Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes

Marseilleviridae members are large dsDNA viruses with icosahedral particles 250 nm in diameter infecting Acanthamoeba. Their 340 to 390 kb genomes encode 450 to 550 protein-coding genes. Since the discovery of marseillevirus (the prototype of the family) in 2009, several strains were isolated from various locations, among which 13 are now fully sequenced. This allows the organization of their genomes to be deciphered through comparative genomics. Here, we first experimentally demonstrate that the Marseilleviridae genomes are circular. We then acknowledge a strong bias in sequence conservation, revealing two distinct genomic regions. One gathers most Marseilleviridae paralogs and has undergone genomic rearrangements, while the other, enriched in core genes, exhibits the opposite pattern. Most of the genes whose protein products compose the viral particles are located in the conserved region. They are also strongly biased toward a late gene expression pattern. We finally discuss the potential advantages of Marseilleviridae having a circular genome, and the possible link between the biased distribution of their genes and the transcription as well as DNA replication mechanisms that remain to be characterized.

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Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

Diversity ◽

10.3390/d13020081 ◽

2021 ◽

Vol 13 (2) ◽

pp. 81

Author(s):

Jakub Sawicki ◽

Katarzyna Krawczyk ◽

Monika Ślipiko ◽

Monika Szczecińska

Keyword(s):

Cryptic Speciation ◽

Editing Event ◽

Protein Coding ◽

Gene Set ◽

Protein Coding Genes ◽

Organellar Genomes ◽

The Family ◽

Leafy Liverwort ◽

Aneura Mirabilis ◽

First Time

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

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Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani

International Journal of Molecular Sciences ◽

10.3390/ijms22042183 ◽

2021 ◽

Vol 22 (4) ◽

pp. 2183

Author(s):

Nurhani Mat Razali ◽

Siti Norvahida Hisham ◽

Ilakiya Sharanee Kumar ◽

Rohit Nandan Shukla ◽

Melvin Lee ◽

...

Keyword(s):

Comparative Genomics ◽

Rhizoctonia Solani ◽

Abiotic Factors ◽

Biotic Factor ◽

Protein Coding ◽

Sustainable Food ◽

Repeat Elements ◽

Gene Sets ◽

Core Genes

Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.

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Genomic Analysis of a Newly Isolated Acidithiobacillus ferridurans JAGS Strain Reveals Its Adaptation to Acid Mine Drainage

Minerals ◽

10.3390/min11010074 ◽

2021 ◽

Vol 11 (1) ◽

pp. 74

Author(s):

Jinjin Chen ◽

Yilan Liu ◽

Patrick Diep ◽

Radhakrishnan Mahadevan

Keyword(s):

Acid Mine Drainage ◽

Mine Drainage ◽

Genomic Structure ◽

Evolutionary Relationship ◽

Genomic Analysis ◽

Protein Coding ◽

Acid Mine ◽

Inorganic Ion ◽

Unique Genes ◽

Core Genes

Acidithiobacillus ferridurans JAGS is a newly isolated acidophile from an acid mine drainage (AMD). The genome of isolate JAGS was sequenced and compared with eight other published genomes of Acidithiobacillus. The pairwise mutation distance (Mash) and average nucleotide identity (ANI) revealed that isolate JAGS had a close evolutionary relationship with A. ferridurans JCM18981, but whole-genome alignment showed that it had higher similarity in genomic structure with A. ferrooxidans species. Pan-genome analysis revealed that nine genomes were comprised of 4601 protein coding sequences, of which 43% were core genes (1982) and 23% were unique genes (1064). A. ferridurans species had more unique genes (205–246) than A. ferrooxidans species (21–234). Functional gene categorizations showed that A. ferridurans strains had a higher portion of genes involved in energy production and conversion while A. ferrooxidans had more for inorganic ion transport and metabolism. A high abundance of kdp, mer and ars genes, as well as mobile genetic elements, was found in isolate JAGS, which might contribute to its resistance to harsh environments. These findings expand our understanding of the evolutionary adaptation of Acidithiobacillus and indicate that A. ferridurans JAGS is a promising candidate for biomining and AMD biotreatment applications.

