 55 (12) ◽  
pp. 835-843
Author(s):  
Benoît Pagé ◽  
Guy Drouin
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Gene Family ◽  
Purifying Selection ◽  
Gene Families ◽  
Lower Number ◽  
Pathogenic Strain ◽  
Helicase Gene ◽  
Nonpathogenic Strain ◽  
S288c Strain ◽  
Gene Conversions

Gene conversions most often have no selective impact, but some are selectively disadvantageous whereas others are selectively advantageous. Although gene conversions have been extensively studied in yeasts, very little is known about their selective impact in pathological yeasts. Here, we used the GENECONV software to compare the characteristics of candidate gene conversions found in a pathogenic strain (YJM789) and a nonpathogenic strain (S288c) of Saccharomyces cerevisiae. Interestingly, the pathogenic strain has fewer gene conversions when compared with the nonpathogenic strain. Of the 123 conversions we identified, 27 were identical or similar between the two strains, 62 were specific to the S288c strain, and 34 were specific to the YJM789 strain. Identical and similar conversions likely represent conversions that are under similar levels of purifying selection in both strains. The lower number of gene conversions in most gene families of the pathogenic strain is likely the result of higher purifying selection in this strain. In contrast, the higher number of conversions found in the YRF1 helicase gene family of the pathogenic strain could represent an example of adaptive gene conversions involved in maintaining its telomeres.

scholarly journals Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence

2019 ◽  
Vol 20 (7) ◽  
pp. 1750 ◽  
Author(s):  
Ghulam Qanmber ◽  
Ji Liu ◽  
Daoqian Yu ◽  
Zhao Liu ◽  
Lili Lu ◽  
...  
Keyword(s):  
Gene Duplication ◽  
Gene Family ◽  
Plant Species ◽  
Functional Divergence ◽  
Rapid Evolution ◽  
Purifying Selection ◽  
Gene Families ◽  
Promoter Regions ◽  
Large Gene ◽  
Receptor Kinases

Proline-rich extensin-like receptor kinases (PERKs) are an important class of receptor kinases in plants. Receptor kinases comprise large gene families in many plant species, including the 15 PERK genes in Arabidopsis. At present, there is no comprehensive published study of PERK genes in G. hirsutum. Our study identified 33 PERK genes in G. hirsutum. Phylogenetic analysis of conserved PERK protein sequences from 15 plant species grouped them into four well defined clades. The GhPERK gene family is an evolutionarily advanced gene family that lost its introns over time. Several cis-elements were identified in the promoter regions of the GhPERK genes that are important in regulating growth, development, light responses and the response to several stresses. In addition, we found evidence for gene loss or addition through segmental or whole genome duplication in cotton. Gene duplication and synteny analysis identified 149 orthologous/paralogous gene pairs. Ka/Ks values show that most GhPERK genes experienced strong purifying selection during the rapid evolution of the gene family. GhPERK genes showed high expression levels in leaves and during ovule development. Furthermore, the expression of GhPERK genes can be regulated by abiotic stresses and phytohormone treatments. Additionally, PERK genes could be involved in several molecular, biological and physiological processes that might be the result of functional divergence.

Evolution and Organization of a Highly Dynamic, Subtelomeric Helicase Gene Family in the Rice Blast Fungus Magnaporthe grisea

Genetics ◽  
2002 ◽  
Vol 162 (1) ◽  
pp. 103-112 ◽  
Author(s):  
Weimin Gao ◽  
Chang Hyun Khang ◽  
Sook-Young Park ◽  
Yong-Hwan Lee ◽  
Seogchan Kang
Keyword(s):  
Gene Family ◽  
Magnaporthe Grisea ◽  
Gene Families ◽  
Mapping Technique ◽  
Telomeric Region ◽  
Cloning And Sequencing ◽  
Fungal Evolution ◽  
Helicase Gene ◽  
Rice Pathogens ◽  
Almost All

Abstract Sequence analysis of a 13-kb telomeric region in O-137, a rice pathogenic isolate of Magnaporthe grisea, uncovered a novel gene, designated TLH1 (telomere-linked helicase 1). The TLH1 gene is a member of a gene family, and the sequences flanking this gene family have also been amplified. Genetic mapping showed that most members of the TLH gene family are tightly linked to the telomeres. A physical mapping technique, termed RecA-mediated Achilles’ heel cleavage, and cloning and sequencing of two additional telomeres of O-137 associated with the TLH gene family confirmed that most members of the TLH gene family are located within 10 kb from the telomeric repeat. A survey of M. grisea strains from diverse hosts revealed that the gene family is ubiquitously present among rice pathogens, but is absent from almost all isolates of hosts other than rice. The gene family appears to be highly dynamic, undergoing frequent deletion/amplification events. Given the presence of similar helicase gene families in chromosome ends of Saccharomyces cerevisiae and Ustilago maydis, the initial association of helicase genes with fungal telomeres might date back to very early stages of the fungal evolution.

