Variation In GC Content Research Articles

The non-canonically organized members of MIR395 gene family in Brassica juncea are associated with developmentally regulated, sulfate-stress responsive bidirectional promoters that exhibit orientation-dependent differential transcriptional activity

Several MICRORNA genes belonging to same family or different families are often found in homologous or non-homologous clusters. Among the various classes, head-to-head arranged genes form one of the largest categories of non-canonically organized genes. Such head-to-head arranged, non-canonically organized genes possibly share cis-regulatory region with the intergenic sequence having the potential to function as bi-directional promoter (BDP). The transcriptional regulation of head-to-head arranged genes, especially with bidirectional promoters, remains an enigma. In the past, bidirectional promoters have been characterized for a small set of protein-coding gene pairs in plants; however, to the best of our knowledge, no such study has been carried so far for MICRORNA genes. The present study thus functionally characterizes bidirectional promoters associated with members of MIR395 family, which is evolutionary conserved and is most frequently occurring cluster across plant kingdom.In Arabidopsis thaliana, the MIR395 gene family contains six members with two head-to-head arranged gene pairs- MIR395A-B and MIR395E-F. This organization was found to be conserved at seven loci for MIR395A-B, and eleven loci for MIR395E-F in five Brassica sps. Sequence analysis of the putative bidirectional promoters revealed variation in length, GC content and distribution of strict TATA-box. Comparatively higher level of conservation at both the ends of the bidirectional promoters, corresponding to ca. 250 bp upstream of 5’end of the respective MIRNA precursor, was observed. These conserved regions harbour several abiotic stress (nutrient, salt, drought) and hormone (ABA, ethylene) responsive cis-motifs. Functional characterization of putative bidirectional promoters associated with MIR395A-B and MIR395E-F from Arabidopsis and their respective orthologs from Brassica juncea (Bj_A08 MIR395A-B, Bj_B03 MIR395A-B, Bj_A07.1 MIR395E-F and Bj_A07.2 MIR395E-F) was carried out using a dual-reporter vector with β-glucuronidase (GUS) and Green Fluorescent Protein (GFP). Analysis of transcriptional regulation of the two reporter genes - GUS and GFP during developmental stages confirmed their bidirectional nature. Orientation-dependent differential reporter activity indicated asymmetric nature of the promoters. Comparison of the reporter activity amongst orthologs, paralogs and homeologs revealed regulatory diversification, an outcome expected in polyploid genomes. Interestingly, reporter gene activities driven by selected bidirectional promoters were also observed in anther and siliques apart vegetative tissues indicating role of miR395 in anther and fruit development. Finally, we evaluated the activity of reporter genes driven under transcriptional regulation of bidirectional promoters under normal and sulfate-deprived conditions which revealed asymmetric inducibility under sulfate-starvation, in agreement with the known role of miR395 in sulfate homeostasis.

The complete annotated plastome sequences of six genera in the tropical woody Polygonaceae.

The Polygonaceae is a family well-known for its weeds, and edible plants, Fagopyrum (buckwheat) and Rheum (rhubarb), which are primarily herbaceous and temperate in distribution. Yet, the family also contains a number of lineages that are principally distributed in the tropics and subtropics. Notably, these lineages are woody, unlike their temperate relatives. To date, full-genome sequencing has focused on the temperate and herbaceous taxa. In an effort to increase breadth of genetic knowledge of the Polygonaceae, we here present six fully assembled and annotated chloroplast genomes from six of the tropical, woody genera: Coccoloba rugosa (a narrow and endangered Puerto Rican endemic), Gymnopodium floribundum, Neomillspaughia emarginata, Podopterus mexicanus, Ruprechtia coriacea, and Triplaris cumingiana. These assemblies represent the first publicly-available assembled and annotated plastomes for the genera Podopterus, Gymnopodium, and Neomillspaughia, and the first assembled and annotated plastomes for the species Coccoloba rugosa, Ruprechtia coriacea, and Triplaris cumingiana. We found the assembled chloroplast genomes to be above the median size of Polygonaceae plastomes, but otherwise exhibit features typical of the family. The features of greatest sequence variation are found among the ndh genes and in the small single copy (SSC) region of the plastome. The inverted repeats show high GC content and little sequence variation across genera. When placed in a phylogenetic context, our sequences were resolved within the Eriogonoideae. These six plastomes from among the tropical woody Polygonaceae appear typical within the family. The plastome assembly of Ruprechtia coriacea presented here calls into question the sequence identity of a previously published plastome assembly of R. albida.

Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective.

Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus.

Rapid Targeted Assembly of the Proteome Reveals Evolutionary Variation of GC Content in Avian Lice.

Nucleotide base composition plays an influential role in the molecular mechanisms involved in gene function, phenotype, and amino acid composition. GC content (proportion of guanine and cytosine in DNA sequences) shows a high level of variation within and among species. Many studies measure GC content in a small number of genes, which may not be representative of genome-wide GC variation. One challenge when assembling extensive genomic data sets for these studies is the significant amount of resources (monetary and computational) associated with data processing, and many bioinformatic tools have not been optimized for resource efficiency. Using a high-performance computing (HPC) cluster, we manipulated resources provided to the targeted gene assembly program, automated target restricted assembly method (aTRAM), to determine an optimum way to run the program to maximize resource use. Using our optimum assembly approach, we assembled and measured GC content of all of the protein-coding genes of a diverse group of parasitic feather lice. Of the 499 426 genes assembled across 57 species, feather lice were GC-poor (mean GC = 42.96%) with a significant amount of variation within and between species (GC range = 19.57%-73.33%). We found a significant correlation between GC content and standard deviation per taxon for overall GC and GC3, which could indicate selection for G and C nucleotides in some species. Phylogenetic signal of GC content was detected in both GC and GC3. This research provides a large-scale investigation of GC content in parasitic lice laying the foundation for understanding the basis of variation in base composition across species.

Distinguishing features of Lycium L. species (family Solanaceae) distributed in Egypt based on their anatomical, metabolic, molecular, and ecological characteristics.

Among the 70-80 species of the genus Lycium (family Solanaceae) disjunctly distributed around the world, only three are frequently distributed in different locations in Egypt. Due to the morphological similarities between these three species, there is a need for alternative tools to distinguish them. Thus, the objective of this study was to revise the taxonomic features of Lycium europaeum L., Lycium shawii Roem. & Schult., and Lycium schweinfurthii var. aschersonii (Dammer) Feinbrun in consideration of their anatomical, metabolic, molecular, and ecological characteristics. In addition to analysis of their anatomical and ecological features, DNA barcoding was performed for molecular characterization through internal transcribed spacer (ITS) sequencing and start codon targeted (SCoT) markers. Furthermore, metabolic profiling of the studied species was conducted based on gas chromatography-mass spectrometry (GC-MS). The observed anatomical features of the adaxial and abaxial epidermal layers, type of mesophyll, crystals, number of palisade and spongy layers, and the vascular system showed variations between the studied species. Beyond this, the anatomy of the leaves showed an isobilateral structure in the studied species, without distinct differences. Species were molecularly identified in terms of ITS sequences and SCoT markers. The ITS sequences were deposited in GenBank with accession numbers ON149839.1, OP597546.1, and ON521125.1 for L. europaeum L., L. shawii, and L. schweinfurthii var. aschersonii, respectively. The sequences showed variations in GC content between the studied species; this was 63.6% in L. europaeum, 61.53% in L. shawii, and 63.55% in L. schweinfurthii var. aschersonii. A total of 62 amplified fragments, including 44 polymorphic fragments with a ratio of 70.97%, were obtained in the SCoT analysis, as well as unique amplicons in L. europaeum L., shawii, and L. schweinfurthii var. aschersonii of 5, 11, and 4 fragments, respectively. Through GC-MS profiling, 38 compounds were identified with clear fluctuations in the extracts of each species. Of these, 23 were distinguishing chemicals that could help in chemical identification of the extracts of the studied species. The present study succeeds in identifying alternative clear and diverse characteristics that can be used to distinguish between L. europaeum, L. shawii, and L. schweinfurthii var. aschersonii.

Genetic Profiling of the Full-Length tprK Gene in Patients with Primary and Secondary Syphilis.

