Comparative Genomics Approach Research Articles

Feature architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii.

The Gram-negative bacterial pathogen Acinetobacter baumannii is a major cause of hospital-acquired opportunistic infections. The increasing spread of pan-drug resistant strains makes A. baumannii top-ranking among the ESKAPE pathogens for which novel routes of treatment are urgently needed. Comparative genomics approaches have successfully identified genetic changes coinciding with the emergence of pathogenicity in Acinetobacter. Genes that are prevalent both in pathogenic and a-pathogenic Acinetobacter species were not considered ignoring that virulence factors may emerge by the modification of evolutionarily old and widespread proteins. Here, we increased the resolution of comparative genomics analyses to also include lineage-specific changes in protein feature architectures. Using type IVa pili (T4aP) as an example, we show that three pilus components, among them the pilus tip adhesin ComC, vary in their Pfam domain annotation within the genus Acinetobacter. In most pathogenic Acinetobacter isolates, ComC displays a von Willebrand Factor type A domain harboring a finger-like protrusion, and we provide experimental evidence that this finger conveys virulence-related functions in A. baumannii. All three genes are part of an evolutionary cassette, which has been replaced at least twice during A. baumannii diversification. The resulting strain-specific differences in T4aP layout suggests differences in the way how individual strains interact with their host. Our study underpins the hypothesis that A. baumannii uses T4aP for host infection as it was shown previously for other pathogens. It also indicates that many more functional complexes may exist whose precise functions have been adjusted by modifying individual components on the domain level.

Genomic and Evolutionary Features of Nine AHPND Positive Vibrio parahaemolyticus Strains Isolated from South American Shrimp Farms.

Vibrio parahaemolyticus is a bacterial pathogen that becomes lethal to Penaeus shrimps when acquiring the pVA1-type plasmid carrying the PirABvp genes, causing acute hepatopancreatic necrosis disease (AHPND). This disease causes significant losses across the world, with outbreaks reported in Southeast Asia, Mexico, and South America. Virulence level and mortality differences have been reported in isolates from different locations, and whether this phenomenon is caused by plasmid-related elements or genomic-related elements from the bacteria remains unclear. Here, nine genomes of South American AHPND-causing V. parahaemolyticus (VPAHPND) isolates were assembled and analyzed using a comparative genomics approach at (i) whole-genome, (ii) secretion system, and (iii) plasmid level, and then included for a phylogenomic analysis with another 86 strains. Two main results were obtained from our analyses. First, all isolates contained pVA1-type plasmids harboring the toxin coding genes, and with high similarity with the prototypical sequence of Mexican-like origin, while phylogenomic analysis showed some level of heterogeneity with discrete clusters and wide diversity compared to other available genomes. Second, although a high genomic similarity was observed, variation in virulence genes and clusters was observed, which might be relevant in the expression of the disease. Overall, our results suggest that South American pathogenic isolates are derived from various genetic lineages which appear to have acquired the plasmid through horizontal gene transfer. Furthermore, pathogenicity seems to be a multifactorial trait where the degree of virulence could be altered by the presence or variations of several virulence factors. IMPORTANCE AHPND have caused losses of over $2.6 billion to the aquaculture industry around the world due to its high mortality rate in shrimp farming. The most common etiological agent is V. parahaemolyticus strains possessing the pVA1-type plasmid carrying the PirABvp toxin. Nevertheless, complete understanding of the role of genetic elements and their impact in the virulence of this pathogen remains unclear. In this work, we analyzed nine South American AHPND-causing V. parahaemolyticus isolates at a genomic level, and assessed their evolutionary relationship with other 86 strains. We found that all our isolates were highly similar and possessed the Mexican-type plasmid, but their genomic content did not cluster with other Mexican strains, but instead were spread across all isolates. These results suggest that South American VPAHPND have different genetic backgrounds, and probably proceed from diverse geographical locations, and acquire the pVA1-type plasmid via horizontal gene transfer at different times.

The novel anti-phage system Shield co-opts an RmuC domain to mediate phage defense across Pseudomonas species.

