GeNeo: A Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction.

High-throughput DNA and RNA sequencing are revolutionizing precision oncology, enabling personalized therapies such as cancer vaccines designed to target tumor-specific neoepitopes generated by somatic mutations expressed in cancer cells. Identification of these neoepitopes from next-generation sequencing data of clinical samples remains challenging and requires the use of complex bioinformatics pipelines. In this paper, we present GeNeo, a bioinformatics toolbox for genomics-guided neoepitope prediction. GeNeo includes a comprehensive set of tools for somatic variant calling and filtering, variant validation, and neoepitope prediction and filtering. For ease of use, GeNeo tools can be accessed via web-based interfaces deployed on a Galaxy portal publicly accessible at https://neo.engr.uconn.edu/. A virtual machine image for running GeNeo locally is also available to academic users upon request.

Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest.

The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.

Microsatellite Variation in the Most Devastating Beetle Pests (Coleoptera: Curculionidae) of Agricultural and Forest Crops.

Weevils, classified in the family Curculionidae (true weevils), constitute a group of phytophagous insects of which many species are considered significant pests of crops. Within this family, the red palm weevil (RPW), Rhynchophorus ferrugineus, has an integral role in destroying crops and has invaded all countries of the Middle East and many in North Africa, Southern Europe, Southeast Asia, Oceania, and the Caribbean Islands. Simple sequence repeats (SSRs), also termed microsatellites, have become the DNA marker technology most applied to study population structure, evolution, and genetic diversity. Although these markers have been widely examined in many mammalian and plant species, and draft genome assemblies are available for many species of true weevils, very little is yet known about SSRs in weevil genomes. Here we carried out a comparative analysis examining and comparing the relative abundance, relative density, and GC content of SSRs in previously sequenced draft genomes of nine true weevils, with an emphasis on R. ferrugineus. We also used Illumina paired-end sequencing to generate draft sequence for adult female RPW and characterized it in terms of perfect SSRs with 1-6 bp nucleotide motifs. Among weevil genomes, mono- to trinucleotide SSRs were the most frequent, and mono-, di-, and hexanucleotide SSRs exhibited the highest GC content. In these draft genomes, SSR number and genome size were significantly correlated. This work will aid our understanding of the genome architecture and evolution of Curculionidae weevils and facilitate exploring SSR molecular marker development in these species.

Mitogenome recovered from a 19 th Century holotype by shotgun sequencing supplies a generic name for an orphaned clade of African weakly electric fishes (Osteoglossomorpha, Mormyridae).

Heteromormyrus Steindachner, 1866, a genus of Mormyridae (Teleostei: Osteoglossomorpha), has been monotypic since the description of Heteromormyruspauciradiatus (Steindacher, 1866) from a single specimen. No type locality other than "Angola" was given and almost no specimens have been subsequently identified to this species. In order to investigate the relationship of this taxon to fresh specimens collected in Angola and elsewhere, whole genome paired-end sequencing of DNA extracted from the holotype specimen of Heteromormyruspauciradiatus was performed and a nearly complete mitogenome assembled from the sequences obtained. Comparison of cytochrome oxidase I and cytochrome b sequences from this mitogenome to sequences from recently collected material reveal that Heteromormyruspauciradiatus is closely related to specimens identified as Hippopotamyrusansorgii (Boulenger, 1905), Hippopotamyrusszaboi Kramer, van der Bank & Wink, 2004, Hippopotamyruslongilateralis Kramer & Swartz, 2010, as well as to several undescribed forms from subequatorial Africa collectively referred to in the literature as the "Hippopotamyrusansorgii species complex" and colloquially known as "slender stonebashers." Previous molecular phylogenetic work has shown that these species are not close relatives of Hippopotamyruscastor Pappenheim, 1906, the type species of genus Hippopotamyrus Pappenheim, 1906 from Cameroon, and are thus misclassified. Hippopotamyrusansorgii species complex taxa and another species shown to have been misclassified, Paramormyropstavernei (Poll, 1972), are placed in genus Heteromormyrus and one genetic lineage from the Kwanza and Lucala rivers of Angola are identified as conspecific Heteromormyruspauciradiatus. Three additional new combinations and a synonymy in Mormyridae are introduced. The morphological characteristics and geographical distribution of the genus Heteromormyrus are reviewed. The electric organ discharges (EODs) of Heteromormyrus species are to be treated in a separate study.

Genome-wide comparative analysis of transposable elements in Palmae genomes.