TprK antigenic variation is acknowledged as an important strategy developed by Treponema pallidum to achieve immune evasion. Previous studies applied short-read sequencing to explore tprK gene sequence diversity in clinical samples; however, due to the limitations of short-read sequencing, it was difficult to determine the linkage between the seven V regions, and crucial information about full-length tprK variants was lost. Although two recent studies explored complete tprK gene profiles in natural human syphilis infection, there are still too few profiled full-length tprK variants among clinical T. pallidum isolates to fully understand the characteristics of TprK coding diversity. Here, Pacific Biosciences (PacBio) long-read sequencing was applied to examine the diversity of full-length tprK variants in 21 clinical T. pallidum isolates from 11 patients with primary syphilis and 10 patients with secondary syphilis. A total of 398 high-confidence full-length sequences, which presented remarkable sequence heterogeneity, were found. However, these full-length tprK variants exhibited limited variation in length and GC content, showing 24 length types and average GC content of 51.5 ± 0.42% and 51.6 ± 0.26% for primary and secondary syphilis samples, respectively. Additionally, the combined patterns of mutated V regions generating new tprK variants were obviously different in primary and secondary syphilis samples. The diversity of tprK gene sequences in primary syphilis samples may represent the underlying variability of the bacterium; conversely, the variability of the tprK gene in secondary syphilis samples may more accurately reflect how T. pallidum escapes host immune clearance. These data highlight the tprK gene as an important coding gene that shows conflicting genetic characteristics but underlies the persistence of spirochete infection. IMPORTANCE The resurgence of syphilis in both low- and high-income countries has attracted attention, and persistent infection by the pathogen has long been a research focus. The tprK gene, encoding the hypervariable outer membrane protein, is thought to be responsible for pathogen immune evasion and persistent infection. Here, PacBio long-read sequencing was applied to examine the diversity of full-length tprK variants in 21 clinical T. pallidum isolates from 11 patients with primary syphilis and 10 patients with secondary syphilis. The results showed that the sequences of the tprK gene were remarkably heterogeneous; however, the sequences presented limited variation in length and GC content. The investigation of the combined patterns of the V regions allowed us to gain insight into the features of the tprK gene generating new variants at different clinical stages. The findings of this study will be helpful for further exploration of the pathogenesis of syphilis.

Mutational Bias and Natural Selection Driving the Synonymous Codon Usage of Single-Exon Genes in Rice (Oryza sativa L.)

The relative abundance of single-exon genes (SEGs) in higher plants is perplexing. Uncovering the synonymous codon usage pattern of SEGs will benefit for further understanding their underlying evolutionary mechanism in plants. Using internal correspondence analysis (ICA), we reveal a significant difference in synonymous codon usage between SEGs and multiple-exon genes (MEGs) in rice. But the effect is weak, accounting for only 2.61% of the total codon usage variability. SEGs and MEGs contain remarkably different base compositions, and are under clearly differential selective constraints, with the former having higher GC content, and evolving relatively faster during evolution. In the group of SEGs, the variability in synonymous codon usage among genes is partially due to the variations in GC content, gene function, and gene expression level, which accounts for 22.03%, 5.99%, and 3.32% of the total codon usage variability, respectively. Therefore, mutational bias and natural selection should work on affecting the synonymous codon usage of SEGs in rice. These findings may deepen our knowledge for the mechanisms of origination, differentiation and regulation of SEGs in plants.

The dynamics of genome size and GC contents evolution in genus Nicotiana.

Hybridization and Polyploidization are most common of the phenomenon observed in plants, especially in the genus Nicotiana leading to the duplication of genome. Although genomic changes associated with these events has been studied at various levels but the genome size and GC content variation is less understood because of absence of sufficient genomic data. In this study the flow cytometry technique was used to uncover the genome size and GC contents of 46 Nicotiana species and we compared the genomic changes associated with the hybridization events along evolutionary time scale. The genome size among Nicotiana species varied between 3.28 pg and 11.88 pg whereas GC contents varied between 37.22% and 51.25%. The tetraploid species in genus Nicotiana including section Polydiclae, Repandae, Nicotiana, Rustica and Sauveolentes revealed both up and downsizing in their genome sizes when compared to the sum of genomes of their ancestral species. The genome sizes of three homoploid hybrids were found near their ancestral species. Loss of large genome sequence was observed in the evolutionary more aged species (>10 Myr) as compared to the recently evolved one's (<0.2 Myr). The GC contents were found homogenous with a mean difference of 2.46% among the Nicotiana species. It is concluded that genome size change appeared in either direction whereas the GC contents were found more homogenous in genus Nicotiana.

The ecological adaptation of the unparalleled plastome character evolution in slipper orchids.