Competitive bacteria-bacteriophage interactions have resulted in the evolution of a plethora of bacterial defense systems preventing phage propagation. In recent years, computational and bioinformatic approaches have underpinned the discovery of numerous novel bacterial defense systems. Anti-phage systems are frequently encoded together in genomic loci termed defense islands. Here we report the identification and characterisation of a novel anti-phage system, that we have termed Shield, which forms part of the Pseudomonas defensive arsenal. The Shield system comprises the core component ShdA, a membrane-bound protein harboring an RmuC domain. Heterologous production of ShdA alone is sufficient to mediate bacterial immunity against several phages. We demonstrate that Shield and ShdA confer population-level immunity and that they can also decrease transformation efficiency. We further show that ShdA homologues can degrade DNA in vitro and, when expressed in a heterologous host, can alter the organisation of the host chromosomal DNA. Use of comparative genomic approaches identified how Shield can be divided into four subtypes, three of which contain additional components that in some cases can negatively affect the activity of ShdA and/or provide additional lines of phage defense. Collectively, our results identify a new player within the Pseudomonas bacterial immunity arsenal that displays a novel mechanism of protection, and reveals a role for RmuC domains in phage defense.

Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing.

Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulatory networks. We found that olfactory receptors were commonly loss and accumulated deleterious mutations, but no purge of deleterious mutations occurred during horse domestication. We examined the potential effects of SVs on the spatial structure of chromatin via topologically associating domains (TADs). Breed-specific TADs were significantly enriched by breed-specific SVs. We identified 4199 unique breakpoint-resolved novel insertions across all chromosomes that account for 2.84 Mb sequences missing from the reference genome. Several novel insertions might have potential functional consequences, as 519 appeared to reside within 449 gene bodies. These genes are primarily involved in pathogen recognition, innate immune responses and drug metabolism. Moreover, 37 diverse horses were resequenced. Combining this with public data, we analysed 97 horses through a comparative population genomics approach to identify the genetic basis underlying breed characteristics using Thoroughbreds as a case study. We provide new scientific evidence for horse domestication, an understanding of the genetic mechanism underlying the phenotypic evolution of horses, and a comprehensive genetic variation resource for further genetic studies of horses.

Comparative genomic assessment of members of genus Tenacibaculum: an exploratory study.

Tenacibaculosis is an ulcerative skin disorder that affects finfish. It is caused by members of the genus Tenacibaculum, resulting in eccentric behavioural changes, including anorexia, lethargy, and abnormal swimming patterns that often result in mortality. Currently, species suspected of causing fish mortality include T. ovolyticum, T. gallaicum, T. discolor, T. finnmarkense, T. mesophilum, T. soleae, T. dicentrarchi, and T. maritimum. However, pathogenic members and the mechanisms involved in disease causation, progression, and transmission are limited due to the inadequate sequencing efforts in the past decade. In this study, we use a comparative genomics approach to investigate the characteristic features of 26 publicly available genomes of Tenacibaculum and report our observations. We propose the reclassification of "T. litoreum HSC 22" to the singaporense species and assignment of "T. sp. 4G03" to the species discolor (species with quotation marks have not been appropriately named). We also report the co-occurrence of several antimicrobial resistance/virulence genes and genes private to a few members. Finally, we mine several non-B DNA forming regions, operons, tandem repeats, high-confidence putative effector proteins, and sortase that might play a pivotal role in bacterial evolution, transcription, and pathogenesis.

Comparative Genomic Analyses of Escherichia coli from a Meat Processing Environment in Relation to Their Biofilm Formation and Persistence.