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Expression of non-protein-coding antisense RNAs in genomic regions related to autism spectrum disorders

Molecular Autism ◽

10.1186/2040-2392-4-32 ◽

2013 ◽

Vol 4 (1) ◽

pp. 32 ◽

Cited By ~ 33

Author(s):

Dmitry Velmeshev ◽

Marco Magistri ◽

Mohammad Faghihi

Keyword(s):

Autism Spectrum Disorders ◽

Autism Spectrum ◽

Protein Coding ◽

Antisense Rnas ◽

Spectrum Disorders ◽

Genomic Regions

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Complete Mitochondrial Genome Sequence Analysis and Phylogenetic Location Determination of Hydropsyche Fryeri (Insecta: Trichoptera)

10.21203/rs.3.rs-437236/v1 ◽

2021 ◽

Author(s):

Yimin Li ◽

Honglin Qin ◽

Xifa Zhong ◽

Jingcai Huang ◽

Yujun Wang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Genome Sequence ◽

Complete Mitochondrial Genome ◽

Phylogenetic Tree Analysis ◽

Protein Coding ◽

Mitochondrial Genome Sequence ◽

Complete Mitochondrial Genome Sequence ◽

Location Determination ◽

The Family

Abstract Hydropsyche fryeri belongs to the Trichopteridae family and builds nests in clean and unpolluted streams using stones. It also can be used as an indicator of water quality. Here, we describe the complete mitochondrial genome sequence of Hydropsyche fryeri. The mitochondrial genome is 15,676 bp long and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs and an AT-rich control region. Phylogenetic tree analysis shows that Hydropsyche fryeri is more closely related to the family Hydroptera than other Trichoptera.

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The Heterochromatin Landscape in Migrating Cells and the Importance of H3K27me3 for Associated Transcriptome Alterations

Cells ◽

10.3390/cells7110205 ◽

2018 ◽

Vol 7 (11) ◽

pp. 205 ◽

Cited By ~ 8

Author(s):

Tamar Segal ◽

Mali Salmon-Divon ◽

Gabi Gerlitz

Keyword(s):

Transcriptome Analysis ◽

Transcriptional Repression ◽

Chromatin Condensation ◽

Opposite Pattern ◽

Protein Coding ◽

Epigenetic Markers ◽

Protein Coding Genes ◽

Global Increase ◽

General Signature ◽

Migrating Cells

H3K9me3, H3K27me3, and H4K20me1 are epigenetic markers associated with chromatin condensation and transcriptional repression. Previously, we found that migration of melanoma cells is associated with and dependent on global chromatin condensation that includes a global increase in these markers. Taken together with more recent reports by others suggests it is a general signature of migrating cells. Here, to learn about the function of these markers in migrating cells, we mapped them by ChIP-seq analysis. This analysis revealed that induction of migration leads to expansion of these markers along the genome and to an increased overlapping between them. Significantly, induction of migration led to a higher increase in H3K9me3 and H4K20me1 signals at repetitive elements than at protein-coding genes, while an opposite pattern was found for H3K27me3. Transcriptome analysis revealed 182 altered genes following induction of migration, of which 33% are dependent on H3K27me3 for these changes. H3K27me3 was also required to prevent changes in the expression of 501 other genes upon induction of migration. Taken together, our results suggest that heterochromatinization in migrating cells is global and not restricted to specific genomic loci and that H3K27me3 is a key component in executing a migration-specific transcriptional plan.

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Preliminary study of the enzyme ubiquitin carboxylterminal hydrolase 14 (UBP6) in Giardia intestinalis: structural bioinformatic analysis and transcriptional profile during encystation

Revista Colombiana de Química ◽

10.15446/rev.colomb.quim.v43n2.53122 ◽

2015 ◽

Vol 43 (2) ◽

pp. 32-40

Author(s):

Magda E Alvarado ◽

Camila A González ◽

Moisés Wasserman ◽

Claudia C Rubiano

Keyword(s):