Plastomes may have undergone adaptive evolution in the process of plant adaptation to diverse environments, whereby species may differ in plastome characters. Cypripedioideae successfully colonized distinct environments and could be an ideal group for studying the interspecific variation and adaptive evolution of plastomes. Comparative study of plastomes, ancestral state reconstruction, phylogenetic-based analysis, ecological niche modelling, and selective pressure analysis were conducted to reveal the evolutionary patterns of plastomes in Cypripedioideae and their relationship with environmental factors. The plastomes of the three evolved genera had reduced plastome size, increased GC content, and compacted gene content compared to the basal group. Variations in plastome size and GC content are proved to have clear relationships with climate regions. Furthermore, ecological niche modelling revealed that temperature and water factors are important climatic factors contributing to the distributional difference which is directly correlated with the climate regions. The temperature-sensitive genes ndh genes, infA, and rpl20 were found to be either lost/pseudogenized or under positive selection in the evolved groups. Unparalleled plastome character variations were discovered in slipper orchids. Our study indicates that variations in plastome characters have adaptive consequences and that temperature and water factors are important climatic factors that affect plastome evolution. This research highlights the expectation that plants can facilitate adaptation to different environmental conditions with the changes in plastome and has added critical insight for understanding the process of plastome evolution in plants.

False gene and chromosome losses in genome assemblies caused by GC content variation and repeats

BackgroundMany short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements.ResultsHere we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna’s hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5′-proximal promoters and 5′ exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies.ConclusionsOur findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.

Categorical edge-based analyses of phylogenomic data reveal conflicting signals for difficult relationships in the avian tree

Phylogenetic analyses fail to yield a satisfactory resolution of some relationships in the tree of life even with genome-scale datasets, so the failure is unlikely to reflect limitations in the amount of data. Gene tree conflicts are particularly notable in studies focused on these contentious nodes, and taxon sampling, different analytical methods, and/or data type effects can further confound analyses. Although many efforts have been made to incorporate biological conflicts, few studies have curated individual genes for their efficiency in phylogenomic studies. Here, we conduct an edge-based analysis of Neoavian evolution, examining the phylogenetic efficacy of two recent phylogenomic bird datasets and three datatypes (ultraconserved elements [UCEs], introns, and coding regions). We assess the potential causes for biases in signal-resolution for three difficult nodes: the earliest divergence of Neoaves, the position of the enigmatic Hoatzin (Opisthocomus hoazin), and the position of owls (Strigiformes). We observed extensive conflict among genes for all data types and datasets even after meticulous curation. Edge-based analyses (EBA) increased congruence and provided information about the impact of data type, GC content variation (GCCV), and outlier genes on each of nodes we examined. First, outlier gene signals appeared to drive different patterns of support for the relationships among the earliest diverging Neoaves. Second, the placement of Hoatzin was highly variable, although our EBA did reveal a previously unappreciated data type effect with an impact on its position. It also revealed that the resolution with the most support here was Hoatzin + shorebirds. Finally, GCCV, rather than data type (i.e., coding vs non-coding) per se, was correlated with a signal that supports monophyly of owls + Accipitriformes (hawks, eagles, and vultures). Eliminating high GCCV loci increased the signal for owls + mousebirds. Categorical EBA was able to reveal the nature of each edge and provide a way to highlight especially problematic branches that warrant a further examination. The current study increases our understanding about the contentious parts of the avian tree, which show even greater conflicts than appreciated previously.

Morphopathological and Molecular Morphometric Characterization of Waitea circinata var. prodigus Causing a Novel Sheath Spot Disease of Maize in India.

Maize brown sheath spot (MBSS), a new disease of maize, was discovered while surveying for maize leaf and sheath blight diseases in the Indian states of Assam, Jharkhand, Meghalaya, Manipur, and Odisha. Maize is the third most important cereal after rice and wheat in India. Unlike banded leaf and sheath blight disease caused by Rhizoctonia solani, MBSS symptoms on maize were discrete and limited to sheaths only. Symptoms of MBSS in the field were initially water-soaked necrotic lesions of 1 to 2 cm in diameter on the lowermost leaf sheaths, which then progressed to the upper sheaths. Lesions coalesced and covered approximately 2 to 5% of the sheath area. Infected dried lower leaves were shed, whereas infected upper leaves remained on the stem. The pathogen was isolated, characterized morphologically, pathologically, and molecularly, and identified as Waitea circinata var. prodigus, a basidiomycete known to cause basal leaf blight of seashore paspalum. The internal transcribed spacer (ITS) sequence 2 (ITS2) of rDNA from MBSS isolates formed a well supported clade with known W. circinata var. prodigus isolates. Molecular morphometric analysis of the ITS2 regions of the five known varieties of W. circinata detected distinguishing variations in GC content, compensatory base changes (CBCs), hemi- CBCs, indels, and altered base-pairing of helices. Variation in these characteristics may indicate that varieties are distinct biological species within W. circinata sensu lato. The geographical distribution and potential impacts of MBSS on the maize crop in India necessitate further investigations of pathogen identification and disease management.

Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage.

In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3′untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.

Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen

Nucleotide composition (GC content) varies across bacteria species, genome regions, and specific genes. In Xylella fastidiosa, a vector-borne fastidious plant pathogen infecting multiple crops, GC content ranges between ∼51-52%; however, these values were gathered using limited genomic data. We evaluated GC content variations across X. fastidiosa subspecies fastidiosa (N = 194), subsp. pauca (N = 107), and subsp. multiplex (N = 39). Genomes were classified based on plant host and geographic origin; individual genes within each genome were classified based on gene function, strand, length, ortholog group, core vs accessory, and recombinant vs non-recombinant. GC content was calculated for each gene within each evaluated genome. The effects of genome and gene-level variables were evaluated with a mixed effect ANOVA, and the marginal-GC content was calculated for each gene. Also, the correlation between gene-specific GC content vs natural selection (dN/dS) and recombination/mutation (r/m) was estimated. Our analyses show that intra-genomic changes in nucleotide composition in X. fastidiosa are small and influenced by multiple variables. Higher AT-richness is observed in genes involved in replication and translation, and genes in the leading strand. In addition, we observed a negative correlation between high-AT and dN/dS in subsp. pauca. The relationship between recombination and GC content varied between core and accessory genes. We hypothesize that distinct evolutionary forces and energetic constraints both drive and limit these small variations in nucleotide composition.

Correlation Analysis Reveals an Important Role of GC Content in Accumulation of Deletion Mutations in the Coding Region of Angiosperm Plastomes.

Variation in GC content is assumed to correlate with various processes, including mutation biases, recombination, and environmental parameters. To date, most genomic studies exploring the evolution of GC content have focused on nuclear genomes, but relatively few have concentrated on organelle genomes. We explored the mechanisms maintaining the GC content in angiosperm plastomes, with a particular focus on the hypothesis of phylogenetic dependence and the correlation with deletion mutations. We measured three genetic traits, namely, GC content, A/T tracts, and G/C tracts, in the coding region of plastid genomes for 1382 angiosperm species representing 350 families and 64 orders, and tested the phylogenetic signal. Then, we performed correlation analyses and revealed the variation in evolutionary rate of selected traits using RRphylo. The plastid GC content in the coding region varied from 28.10% to 43.20% across angiosperms, with a few non-photosynthetic species showing highly reduced values, highlighting the significance of functional constraints. We found strong phylogenetic signal in A/T tracts, but weak ones in GC content and G/C tracts, indicating adaptive potential. GC content was positively and negatively correlated with G/C and A/T tracts, respectively, suggesting a trade-off between these two deletion events. GC content evolved at various rates across the phylogeny, with significant increases in monocots and Lamiids, and a decrease in Fabids, implying the effects of some other factors. We hypothesize that variation in plastid GC content might be a mixed strategy of species to optimize fitness in fluctuating climates, partly through influencing the trade-off between AT → GC and GC → AT mutations.

A simple stochastic model describing genomic evolution over time of GC content in microbial symbionts

An organism’s genomic base composition is usually summarized by its AT or GC content due to Chargaff’s parity laws. Variation in prokaryotic GC content can be substantial between taxa but is generally small within microbial genomes. This variation has been found to correlate with both phylogeny and environmental factors. Since novel single-nucleotide polymorphisms (SNPs) within genomes are at least partially linked to the environment through natural selection, SNP GC content can be considered a compound measure of an organism’s environmental influences, lifestyle, phylogeny as well as other more or less random processes. While there are several models describing genomic GC content few, if any, consider AT/GC mutation rates subjected to random perturbations. We present a mathematical model that describes how GC content in microbial genomes evolves over time as a function of the AT → GC and GC → AT mutation rates with Gaussian white noise disturbances. The model, which is suited specifically to non-recombining vertically transmitted prokaryotic symbionts, suggests that small differences in the AT/GC mutation rates can lead to profound differences in outcome due to the ensuing stochastic process. In other words, the model indicates that time to extinction could be a consequence of the mutation rate trajectory on which the symbiont embarked early on in its evolutionary history.