Background: Transposable elements (TEs) are the largest component of the genetic material of most eukaryotes and can play roles in shaping genome architecture and regulating phenotypic variation; thus, understanding genome evolution is only possible if we comprehend the contributions of TEs. However, the quantitative and qualitative contributions of TEs can vary, even between closely related lineages. For palm species, in particular, the dynamics of the process through which TEs have differently shaped their genomes remains poorly understood because of a lack of comparative studies. Materials and methods: We conducted a genome-wide comparative analysis of palm TEs, focusing on identifying and classifying TEs using the draft assemblies of four palm species: Phoenix dactylifera, Cocos nucifera, Calamus simplicifolius, and Elaeis oleifera. Our TE library was generated using both de novo structure-based and homology-based methodologies. Results: The generated libraries revealed the TE component of each assembly, which varied from 41-81%. Class I retrotransposons covered 36-75% of these species' draft genome sequences and primarily consisted of LTR retroelements, while non-LTR elements covered about 0.56-2.31% of each assembly, mainly as LINEs. The least represented were Class DNA transposons, comprising 1.87-3.37%. Conclusion: The current study contributes to a detailed identification and characterization of transposable elements in Palmae draft genome assemblies.

Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus.

BACKGROUND: Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. To date, details regarding the presence and characteristics of TEs in camelid genomes have not been made available. RESULTS: We conducted a genome-wide comparative analysis of camelid TEs, focusing on the identification of TEs and elucidation of transposition histories in four species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. Our TE library was created using both de novo structure-based and homology-based searching strategies ( https://github.com/kacst-bioinfo-lab/TE_ideintification_pipeline ). Annotation results indicated a similar proportion of each genomes comprising TEs (35-36%). Class I LTR retrotransposons comprised 16-20% of genomes, and mostly consisted of the endogenous retroviruses (ERVs) groups ERVL, ERVL-MaLR, ERV_classI, and ERV_classII. Non-LTR elements comprised about 12% of genomes and consisted of SINEs (MIRs) and the LINE superfamilies LINE1, LINE2, L3/CR1, and RTE clades. Least represented were the Class II DNA transposons (2%), consisting of hAT-Charlie, TcMar-Tigger, and Helitron elements and comprising about 1-2% of each genome. CONCLUSIONS: The findings of the present study revealed that the distribution of transposable elements across camelid genomes is approximately similar. This investigation presents a characterization of TE content in four camelid to contribute to developing a better understanding of camelid genome architecture and evolution.

On the Prevalence and Potential Functionality of an Intrinsic Disorder in the MERS-CoV Proteome.

Middle East respiratory syndrome is a severe respiratory illness caused by an infectious coronavirus. This virus is associated with a high mortality rate, but there is as of yet no effective vaccine or antibody available for human immunity/treatment. Drug design relies on understanding the 3D structures of viral proteins; however, arriving at such understanding is difficult for intrinsically disordered proteins, whose disorder-dependent functions are key to the virus's biology. Disorder is suggested to provide viral proteins with highly flexible structures and diverse functions that are utilized when invading host organisms and adjusting to new habitats. To date, the functional roles of intrinsically disordered proteins in the mechanisms of MERS-CoV pathogenesis, transmission, and treatment remain unclear. In this study, we performed structural analysis to evaluate the abundance of intrinsic disorder in the MERS-CoV proteome and in individual proteins derived from the MERS-CoV genome. Moreover, we detected disordered protein binding regions, namely, molecular recognition features and short linear motifs. Studying disordered proteins/regions in MERS-CoV could contribute to unlocking the complex riddles of viral infection, exploitation strategies, and drug development approaches in the near future by making it possible to target these important (yet challenging) unstructured regions.

Draft Genome Sequence of Lactobacillus rhamnosus NRRL B-442, a Potential Probiotic Strain.

Lactic acid bacteria are known to exhibit probiotic properties through various mechanisms, including competitive exclusion, pathogen inhibition, production of antimicrobial substances, and maintenance of eubiosis. Here, we present the draft genome sequence of a novel probiotic strain, Lactobacillus rhamnosus strain NRRL B-442, which exhibits potent antivirulence activity against Salmonella enterica.

Draft Genome Sequence of Lactobacillus paracasei DUP 13076, Which Exhibits Potent Antipathogenic Effects against Salmonella enterica Serovars Enteritidis, Typhimurium, and Heidelberg.

Lactobacillus paracasei DUP 13076 demonstrates antagonistic effects against the foodborne pathogens Salmonella enterica serovars Enteritidis, Typhimurium, and Heidelberg in coculture and in vitro experiments. Here, we report the draft genome sequence of Lactobacillus paracasei DUP 13076, which has a circular chromosome of 3,048,314 bp and a G+C content of 46.3%.