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 Preferential use of the VH4 Ig gene family by diffuse large-cell lymphoma

Blood ◽  
1995 ◽  
Vol 86 (8) ◽  
pp. 3072-3082 ◽  
Author(s):  
FJ Hsu ◽  
R Levy
Keyword(s):  
Gene Family ◽  
Cell Lymphoma ◽  
Variable Region ◽  
Gene Families ◽  
Large Cell ◽  
Germline Gene ◽  
Diffuse Large Cell Lymphoma ◽  
Vh Genes ◽  
Large Cell Lymphoma ◽  
Almost All

Abstract Ig heavy chain variable region (VH) genes expressed by human diffuse large-cell lymphoma (DLC) and follicular lymphoma (FL) were identified and analyzed with respect to germline gene families. In 67 cases of FL, VH region genes were expressed in a pattern similar to that of normal B cells, with a predominance of the large VH3 gene family being used. In contrast, of the 17 cases of DLC, there was an extremely biased use of VH genes. Of these DLC tumors, 88% expressed genes from the small VH4 gene family; and even among these tumors, there was a limited use of genes, with 11 cases producing Igs derived from the VH4.21 germline gene. Although most of the VH genes expressed by DLC tumor cells contained mutations with respect to their germline counterparts, almost all of these mutations occurred before the clonal expansion of the tumor. This contrasts with our previous findings of ongoing mutations in FL and represents a fundamental difference between these two malignancies. This preferential gene use implies an important role for the VH4 gene family, and specifically for VH4.21, in the genesis of DLC.

scholarly journals Preferential use of the VH4 Ig gene family by diffuse large-cell lymphoma

Blood ◽  
1995 ◽  
Vol 86 (8) ◽  
pp. 3072-3082 ◽  
Author(s):  
FJ Hsu ◽  
R Levy
Keyword(s):  
Gene Family ◽  
Cell Lymphoma ◽  
Variable Region ◽  
Gene Families ◽  
Large Cell ◽  
Germline Gene ◽  
Diffuse Large Cell Lymphoma ◽  
Vh Genes ◽  
Large Cell Lymphoma ◽  
Almost All

Ig heavy chain variable region (VH) genes expressed by human diffuse large-cell lymphoma (DLC) and follicular lymphoma (FL) were identified and analyzed with respect to germline gene families. In 67 cases of FL, VH region genes were expressed in a pattern similar to that of normal B cells, with a predominance of the large VH3 gene family being used. In contrast, of the 17 cases of DLC, there was an extremely biased use of VH genes. Of these DLC tumors, 88% expressed genes from the small VH4 gene family; and even among these tumors, there was a limited use of genes, with 11 cases producing Igs derived from the VH4.21 germline gene. Although most of the VH genes expressed by DLC tumor cells contained mutations with respect to their germline counterparts, almost all of these mutations occurred before the clonal expansion of the tumor. This contrasts with our previous findings of ongoing mutations in FL and represents a fundamental difference between these two malignancies. This preferential gene use implies an important role for the VH4 gene family, and specifically for VH4.21, in the genesis of DLC.

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 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.

scholarly journals Genome-wide search and structural and functional analyses for late embryogenesis-abundant (LEA) gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zihan Cheng ◽  
Xuemei Zhang ◽  
Wenjing Yao ◽  
Kai Zhao ◽  
Lin Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Abiotic Stress Tolerance ◽  
Gene Families ◽  
Regulatory Elements ◽  
Late Embryogenesis Abundant ◽  
Genome Wide ◽  
Lea Gene ◽  
Late Embryogenesis ◽  
Genome Wide Search

Abstract Background The Late Embryogenesis-Abundant (LEA) gene families, which play significant roles in regulation of tolerance to abiotic stresses, widely exist in higher plants. Poplar is a tree species that has important ecological and economic values. But systematic studies on the gene family have not been reported yet in poplar. Results On the basis of genome-wide search, we identified 88 LEA genes from Populus trichocarpa and renamed them as PtrLEA. The PtrLEA genes have fewer introns, and their promoters contain more cis-regulatory elements related to abiotic stress tolerance. Our results from comparative genomics indicated that the PtrLEA genes are conserved and homologous to related genes in other species, such as Eucalyptus robusta, Solanum lycopersicum and Arabidopsis. Using RNA-Seq data collected from poplar under two conditions (with and without salt treatment), we detected 24, 22 and 19 differentially expressed genes (DEGs) in roots, stems and leaves, respectively. Then we performed spatiotemporal expression analysis of the four up-regulated DEGs shared by the tissues, constructed gene co-expression-based networks, and investigated gene function annotations. Conclusion Lines of evidence indicated that the PtrLEA genes play significant roles in poplar growth and development, as well as in responses to salt stress.