We investigated the phylogeny of biofilm forming (BF) and nonbiofilm forming (NBF) Escherichia coli (n = 114) from a beef processing environment as well as genetic elements in their BF and persistence via a comparative genomic analysis. Phylogroup B1 made up the largest proportion of both the BF (73.8%) and NBF (50.9%) groups. E. coli from all of the sources that were examined had mixed phylogroups, except for those that were recovered from equipment after cleaning, which were exclusively from phylogroup B1. Both the core genome and gene content trees showed a tree-wide spread of BF strains, with clusters, including both BF and NBF strains. Genome-wide association studies (GWAS) via Scoary or Pyseer did not find any genes or mutations that were overrepresented in the BF group. A retrospective analysis of phenotypes found a significant correlation (P < 0.05) between BF ability and curli production, cellulose synthesis, and/or mobility. However, the BF group also included strains that were negative for curli and cellulose and/or missing encoding genes for the two traits. All curli and cellulose encoding genes were present in most genomes, regardless of their BF status. The degree of motility was correlated with both curli and cellulose production, and 80 common genes were overrepresented in all three of the trait-positive groups. A PTS enzyme II, a subsidiary gluconate catabolism pathway, and an iron-dicitrate transport system were more abundant in the persisting E. coli group. These findings suggest gene function redundancy in E. coli for biofilm formation as well as additional substrate utilization and iron acquisition in its persistence. IMPORTANCE The persistence of potentially hazardous bacteria is a major challenge for meat processing environments, which are conducive for biofilm formation. Marker genes/phenotypes are commonly used to differentiate biofilm forming E. coli strains from their nonbiofilm forming counterparts. We took a comparative genomic analysis approach to analyze E. coli strains that were from the same environment but were differentiated by their biofilm forming ability. A diversification of the genes involved in the biofilm formation of E. coli was observed. Even though there is a correlation on the population level between biofilm formation and the expression of curli and cellulose, uncertainties exist on the individual strain level. Novel substrate utilization and iron acquisition could contribute to the persistence of E. coli. These findings not only advance our understanding of the ecology of E. coli with respect to its persistence but also show that a marker gene/phenotype driven approach for the biofilm control of E. coli may not be prudent.

Northern Wild Rice (Zizania palustris L.) breeding, genetics, and conservation

AbstractCultivated Northern Wild Rice (NWR; Zizania palustris L.) is a high‐value, small commodity crop grown in irrigated paddies, primarily in Minnesota and California. Domestication of the species began ∼60 years ago as demand for the nutritional grain outpaced hand‐harvesting efforts from lakes and rivers in the Great Lakes region of the United States and Canada. Cultivated NWR cultivars are open‐pollinated and highly heterogeneous and have primarily been bred for seed retention, yield, and seed size. As a lowland crop, NWR's life cycle, particularly its unique seed physiology, poses challenges to breeding efforts, limiting selection cycles per year, and requiring annual grow‐outs of all germplasm. Recent efforts have increased the genomic resources available to NWR researchers, including a reference genome assembly and methodology optimization for genotyping‐by‐sequencing technologies. The species’ close phylogenetic relationship with white rice (Oryza sativa) also provides a unique opportunity to utilize comparative genomic approaches to identify genes conferring agronomic traits of interest in NWR, particularly domestication traits such as seed retention. Z. palustris is an enigmatic species with regional ecological, cultural, and agricultural significance in the Great Lakes. As NWR is grown in both the centers of origin and diversity, it is important for NWR plant breeders to be good stewards of our domesticated plants and include a diversity of stakeholders in our decision‐making processes. In this work, we have aimed to unpack some of the disputes regarding the breeding of cultivated NWR and the science behind our work. Additionally, we have discussed conservation efforts for natural stands of NWR which will help preserve the many ecosystem, nutritional, spiritual, and economic services provided by this important species.

A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event

BackgroundHorizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes.ResultsThrough a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces.ConclusionsThe presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.

Evolutionarily conserved mechanisms regulating hypoxia tolerance in Drosophila melanogaster