Protein Turnover ◽

Bioinformatic Analysis ◽

Giardia Intestinalis ◽

Deubiquitinating Enzyme ◽

Combined Approach ◽

Protein Coding ◽

Starting Point ◽

The Family ◽

Preliminary Study ◽

Carboxyl Terminal

This paper presents a combined approach with two aims. The first is to analyze the reported sequence of the enzyme ubiquitin carboxyl-terminal hydrolase 14 of Giardia intestinalis (UBP6) through computational methods to find components related with its hypothetical function. The second is to determine if the protein-coding gene is expressed in G. intestinalis and, if such is the case, also determine its transcription pattern along the life cycle of the parasite. It was established that the protein belongs to the family of Cys-dependent deubiquitinases and more specifically to ubiquitin specific proteases (USPs). Moreover, the catalytic center with the complete triad as well as typical features of the USP motif were also identified. Since the computational findings suggest that the enzyme could be functional, reverse transcription coupled to PCR was used as a first approach to establish if in fact the coding gene is expressed in the parasite. Interestingly, it was found not only that the gene is expressed, but also that there is a transcription variation along the life cycle of the parasite. These two findings are the starting point for further studies since they tentatively suggest that this enzyme could be involved in the protein turnover that occurs during parasite encystation. Although preliminary, this study is the first report concerning the study of a specific deubiquitinating enzyme in the parasite G. intestinalis.

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Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

10.1101/079137 ◽

2016 ◽

Cited By ~ 1

Author(s):

Kevin S. Bonham ◽

Benjamin E. Wolfe ◽

Rachel J. Dutton

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Molecular Mechanisms ◽

Protein Coding ◽

Associated Bacteria ◽

The Us ◽

Selective Forces ◽

Genomic Regions ◽

Microbiome Assembly ◽

Insight Into

AbstractAcquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

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The Draft Genome Sequence of The Endophytic Streptomyces Strain VITGV156

10.21203/rs.3.rs-791591/v1 ◽

2021 ◽

Author(s):

Veilumuthu P ◽

Nagarajan T ◽

Sasikumar S ◽

Siva R ◽

J Godwin Christopher

Keyword(s):

Secondary Metabolites ◽

Draft Genome ◽

Gc Content ◽

Gene Clusters ◽

Dominant Group ◽

Protein Coding ◽

Peptide Synthetase ◽

The Family ◽

Modified Peptides ◽

Endophytic Streptomyces

Abstract Streptomyces species is one among the dominant group of bacteria in the family Actinobacteria with a rich repertoire of secondary metabolites. Secondary metabolites with antimicrobial activity and plant growth promotor have been isolated from various Streptomyces sp. Here in this investigation, we present the draft genome of a new species, Streptomyces sp. VITGV156 isolated from healthy tomato plant (Lycopersicon esculentum) which has some rare antimicrobial secondary metabolites, like coelichelin, fluostatins, vicenistatin, nystatin, sipanmycin, and informatipeptin. The genome is 8.18 Mb in size with 6,259 protein coding genes. The average GC content of the genome is 72.61 %. Preliminary analysis with antiSMASH 6.0 revealed the presence of 29 biosynthetic gene clusters for the synthesis of potential secondary metabolites. These includes 4 NRPS (non – ribosomal peptide synthetase), 7 PKS (Polyketide Synthases), 2 RiPP (Ribosomally synthesized and post-translationally modified peptides) clusters. When we look into genes associated with secondary metabolites, 406 genes are present which includes 184 genes for cofactor and vitamins, 72 genes for terpenoids and polyketides, 70 genes for xenobiotics and 80 genes for other metabolites are present. Comparative genome analysis of VITGV156 with its closest neighbor Streptomyces luteus strain TRM45540 revealed ANI 91.22% and dDDH value 44.00%.

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Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

Systematic Botany ◽

10.1600/036364421x16128061189576 ◽

2021 ◽

Vol 46 (1) ◽

pp. 162-174

Author(s):

Ming-Hui Yan ◽

Chun-Yang Li ◽

Peter W. Fritsch ◽

Jie Cai ◽

Heng-Chang Wang

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Signal ◽

Strong Support ◽

Single Copy ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

The Family ◽

Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

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