An in silico comparative genomic report on transcription factors in three Arabidopsis species

Transcription factors (TF) are the elements, which regulate gene expression. Regulatory function of TFs play an important role in plant biological processes and mechanisms. They may interconnect with other transcription factors or functional genes to modulate their expression in response to an internal/external factor like life cycle stage, growth, development and stress. Arabidopsis is the well-known and the most used model organism. Transcription factors of three Arabidopsis species including A. halleri, A. lyrata and A. thaliana, were compared. basic/helix-loop-helix (bHLH) with 220 TFs was the most abundant family among three Arabidopsis species while MYB and MYB related families considering as a whole group were more than bHLH with 308 TFs. No STERILE APETALA (SAP) TF homolog was found for A.halleri. The common transcription factors among three species were 4,172 grouped in 1,212 clusters. The species-specific clustered TFs were 12, 30 and 58 for A. halleri, A. lyrata and A. thaliana respectively. Eight hundred ninety two single-copy gene clusters those have one gene copy from each species, i.e. 2,676 genes, were listed. Four hundred forty five TF singletons were not clustered and are unique among three species. For clustered TF belonging to each species, GO terms and SwissProt hits showed that A. halleri has two species-specific TFs involved in heavy metal response including Zinc finger protein AZF2 and two-component response regulator ARR11 while for A. lyrata specific TFs are involved in stress response and plant development. A. thaliana specific clustered TFs work on plant flower development and acclimation.

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An in silico comparative genomic report on transcription factors in three Arabidopsis species

Ciencia y Tecnología ◽

10.18779/cyt.v11i1.215 ◽

2018 ◽

Vol 11 (1) ◽

pp. 1-9

Author(s):

Seyed Mehdi Jazayeri ◽

Mahtab Pooralinaghi ◽

Ronald Villamar Torres ◽

Luz García Cruzatty

Keyword(s):

Transcription Factors ◽

Zinc Finger Protein ◽

Response Regulator ◽

Model Organism ◽

Gene Clusters ◽

Gene Copy ◽

Regulatory Function ◽

Comparative Genomic ◽

Species Specific ◽

Arabidopsis Species

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Gene expression and DNA methylation altering lead to the high oil content in wild allotetraploid peanut (A. monticola)

10.21203/rs.3.rs-1222296/v1 ◽

2022 ◽

Author(s):

Nian Liu ◽

Manish Pandey ◽

Bei Wu ◽

Li Huang ◽

Huaiyong Luo ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Transcription Factors ◽

Arachis Hypogaea ◽

Oil Content ◽

Expression Patterns ◽

Gene Clusters ◽

Oil Accumulation ◽

Species Specific ◽

Wild Peanut

Abstract The wild allotetraploid peanut Arachis monticola contains higher oil content than cultivated allotetraploid Arachis hypogaea. To investigate its molecular mechanism controlling oil accumulation, we performed comparative transcriptomics from developing seeds between three Arachis monticola and five Arachis hypogaea varieties. The analysis not only showed species-specific grouping based on transcriptional profiles but also detected two gene clusters with divergent expression patterns enriched in lipid metabolism. Further, the differential expression gene analysis also indicated expression alteration in wild peanut leading to enhanced activity of oil biogenesis and limiting the rate of lipid degradation. We also constructed a regulatory network of lipid metabolic DEGs with co-expressed transcription factors. In addition, bisulfite sequencing was conducted to characterize the variation of DNA methylation between wild allotetraploid (245, WH 10025) and cultivated allotetraploid (Z16, Zhh 7720) genotypes. Genome-wide DNA methylation was found antagonistically correlated with gene expression during seed development. The results indicated that CG and CHG contexts methylation may negatively regulate specific lipid metabolic genes and transcription factors to subtly affect the difference of oil accumulation. Our work provided the first glimpse on the regulatory mechanism of gene expression altering for oil accumulation in wild peanut and gene resources for future breeding applications.

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Significant Natural Product Biosynthetic Potential of Actinorhizal Symbionts of the Genus Frankia, as Revealed by Comparative Genomic and Proteomic Analyses

Applied and Environmental Microbiology ◽

10.1128/aem.00038-11 ◽

2011 ◽

Vol 77 (11) ◽

pp. 3617-3625 ◽

Cited By ~ 66

Author(s):

Daniel W. Udwary ◽

Erin A. Gontang ◽

Adam C. Jones ◽

Carla S. Jones ◽

Andrew W. Schultz ◽

...