Hypoxia is one of the critical pathological elements in many human diseases, including ischemic stroke, myocardial infarction and solid tumors. Understanding the mechanisms regulating hypoxia tolerance or susceptibility is essential for developing effective strategies for medical therapy. In this regard, we generated hypoxia-tolerant Drosophila melanogaster populations through experimental hypoxia-directed evolution in the laboratory, sequenced and analyzed their genomes. In parallel, we took advantage of the natural evolution of humans at high-altitude regions and analyzed the whole genomes of Ethiopian and Andean highlanders. Through a comparative genomic approach, we obtained a group of evolutionarily conserved genes (28 human/23 Drosophila genes) that are potentially involved in regulating hypoxia tolerance in both human highlanders and the hypoxia-tolerant flies. We confirmed that ubiquitous knocking down of the conserved genes, such as grn/ GATA3, inv/ EN1, Mkk4/MAP2K4, Pxt/DUOX1/DUOX2, pyd/TJP1, RapGAP1/RAP1GAP2, Shal/KCN and shep/RBMS3 dramatically enhanced hypoxia tolerance in vivo in Drosophila melanogaster. In addition, we found that glial-specific knocking down of Egfr, grn, pyd and Shal rescued hypoxia-induced lethality. Furthermore, we found that some of these conserved genes (i.e., bnl, croc, Mkk4 and shep) are required by Notch activation-conferred survival in hypoxic environment, whereas Egfr, grn, pyd and Shal regulating hypoxia tolerance through Notch-independent mechanisms. We believe that these evolutionarily conserved mechanisms are novel targets that have a strong potential to be translated into therapeutic strategies to treat or prevent hypoxia-related diseases. This project is supported by NIH grant 1R21NS120023-01A1. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Small open reading frames: a comparative genetics approach to validation

Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the human genome, but the true number and the biological significance of the micropeptides they encode remain uncertain. Here, we used a comparative genomics approach to identify high-confidence smORFs that are likely protein-coding. We identified 3,326 high-confidence smORFs using constraint within human populations and evolutionary conservation as additional lines of evidence. Next, we validated that, as a group, our high-confidence smORFs are conserved at the amino-acid level rather than merely residing in highly conserved non-coding regions. Finally, we found that high-confidence smORFs are enriched among disease-associated variants from GWAS. Overall, our results highlight that smORF-encoded peptides likely have important functional roles in human disease.

Identification of conserved miRNAs and their targets in Jatropha curcas: an in silico approach

BackgroundMicroRNAs (miRNAs) are small endogenous RNAs with an approximate length of 18–22 nucleotides and involved in the regulation of gene expression in transcriptional or post-transcriptional levels. They were found to be associated with leaf morphogenesis, flowering time, vegetative phase change, and response to environmental cues in plants, where they act as a critical regulatory factor. The nature of high conservancy of plant miRNAs within the plant species made it possible to detect the conserved miRNAs by computational approaches. Expressed Sequence Tags (EST) based comparative genomic approaches provide advantages over wet lab approaches as it is convenient, easy to carry out and less time consuming. EST-based in silico approach can unravel new conserved miRNAs in plants, even when the complete genome sequence is not available. ResultsTo identify the novel miRNAs, a total of 46,865 ESTs from Jatropha curcas were searched for homology to all available 6746 mature miRNAs of plant eudicotyledons. Finally, we ended up with 12 novel miRNAs in Jatropha that range from 18 to 19 nucleotides where their respective precursor miRNAs had 54.11–71.76% (A + U) content. The putative miRNAs belong to 12 individual miRNA family and most of them have higher (A + U) content ranging from 47.36 to 77.77% than their respective miRNA homologs. Many of the target genes by the newly identified miRNAs were associated with plant growth and development, stress response, defense and hormone signaling, and oil synthesis pathways. ConclusionThese findings have the potential to speed up miRNA identification and expand our understanding of miRNA functions in J. curcas.

Use of Arabidopsis thaliana as a model to understand specific carcinogenic events: Comparison of the molecular machinery associated with cancer-hallmarks in plants and humans