scholarly journals Identification and Evolution Analysis of the JAZ Gene Family in Maize

2021 ◽  
Author(s):  
Yang Han ◽  
Dawn Luthe
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Gene Families ◽  
Defense Responses ◽  
Maize Genome ◽  
Synteny Analysis ◽  
Genetic Redundancy ◽  
Duplication Events

Abstract Background: Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results: In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds.Conclusions: Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

scholarly journals Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions

2019 ◽  
Vol 20 (8) ◽  
pp. 1945 ◽  
Author(s):  
Jiadai He ◽  
Hua Zhao ◽  
Zhilu Cheng ◽  
Yuwei Ke ◽  
Jiaxi Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Populus Trichocarpa ◽  
Purifying Selection ◽  
Gene Families ◽  
Arabinogalactan Proteins ◽  
Plant Evolution ◽  
Land Plants ◽  
Arabinogalactan Protein ◽  
Gene Copy

The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the FLA gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 FLA genes are identified with gene copy numbers ranging from one (Chondrus crispus) to 49 (Populus trichocarpa). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in FLA genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of FLA gene families. The duplicated gene pairs in FLA gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the FLA gene family and help us understand their functions during the process of evolution.

scholarly journals Genome-Wide Identification, Molecular Evolution, and Expression Divergence of Aluminum-Activated Malate Transporters in Apples

2018 ◽  
Vol 19 (9) ◽  
pp. 2807 ◽  
Author(s):  
Baiquan Ma ◽  
Yangyang Yuan ◽  
Meng Gao ◽  
Tonghui Qi ◽  
Mingjun Li ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Gene Duplication ◽  
Gene Family ◽  
Functional Divergence ◽  
Aluminum Tolerance ◽  
Evolutionary Process ◽  
Purifying Selection ◽  
Gene Families ◽  
Biochemical Properties ◽  
Evolutionary Pattern

Aluminum-activated malate transporters (ALMTs) play an important role in aluminum tolerance, stomatal opening, and fruit acidity in plants. However, the evolutionary pattern of the ALMT gene family in apples remains relatively unknown. In this study, a total of 25 MdALMT genes were identified from the apple reference genome of the “Golden Delicious” doubled-haploid tree (GDDH13). The physiological and biochemical properties, gene structure, and conserved motifs of MdALMT genes were examined. Chromosome location and gene-duplication analysis indicated that whole-genome duplication/segmental duplication played an important role in the expansion of the MdALMT gene family. The Ka/Ks ratio of duplicated MdALMT genes showed that members of this family have undergone strong purifying selection. Through exploration of the phylogenetic relationships, seven subgroups were classified, and higher old gene duplication frequency and significantly different evolutionary rates of the ALMT gene families were detected. In addition, the functional divergence of ALMT genes occurred during the evolutionary process of Rosaceae species. Furthermore, the functional divergence of MdALMT genes was confirmed by expression discrepancy and different subcellular localizations. This study provides the foundation to better understand the molecular evolution of MdALMT genes and further facilitate functional analysis to unravel their exact role in apples.

scholarly journals Gene conversions are frequent but not under positive selection in the Siglec gene families of primates

Genome ◽  
2014 ◽  
Vol 57 (6) ◽  
pp. 317-325 ◽  
Author(s):  
Mouldi Zid ◽  
Guy Drouin
Keyword(s):  
Sequence Similarity ◽  
Purifying Selection ◽  
Gene Families ◽  
Surface Proteins ◽  
Primate Species ◽  
Immunoglobulin Superfamily ◽  
Sialic Acid Binding ◽  
High Degree ◽  
Gene Conversions

Siglecs are cell surface proteins that belong to the immunoglobulin superfamily and which bind sialic acids. They are composed of two groups, the conserved Siglecs and the CD33-related Siglecs. Previous studies have reported the occurrence of gene conversions between human CD33-related Siglecs and suggested that these conversions are adaptive because they increase the diversity of these immunoglobulin-related genes. Here, we analyze the Siglec genes of five primate species and show that gene conversions are not observed between conserved Siglec genes but that they are frequent between primate CD33-related Siglecs. The gene conversions between CD33-related Siglec genes only occur between similar genes and equally frequently in sialic acid binding and nonbinding domains. Furthermore, dN/dS ratio tests show that most of the Ig-like V-type 1 and the Ig-like C2-type 1 domains of Siglec genes evolve either neutrally or under purifying selection and that gene conversions were not responsible for the positively selected regions detected in the Ig-like V-type1 domain of the human SIGLEC7 and SIGLEC9 genes. Our results suggest that the frequent gene conversions between CD33-related Siglec genes are simply a consequence of the high degree of sequence similarity of these genes and that they are not adaptive.

scholarly journals Identification and evolution analysis of the JAZ gene family in maize

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yang Han ◽  
Dawn Luthe
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Gene Families ◽  
Defense Responses ◽  
Maize Genome ◽  
Synteny Analysis ◽  
Genetic Redundancy ◽  
Duplication Events