Keyword(s):

Natural Products ◽

Cyclic Peptides ◽

Intact Cell ◽

Gene Clusters ◽

Mass Range ◽

Bioinformatic Analysis ◽

Comparative Genomic ◽

Ionization Mass ◽

Content Type ◽

Species Specific

ABSTRACTBacteria of the genusFrankiaare mycelium-forming actinomycetes that are found as nitrogen-fixing facultative symbionts of actinorhizal plants. Although soil-dwelling actinomycetes are well-known producers of bioactive compounds, the genusFrankiahas largely gone uninvestigated for this potential. Bioinformatic analysis of the genome sequences ofFrankiastrains ACN14a, CcI3, and EAN1pec revealed an unexpected number of secondary metabolic biosynthesis gene clusters. Our analysis led to the identification of at least 65 biosynthetic gene clusters, the vast majority of which appear to be unique and for which products have not been observed or characterized. More than 25 secondary metabolite structures or structure fragments were predicted, and these are expected to include cyclic peptides, siderophores, pigments, signaling molecules, and specialized lipids. Outside the hopanoid gene locus, no cluster could be convincingly demonstrated to be responsible for the few secondary metabolites previously isolated from otherFrankiastrains. Few clusters were shared among the three species, demonstrating species-specific biosynthetic diversity. Proteomic analysis ofFrankiasp. strains CcI3 and EAN1pec showed that significant and diverse secondary metabolic activity was expressed in laboratory cultures. In addition, several prominent signals in the mass range of peptide natural products were observed inFrankiasp. CcI3 by intact-cell matrix-assisted laser desorption-ionization mass spectrometry (MALDI-MS). This work supports the value of bioinformatic investigation in natural products biosynthesis using genomic information and presents a clear roadmap for natural products discovery in theFrankiagenus.

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Denaturing High Performance Liquid Chromatography and Bioinformatics - Two Modern Tools for Extracellular Superoxide Dismutase (SOD3) Gene Promoter Analysis

Revista de Chimie ◽

10.37358/rc.08.7.1893 ◽

2008 ◽

Vol 59 (7) ◽

Author(s):

Corina Samoila ◽

Alfa Xenia Lupea ◽

Andrei Anghel ◽

Marilena Motoc ◽

Gabriela Otiman ◽

...

Keyword(s):

High Performance Liquid Chromatography ◽

Transcription Factors ◽

Liquid Chromatography ◽

Dna Sequences ◽

High Performance ◽

Zinc Finger Protein ◽

High Capacity ◽

Gene Promoter ◽

Experimental Approaches ◽

Myeloid Zinc Finger

Denaturing High Performance Liquid Chromatography (DHPLC) is a relatively new method used for screening DNA sequences, characterized by high capacity to detect mutations/polymorphisms. This study is focused on the Transgenomic WAVETM DNA Fragment Analysis (based on DHPLC separation method) of a 485 bp fragment from human EC-SOD gene promoter in order to detect single nucleotide polymorphism (SNPs) associated with atherosclerosis and risk factors of cardiovascular disease. The fragment of interest was amplified by PCR reaction and analyzed by DHPLC in 100 healthy subjects and 70 patients characterized by atheroma. No different melting profiles were detected for the analyzed DNA samples. A combination of computational methods was used to predict putative transcription factors in the fragment of interest. Several putative transcription factors binding sites from the Ets-1 oncogene family: ETS member Elk-1, polyomavirus enhancer activator-3 (PEA3), protein C-Ets-1 (Ets-1), GABP: GA binding protein (GABP), Spi-1 and Spi-B/PU.1 related transcription factors, from the Krueppel-like family: Gut-enriched Krueppel-like factor (GKLF), Erythroid Krueppel-like factor (EKLF), Basic Krueppel-like factor (BKLF), GC box and myeloid zinc finger protein MZF-1 were identified in the evolutionary conserved regions. The bioinformatics results need to be investigated further in others studies by experimental approaches.

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Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

Journal of Fungi ◽

10.3390/jof7050337 ◽

2021 ◽

Vol 7 (5) ◽

pp. 337

Author(s):

Daniel Peterson ◽

Tang Li ◽

Ana M. Calvo ◽

Yanbin Yin

Keyword(s):

Comparative Genomics ◽

Orthologous Gene ◽

Gene Clusters ◽

Phytopathogenic Fungi ◽

Secreted Proteins ◽

Economic Losses ◽

Comparative Genomic ◽

Signal Peptides ◽

Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

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Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Marine Drugs ◽

10.3390/md19060298 ◽

2021 ◽

Vol 19 (6) ◽

pp. 298

Author(s):

Despoina Konstantinou ◽

Rafael V. Popin ◽

David P. Fewer ◽

Kaarina Sivonen ◽

Spyros Gkelis

Keyword(s):

Natural Products ◽

Microbial Communities ◽

Genomic Analysis ◽

Gene Clusters ◽

Marine Sponges ◽

Genome Reduction ◽

Extracellular Polysaccharides ◽

Comparative Genomic ◽

Symbiotic Relationships ◽

Genes Encoding

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.