Model organisms are fundamental in cancer research given that they rise the possibility to characterize in a quantitative-objective fashion the organisms as a whole in ways that are infeasible in humans. From this perspective, model organisms with short generation times and established protocols for genetic manipulation allow the understanding of basic biology principles that might guide carcinogenic onset. The cancer-hallmarks (CHs) approach, a modular perspective for cancer understanding, stands that underlying the variability among different cancer types, critical events support the carcinogenic origin and progression. Thus, CHs as interconnected genetic circuitry, have a causal effect over cancer biogenesis and might represent a comparison scaffold among model organisms to identify and characterize evolutionarily conserved modules to understand cancer. Nevertheless, the identification of novel cancer regulators by comparative genomics approaches relies on selecting specific biological processes or related signaling cascades that limit the type of detected regulators, even more, holistic analysis from a systemic perspective is absent. Similarly, although the plant Arabidopsis thaliana has been used as a model organism to dissect specific disease-associated mechanisms, given the evolutionary distance between plants and humans, a general concern about the utility of using A. thaliana as a cancer model persists. In the present research, we take advantage of the CHs paradigm as a framework to establish a functional systemic comparison between plants and humans, that allowed the identification not only of specific novel key genetic regulators, but also, biological processes, metabolic systems, and genetic modules that might contribute to the neoplastic transformation. We propose five cancer-hallmarks that overlapped in conserved mechanisms and processes between Arabidopsis and human and thus, represent mechanisms which study can be prioritized in A. thaliana as an alternative model for cancer research. Additionally, derived from network analyses and machine learning strategies, a new set of potential candidate genes that might contribute to neoplastic transformation is described. These findings postulate A. thaliana as a suitable model to dissect, not all, but specific cancer properties, highlighting the importance of using alternative complementary models to understand carcinogenesis.

Comparative Analysis of the Alkaline Proteolytic Enzymes of Yarrowia Clade Species and Their Putative Applications

Proteolytic enzymes are commercially valuable and have multiple applications in various industrial sectors. The most studied proteolytic enzymes produced by Yarrowia lipolytica, extracellular alkaline protease (Aep) and extracellular acid protease (Axp), were shown to be good candidates for different biotechnological applications. In this study, we performed a comprehensive analysis of the alkaline proteolytic enzymes of Yarrowia clade species, including phylogenetic studies, synteny analysis, and protease production and application. Using a combination of comparative genomics approaches based on sequence similarity, synteny conservation, and phylogeny, we reconstructed the evolutionary scenario of the XPR2 gene for species of the Yarrowia clade. Furthermore, except for the proteolytic activity of the analyzed Yarrowia clade strains, the brewers' spent grain (BSG) was used as a substrate to obtain protein hydrolysates with antioxidant activity. For each culture, the degree of hydrolysis was calculated. The most efficient protein hydrolysis was observed in the cultures of Y. lipolytica, Y. galli, and Y. alimentaria. In contrast, the best results obtained using the 2,2-azinobis (3-ethyl-benzothiazoline-6-sulfonic acid (ABTS) method were observed for the culture medium after the growth of Y. divulgata, Y. galli, and Y. lipolytica on BSG.

Discovery of novel virulence mechanisms in Clostridium botulinum type A3 using genome-wide analysis

ObjectiveClostridium botulinum type A is a neurotoxin-producing, spore-forming anaerobic bacterium that causes botulism in humans. The evolutionary genomic context of this organism is not yet known to understand its molecular virulence mechanisms in the human intestinal tract. Hence, this study aimed to investigate the mechanisms underlying virulence and pathogenesis by comparing the genomic contexts across species, serotypes, and subtypes. MethodsA comparative genomic approach was used to analyze evolutionary genomic relationships, intergenomic distances, syntenic blocks, replication origins, and gene abundance with phylogenomic neighbors. ResultsType A strains have shown genomic proximity to group I strains with distinct accessory genes and vary even within subtypes. Phylogenomic data showed that type C and D strains were distantly related to a group I and group II strains. Synthetic plots indicated that orthologous genes might have evolved from Clostridial ancestry to subtype A3 strains, whereas syntonic out-paralogs might have emerged between subtypes A3 and A1 through α-events. Gene abundance analysis revealed the key roles of genes involved in biofilm formation, cell–cell communication, human diseases, and drug resistance compared to the pathogenic Clostridia. Moreover, we identified 43 unique genes in the type A3 genome, of which 29 were involved in the pathophysiological processes and other genes contributed to amino acid metabolism. The C. botulinum type A3 genome contains 14 new virulence proteins that can provide the ability to confer antibiotic resistance, virulence exertion and adherence to host cells, the host immune system, and mobility of extrachromosomal genetic elements. ConclusionThe results of our study provide insight into the understanding of new virulence mechanisms to discover new therapeutics for the treatment of human diseases caused by type A3 strains.