M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data

Large-scale mining and analysis of bacterial datasets contribute to the comprehensive characterization of complex microbial dynamics within a microbiome and among different bacterial strains, e.g., during disease outbreaks. The study of large-scale bacterial evolutionary dynamics poses many challenges. These include data-mining steps, such as gene annotation, ortholog detection, sequence alignment, and phylogeny reconstruction. These steps require the use of multiple bioinformatics tools and ad-hoc programming scripts, making the entire process cumbersome, tedious and error-prone due to manual handling. This motivated us to develop the M1CR0B1AL1Z3R web server, a ‘one-stop shop’ for conducting microbial genomics data analyses via a simple graphical user interface (Avram, et al., Nucleic Acids Res., 2019). Some of the features implemented in M1CR0B1AL1Z3R are: (i) extracting putative open reading frames and comparative genomics analysis of gene content; (ii) extracting orthologous sets and analyzing their size distribution; (iii) analyzing gene presence-absence patterns; (iv) reconstructing a phylogenetic tree based on the extracted orthologous set; (v) inferring GC-content variation among lineages. M1CR0B1AL1Z3R facilitates the mining and analysis of dozens of bacterial genomes using advanced techniques, with the click of a button. M1CR0B1AL1Z3R is freely available at https://microbializer.tau.ac.il/ [https://microbializer.tau.ac.il/].

Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon.

Summary Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary.Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR‐RT) families in the 272‐Mb genome of the Mediterranean grass Brachypodium distachyon. We find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half‐life as low as 66 kyr, the latter are the most dynamic part of the genome and an important source of within‐species polymorphisms. Second, GC‐rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains > 20% of the genome‐wide variation in GC content and is associated with higher methylation levels.Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.

Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life-history traits and climatic conditions.

In angiosperms, genome size and nucleobase composition (GC content) exhibit pronounced variation with possible adaptive consequences. The hyperdiverse orchid family possessing the unique phenomenon of partial endoreplication (PE) provides a great opportunity to search for interactions of both genomic traits with the evolutionary history of the family. Using flow cytometry, we report values of both genomic traits and the type of endoreplication for 149 orchid species and compare these with a suite of life-history traits and climatic niche data using phylogeny-based statistics. The evolution of genomic traits was further studied using the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to access their adaptive potential. Pronounced variation in genome size (341-54878Mb), and especially in GC content (23.9-50.5%), was detected among orchids. Diversity in both genomic traits was closely related to the type of endoreplication, plant growth form and climatic conditions. GC content was also associated with the type of dormancy. In all tested scenarios, OU models always outperformed BM models. Unparalleled GC content variation was discovered in orchids, setting new limits for plants. Our study indicates that diversity in both genome size and GC content has adaptive consequences and is tightly linked with evolutionary transitions to PE.

Extracting phylogenetic signal from phylogenomic data: Higher-level relationships of the nightbirds (Strisores)

A well-resolved phylogeny would facilitate study of adaptation to nocturnality in the avian superorder Strisores, a group that includes both nocturnal and diurnal lineages. Based on previous estimates, it could be hypothesized that there were multiple independent origins of nocturnality in this group. In order to refine the Strisores phylogeny, we generated genome-scale datasets of 2289–4243 ultraconserved elements for 23 taxa representing all major living lineages in the group. Among the considerations for using genome-scale, molecular sequence data in phylogenomic analyses are issues related to GC content, GC variance and their effects on model selection. In this study, we employed a variety of analytical techniques to empirically investigate those issues in our data, as well as biases and errors resulting from alignment trimming, taxon selection, matrix completeness and evolutionary rate variation among sites and across lineages. Extensive analyses revealed conflict within the data, especially in regard to variation in GC content, that would not have been detected by more cursory study. Our results indicate that readily available models of molecular evolution are insufficient to encapsulate all phenomena present in genome-scale matrices, and that this problem may be at the root of many current issues in phylogenomic analysis. The analytical methods employed in this study are relevant to phylogenomic analysis of any large, heterogeneous matrix. In conclusion, we present a strongly supported estimate of the Strisores tree, and discuss visual adaptations for, and potential evolutionary pathways to, nocturnality in this clade.