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In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data

Animals ◽

10.3390/ani11082226 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2226

Author(s):

Sazia Kunvar ◽

Sylwia Czarnomska ◽

Cino Pertoldi ◽

Małgorzata Tokarska

Keyword(s):

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Model Organism ◽

Genotyping By Sequencing ◽

Model Organisms ◽

European Bison ◽

Model Animal ◽

Pcr Duplicates ◽

Species Specific

The European bison is a non-model organism; thus, most of its genetic and genomic analyses have been performed using cattle-specific resources, such as BovineSNP50 BeadChip or Illumina Bovine 800 K HD Bead Chip. The problem with non-specific tools is the potential loss of evolutionary diversified information (ascertainment bias) and species-specific markers. Here, we have used a genotyping-by-sequencing (GBS) approach for genotyping 256 samples from the European bison population in Bialowieza Forest (Poland) and performed an analysis using two integrated pipelines of the STACKS software: one is de novo (without reference genome) and the other is a reference pipeline (with reference genome). Moreover, we used a reference pipeline with two different genomes, i.e., Bos taurus and European bison. Genotyping by sequencing (GBS) is a useful tool for SNP genotyping in non-model organisms due to its cost effectiveness. Our results support GBS with a reference pipeline without PCR duplicates as a powerful approach for studying the population structure and genotyping data of non-model organisms. We found more polymorphic markers in the reference pipeline in comparison to the de novo pipeline. The decreased number of SNPs from the de novo pipeline could be due to the extremely low level of heterozygosity in European bison. It has been confirmed that all the de novo/Bos taurus and Bos taurus reference pipeline obtained SNPs were unique and not included in 800 K BovineHD BeadChip.

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Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

Journal of Fungi ◽

10.3390/jof7060485 ◽

2021 ◽

Vol 7 (6) ◽

pp. 485

Author(s):

Boxun Li ◽

Yang Yang ◽

Jimiao Cai ◽

Xianbao Liu ◽

Tao Shi ◽

...

Keyword(s):

Comparative Genomics ◽

Single Molecule ◽

Rubber Tree ◽

Gene Families ◽

Gene Clusters ◽

The Philippines ◽

Tree Plantations ◽

Comparative Genomic ◽

Corynespora Cassiicola ◽

Leaf Fall

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.

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An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

Genetics ◽

10.1093/genetics/iyab066 ◽

2021 ◽

Author(s):

Matthew E Mead ◽

Jacob L Steenwyk ◽

Lilian P Silva ◽

Patrícia A de Castro ◽

Nauman Saeed ◽

...

Keyword(s):

Human Disease ◽

Evolutionary Rate ◽

Fungal Disease ◽

Comparative Genomic ◽

Genetic Elements ◽

Genomic Approach ◽

Evolutionary Genomic ◽

Repeated Evolution ◽

Species Specific ◽

Encoding Genes

Abstract Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus Aspergillus. Roughly 70% of infections are caused by Aspergillus fumigatus, with the rest stemming from approximately a dozen other Aspergillus species. Several of these pathogens are closely related to A. fumigatus and belong in the same taxonomic section, section Fumigati. Pathogenic species are frequently most closely related to non-pathogenic ones, suggesting Aspergillus pathogenicity evolved multiple times independently. To understand the repeated evolution of Aspergillus pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in section Fumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and non-pathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1,700 genes whose evolutionary rate differed between pathogens and non-pathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and non-pathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in Aspergillus involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.

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Identification of the kinanthraquinone biosynthetic gene cluster by expression of an atypical response regulator

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbaa082 ◽

2021 ◽

Vol 85 (3) ◽

pp. 714-721

Author(s):

Risa Takao ◽

Katsuyuki Sakai ◽

Hiroyuki Koshino ◽

Hiroyuki Osada ◽

Shunji Takahashi

Keyword(s):

Heterologous Expression ◽

Gene Cluster ◽

Secondary Metabolite ◽

Response Regulator ◽

Bac Library ◽

Gene Clusters ◽

Biosynthetic Gene Cluster ◽

Gene Organization ◽

Biosynthetic Gene ◽

Streptomyces Sp

ABSTRACT Recent advances in genome sequencing have revealed a variety of secondary metabolite biosynthetic gene clusters in actinomycetes. Understanding the biosynthetic mechanism controlling secondary metabolite production is important for utilizing these gene clusters. In this study, we focused on the kinanthraquinone biosynthetic gene cluster, which has not been identified yet in Streptomyces sp. SN-593. Based on chemical structure, 5 type II polyketide synthase gene clusters were listed from the genome sequence of Streptomyces sp. SN-593. Among them, a candidate gene cluster was selected by comparing the gene organization with grincamycin, which is synthesized through an intermediate similar to kinanthraquinone. We initially utilized a BAC library for subcloning the kiq gene cluster, performed heterologous expression in Streptomyces lividans TK23, and identified the production of kinanthraquinone and kinanthraquinone B. We also found that heterologous expression of kiqA, which belongs to the DNA-binding response regulator OmpR family, dramatically enhanced the production of kinanthraquinones.

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