Genome-Wide Meta-Analysis of QTLs Associated with Root Traits and Implications for Maize Breeding.

Root system architecture (RSA), also known as root morphology, is critical in plant acquisition of soil resources, plant growth, and yield formation. Many QTLs associated with RSA or root traits in maize have been identified using several bi-parental populations, particularly in response to various environmental factors. In the present study, a meta-analysis of QTLs associated with root traits was performed in maize using 917 QTLs retrieved from 43 mapping studies published from 1998 to 2020. A total of 631 QTLs were projected onto a consensus map involving 19,714 markers, which led to the prediction of 68 meta-QTLs (MQTLs). Among these 68 MQTLs, 36 MQTLs were validated with the marker-trait associations available from previous genome-wide association studies for root traits. The use of comparative genomics approaches revealed several gene models conserved among the maize, sorghum, and rice genomes. Among the conserved genomic regions, the ortho-MQTL analysis uncovered 20 maize MQTLs syntenic to 27 rice MQTLs for root traits. Functional analysis of some high-confidence MQTL regions revealed 442 gene models, which were then subjected to in silico expression analysis, yielding 235 gene models with significant expression in various tissues. Furthermore, 16 known genes viz., DXS2, PHT, RTP1, TUA4, YUC3, YUC6, RTCS1, NSA1, EIN2, NHX1, CPPS4, BIGE1, RCP1, SKUS13, YUC5, and AW330564 associated with various root traits were present within or near the MQTL regions. These results could aid in QTL cloning and pyramiding in developing new maize varieties with specific root architecture for proper plant growth and development under optimum and abiotic stress conditions.

The identification of retro-DNAs in primate genomes as DNA transposons mobilizing via retrotransposition

Background: Mobile elements (MEs) constitute a major portion of the genome in primates and other higher eukaryotes, and they play important role in genome evolution and gene function. MEs can be divided into two fundamentally different classes: DNA transposons which transpose in the genome in a “cut-and-paste” style, and retrotransposons which propagate in a “copy-and-paste” fashion via a process involving transcription and reverse-transcription. In primate genomes, DNA transposons are mostly dead, while many retrotransposons are still highly active. We report here the identification of a new type of MEs, which we call “retro-DNAs”, for their combined characteristics of these two fundamentally different ME classes. Methods: A comparative computational genomic approach was used to analyze the reference genome sequences of 10 primate species consisting of five apes, four monkeys, and marmoset. Results: From our analysis, we identified a total of 1,750 retro-DNAs, representing 748 unique insertion events in the genomes of ten primate species including human. These retro-DNAs contain sequences of DNA transposons but lack the terminal inverted repeats (TIRs), the hallmark of DNA transposons. Instead, they show characteristics of retrotransposons, such as polyA tails, longer target-site duplications (TSDs), and the “TT/AAAA” insertion site motif, suggesting the use of the L1-based target-primed reverse transcription (TPRT) mechanism. At least 40% of these retro-DNAs locate into genic regions, presenting potentials for impacting gene function. More interestingly, some retro-DNAs, as well as their parent sites, show certain levels of expression, suggesting that they have the potential to create more retro-DNA copies in the present primate genomes. Conclusions: Although small in number, the identification of these retro-DNAs reveals a new mechanism for propagating DNA transposons in primate genomes without active canonical DNA transposon activity. Our data also suggest that the TPRT machinery may transpose a wider variety of DNA sequences in the genomes.

Robust 3D modeling reveals spatiosyntenic properties of animal genomes.