scholarly journals The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Tengcheng Que ◽  
Huifeng Wang ◽  
Weifei Yang ◽  
Jianbao Wu ◽  
Chenyang Hou ◽  
...  
Keyword(s):  
De Novo ◽  
Great Majority ◽  
Gene Families ◽  
Functional Enrichment ◽  
Mineral Absorption ◽  
Iron Storage ◽  
Trachypithecus Leucocephalus ◽  
Karst Environment ◽  
Alkali Tolerance ◽  
Almost All

Abstract Background Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche. Results In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies. Conclusions These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.

scholarly journals Shoot Regeneration Is Not a Single Cell Event

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 58
Author(s):  
Patharajan Subban ◽  
Yaarit Kutsher ◽  
Dalia Evenor ◽  
Eduard Belausov ◽  
Hanita Zemach ◽  
...  
Keyword(s):  
Gene Family ◽  
Single Cell ◽  
Shoot Regeneration ◽  
Major Gene ◽  
Molecular Genetic ◽  
Plant Biotechnology ◽  
Gene Families ◽  
Regeneration Medium ◽  
Developmental Processes ◽  
Leaf Segments

Shoot regeneration is a key tool of modern plant biotechnology. While many researchers use this process empirically, very little is known about the early molecular genetic factors and signaling events that lead to shoot regeneration. Using tobacco as a model system, we found that the inductive events required for shoot regeneration occur in the first 4–5 days following incubation on regeneration medium. Leaf segments placed on regeneration medium did not produce shoots if removed from the medium before four days indicating this time frame is crucial for the induction of shoot regeneration. Leaf segments placed on regeneration medium for longer than five days maintain the capacity to produce shoots when removed from the regeneration medium. Analysis of gene expression during the early days of incubation on regeneration medium revealed many changes occurring with no single expression pattern evident among major gene families previously implicated in developmental processes. For example, expression of Knotted gene family members increased during the induction period, whereas transcription factors from the Wuschel gene family were unaltered during shoot induction. Expression levels of genes involved in cell cycle regulation increased steadily on regeneration medium while expression of NAC genes varied. No obvious possible candidate genes or developmental processes could be identified as a target for the early events (first few days) in the induction of shoot regeneration. On the other hand, observations during the early stages of regeneration pointed out that regeneration does not occur from a single cell but a group of cells. We observed that while cell division starts just as leaf segments are placed on regeneration medium, only a group of cells could become shoot primordia. Still, these primordia are not identifiable during the first days.

scholarly journals Sexually Fertile Magnaporthe grisea Rice Pathogens in Thailand

Plant Disease ◽  
1999 ◽  
Vol 83 (10) ◽  
pp. 939-943 ◽  
Author(s):  
Poonsak Mekwatanakarn ◽  
Wichai Kositratana ◽  
Tawatchai Phromraksa ◽  
R. S. Zeigler
Keyword(s):  
Mating Type ◽  
Male Fertility ◽  
Magnaporthe Grisea ◽  
Female Sterility ◽  
Diverse Populations ◽  
Type Distribution ◽  
Northern Regions ◽  
Rice Pathogens ◽  
Central Thailand

Sexual fertility and mating type distribution of Magnaporthe grisea field isolates collected in Thailand were analyzed from sites previously found to harbor diverse populations of the pathogen. Three hundred forty-one single conidium isolates of M. grisea collected from five sites in north, northeast, and central Thailand were evaluated for in vitro sexual fertility and mating type by pairing with strains of known mating type. Most isolates (67%) were infertile when crossed with the hermaphrodite tester strains; but fertile isolates of each mating type that yielded viable ascospores were detected in all sites from the northeastern and northern regions. MAT1-2 predominated over MAT1-1 in bioassay mating type. Male fertility (female sterility) predominated in fertile MAT1-1 (50 to 75%) and MAT1-2 (50 to 85%) isolates from all locations in Thailand; however, hermaphroditic and/or female fertile isolates were also detected in all but one site. Fertility, as determined by perithecia density, was low (<10 perithecia cm-2) for most isolates, although a few produced in excess of 20 perithecia cm-2.

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