Abstract Background Jasmonates (JAs) are important for plants to coordinate growth, reproduction, and defense responses. In JA signaling, jasmonate ZIM-domain (JAZ) proteins serve as master regulators at the initial stage of herbivores attacks. Although discovered in many plant species, little in-depth characterization of JAZ gene expression has been reported in the agronomically important crop, maize (Zea mays L.). Results In this study 16 JAZ genes from the maize genome were identified and classified. Phylogenetic analyses were performed from maize, rice, sorghum, Brachypodium, and Arabidopsis using deduced protein sequences, total six clades were proposed and conservation was observed in each group, such as similar gene exon/intron structures. Synteny analysis across four monocots indicated these JAZ gene families had a common ancestor, and duplication events in maize genome may drive the expansion of JAZ gene family, including genome-wide duplication (GWD), transposon, and/or tandem duplication. Strong purifying selection acted on all JAZ genes except those in group 4, which were under neutral selection. Further, we cloned three paralogous JAZ gene pairs from two maize inbreds differing in JA levels and insect resistance, and gene polymorphisms were observed between two inbreds. Conclusions Here we analyzed the composition and evolution of JAZ genes in maize with three other monocot plants. Extensive phylogenetic and synteny analysis revealed the expansion and selection fate of maize JAZ. This is the first study comparing the difference between two inbreds, and we propose genotype-specific JAZ gene expression might be present in maize plants. Since genetic redundancy in JAZ gene family hampers our understanding of their role in response to specific elicitors, we hope this research could be pertinent to elucidating the defensive responses in plants.

scholarly journals Isolation and Characterization Of Rice R Genes: Evidence for Distinct Evolutionary Paths in Rice and Maize

Genetics ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 1021-1031 ◽  
Author(s):  
Jianping Hu ◽  
Beth Anderson ◽  
Susan R Wessler
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Chromosome 1 ◽  
R Gene ◽  
R Genes ◽  
Helix Loop Helix ◽  
Isolation And Characterization ◽  
Undetermined Function ◽  
Evolutionary Paths

Abstract R and B genes and their homologues encode basic helix-loop-helix (bHLH) transcriptional activators that regulate the anthocyanin biosynthetic pathway in flowering plants. In maize, R/B genes comprise a very small gene family whose organization reflects the unique evolutionary history and genome architecture of maize. To know whether the organization of the R gene family could provide information about the origins of the distantly related grass rice, we characterized members of the R gene family from rice Oryza sativa. Despite being a true diploid, O. sativa has at least two R genes. An active homologue (Ra) with extensive homology with other R genes is located at a position on chromosome 4 previously shown to be in synteny with regions of maize chromosomes 2 and 10 that contain the B and R loci, respectively. A second rice R gene (Rb) of undetermined function was identified on chromosome 1 and found to be present only in rice species with AA genomes. All non-AA species have but one R gene that is Ra-like. These data suggest that the common ancestor shared by maize and rice had a single R gene and that the small R gene families of grasses have arisen recently and independently.

scholarly journals Expression of a gene duplication encoding conserved sperm tail proteins is translationally regulated in Drosophila melanogaster.

1993 ◽  
Vol 13 (3) ◽  
pp. 1708-1718 ◽  
Author(s):  
M Schäfer ◽  
D Börsch ◽  
A Hülster ◽  
U Schäfer
Keyword(s):  
Drosophila Melanogaster ◽  
Gene Family ◽  
Translational Control ◽  
Germ Line ◽  
Gene Families ◽  
Homologous Gene ◽  
Male Sterile ◽  
Sperm Tail ◽  
Repetitive Motif ◽  
Carboxy Terminal

We have analyzed a locus of Drosophila melanogaster located at 98C on chromosome 3, which contains two tandemly arranged genes, named Mst98Ca and Mst98Cb. They are two additional members of the Mst(3)CGP gene family by three criteria. (i) Both genes are exclusively transcribed in the male germ line. (ii) Both transcripts encode a protein with a high proportion of the repetitive motif Cys-Gly-Pro. (iii) Their expression is translationally controlled; while transcripts can be detected in diploid stages of spermatogenesis, association with polysomes can be shown only in haploid stages of sperm development. The genes differ markedly from the other members of the gene family in structure; they do not contain introns, they are of much larger size, and they have the Cys-Gly-Pro motifs clustered at the carboxy-terminal end of the encoded proteins. An antibody generated against the Mst98Ca protein recognizes both Mst98C proteins in D. melanogaster. In a male-sterile mutation in which spermiogenesis is blocked before individualization of sperm, both of these proteins are no longer synthesized. This finding provides proof of late translation for the Mst98C proteins and thereby independent proof of translational control of expression. Northern (RNA) and Western immunoblot analyses indicate the presence of homologous gene families in many other Drosophila species. The Mst98C proteins share sequence homology with proteins of the outer dense fibers in mammalian spermatozoa and can be localized to the sperm tail by immunofluorescence with an anti-Mst98Ca antibody.

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