Animal genomes are organized into chromosomes that are remarkably conserved in their gene content, forming distinct evolutionary units (synteny). Using versatile chromosomal modeling, we infer three-dimensional topology of genomes from representative clades spanning the earliest animal diversification. We apply a partitioning approach using interaction spheres to compensate for varying quality of topological data. Using comparative genomics approaches, we test whether syntenic signal at gene pair, local, and whole chromosomal scale is reflected in the reconstructed spatial organization. We identify evolutionarily conserved three-dimensional networks at all syntenic scales revealing novel evolutionarily maintained interactors associated with known conserved local gene linkages (such as hox). We thus present evidence for evolutionary constraints that are associated with three-, rather than just two-, dimensional animal genome organization, which we term spatiosynteny. As more accurate topological data become available, together with validation approaches, spatiosynteny may become relevant in understanding the functionality behind the observed conservation of animal chromosomes.

Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches.

Bifidobacteria are extensively exploited for the formulation of probiotic food supplements due to their claimed ability to exert health-beneficial effects upon their host. However, most commercialized probiotics are tested and selected for their safety features rather than for their effective abilities to interact with the host and/or other intestinal microbial players. In this study, we applied an ecological and phylogenomic-driven selection to identify novel B. longum subsp. longum strains with a presumed high fitness in the human gut. Such analyses allowed the identification of a prototype microorganism to investigate the genetic traits encompassed by the autochthonous bifidobacterial human gut communities. B. longum subsp. longum PRL2022 was selected due to its close genomic relationship with the calculated model representative of the adult human-gut associated B. longum subsp. longum taxon. The interactomic features of PRL2022 with the human host as well as with key representative intestinal microbial members were assayed using in vitro models, revealing how this bifidobacterial gut strain is able to establish extensive cross-talk with both the host and other microbial residents of the human intestine.

Pyridoxal 5'-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes.

Pyridoxal 5’-phosphate or PLP is a cofactor derived from B6 vitamers and essential for growth in all known organisms. PLP synthesis and salvage pathways are well characterized in a few model species even though key components, such as the vitamin B6 transporters, are still to be identified in many organisms including the model bacteria Escherichia coli or Bacillus subtilis . Using a comparative genomic approach, PLP synthesis and salvage pathways were predicted in 5840 bacterial and archaeal species with complete genomes. The distribution of the two known de novo biosynthesis pathways and previously identified cases of non-orthologous displacements were surveyed in the process. This analysis revealed that several PLP de novo pathway genes remain to be identified in many organisms, either because sequence similarity alone cannot be used to discriminate among several homologous candidates or due to non-orthologous displacements. Candidates for some of these pathway holes were identified using published TnSeq data, but many remain. We find that ~10 % of the analysed organisms rely on salvage but further analyses will be required to identify potential transporters. This work is a starting point to model the exchanges of B6 vitamers in communities, predict the sensitivity of a given organism to drugs targeting PLP synthesis enzymes, and identify numerous gaps in knowledge that will need to be tackled in the years to come.

Isolation and characterization of full-length coding sequences of gibberellic acid biosynthetic genes in coconut (Cocos nucifera L.) and their expression analysis

Gibberellic acid (GA) is intricately associated with plant growth and developmental pathways. To elucidate GA metabolism in coconut, we cloned full-length coding regions of the seven GA biosynthetic pathway genes (CPS, KS, KO, KAO, GA20ox, GA3ox and GA2ox) using a comparative genomics approach, using sequences from oil palm and date palm. The predicted amino acid sequences of the seven coconut GA biosynthetic genes shared high identities with oil palm and date palm GA biosynthetic genes. In silico structural and functional analyses were performed, and secondary and tertiary structures were predicted. Compared to the other two palms, the evolutionary analysis of the seven genes in coconut revealed that these genes may not be evolving rapidly enough to keep pace with occurring mutations. Additionally, we performed expression profiling of these seven genes during germination of mature zygotic embryos under in vitro conditions in two phenotypically contrasting coconut accessions (West Coast Tall and Chowghat Green Dwarf) and in response to exogenously supplemented GA3 and paclobutrazol (PBZ) in the embryo culture medium. While PBZ had an antagonistic effect on the GA biosynthesis pathway, GA3 enhanced the overall GA production. These results provide the first insights into GA biosynthesis in coconut, laying the foundation for future studies to decipher the genetics of dwarfism in coconut.