GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses

Whole-genome sequence of subcluster BE1 Streptomyces lividans bacteriophage Persimmon

Persimmon is a BE1 subcluster bacteriophage infecting Streptomyces lividans with siphoviral morphology and was isolated from a soil sample. The genome of Persimmon has a length of 131,421 bp, 231 protein-coding genes, and a 50.0% GC content that differs from the isolation host with high GC content.

Isolation and genomic characterization of Psychrobacillus isolate L3 and bacteriophage Spoks: a new phage-host pair from Antarctic soil

BACKGROUND

Most habitats on Earth house unfathomable microbial diversity, yet much of it remains uncultured. The same applies to temperate phages, most of which documented to date are predicted purely in silico from the prophage-like genomic regions of the bacteria, lacking any experimental evidence of their functional integrity (e.g., the ability to undergo lytic replication). Hard-to-access parts of our planet with unique environments serve as especially promising places to collect samples for the isolation of novel microbes highly divergent from those isolated thus far. Antarctica, a continent mostly covered by a thick ice sheet, is one such area of our planet rife with novel microbiological entities. In this study, we aimed to isolate and characterize a novel culturable phage-host pair from Antarctic soils.

RESULTS

Psychrobacillus phage Spoks was retrieved alongside its host bacterial strain designated as "L3" from an ice-free soil sample collected at Waddington Bay, Graham Coast, Antarctica. Whole-genome sequencing of both the phage and the host revealed that they are divergent from, respectively, viruses and bacteria cultured and characterized thus far, and the intergenomic differences suggest that both might represent novel taxa. The genome of siphophage Spoks is a 36,472 bp long linear double-stranded DNA molecule with 11 base long 3' cohesive overhangs. Spoks can integrate into the chromosome of its isolation host strain in a site-specific fashion. Integration takes place in the genomic region of the host chromosome between the ORFs predicted to encode a DNA topoisomerase III and a BlaI/MecI/CopY family transcriptional regulator via recombination between attP and attB, which share a 19 bp "core" overlap sequence. L3 lysogens containing Spoks are not stable, with regular spontaneous induction occurring. Although the attachment site overlap sequence was found in the publicly available genomic sequences of several other Psychrobacillus spp. strains isolated from different habitats, none were found to contain a Spoks-like prophage.

CONCLUSIONS

The isolation and characterization of Psychrobacillus temperate phage Spoks and its host strain L3 from Antarctica highlight the potential for discovering novel biological entities divergent from their closest cultured relatives with relative ease, given access to such difficult-to-access undersampled environments, and are expected to encourage similar studies.

Lytic bacteriophages of Gordonia rubripertincta from topsoil in Lubbock, Texas: FlyingTortilla and ScarletRaider

We isolated two environmental phages, as part of the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Sciences program, that infect Gordonia rubripertincta from topsoil in Lubbock, Texas. We report the complete genome sequences of lytic bacteriophages FlyingTortilla and ScarletRaider. Sequence similarity analysis reveals the viruses as a part of an unclassified order within the Caudoviricetes class.

Sequence analysis of two F1 mycobacteriophages, Deb65 and DocMcStuffins

Isolated from wetland soil, Deb65 and DocMcStuffins are bacteriophages with a siphoviral morphology that infect Mycobacterium smegmatis. Deb65 and DocMcStuffins encode 97 and 91 putative genes, 41 of which are shared. Based on gene content similarity to actinobacteriophages more broadly, both phages are assigned to subcluster F1.

Genome sequence of cluster A6 bacteriophage Lilbunny, isolated using Mycobacterium smegmatis mc2155

Bacteriophage Lilbunny is a siphovirus infecting Mycobacterium smegmatis strain mc2155. It was isolated from compost of rabbit fecal matter. The genome of Lilbunny belongs to the A6 subcluster and is 50,789 bp, containing 95 open reading frames, 52.6% of which encode proteins with predicted functions, and three tRNA genes.

Genome sequences of G. rubripertincta bacteriophages Eddiemania and UBSmoodge isolated in Las Vegas, Nevada

Eddiemania and UBSmoodge are bacteriophages isolated on Gordonia rubripertincta NRRL B-16540. Eddiemania has a 3' sticky overhang, a 61,427 bp genome predicted to encode 92 putative genes, and a siphovirus virion morphology. The UBSmoodge genome was identified as a circularly permuted, 92,786 bp long genome predicted to encode 130 putative genes and having a myovirus virion morphology.

Genome sequences of four A1 subcluster Mycobacterium smegmatis bacteriophages

Payneful, Marchy, Hami1, and Sorpresa are A1 subcluster tailed bacteriophages belonging to the Caudoviricetes class that infect Mycobacterium smegmatis strain mc2155. They are consistent with other A1 subcluster phages based on their genome length and guanine-cytosine content. Their genomes contain six novel open reading frames.

Genome sequence of cluster F1 Mycobacterium smegmatis phage Fastidio

Fastidio is an F1 subcluster bacteriophage in the Caudoviricetes class, infecting Mycobacterium smegmatis strain mc²155. The genome is 55,839 base pairs in length and contains several putative novel open reading frames. The isolation, annotation, and analysis of Fastidio, together with other bacteriophages, improve our knowledge of phage diversity.

Chromosome-level genome assembly and annotation of Anthurium amnicola

Anthurium amnicola is in the monocot family Araceae, subfamily Pothoideae and is a contributing species in Hawaii floriculture industry hybrids. To support future genetic improvements to this commodity, we sequenced and assembled the A. amnicola genome to chromosome-scale using PacBio HiFi and short-read Hi-C sequencing. A total of 98.51% of the 4.79 Gb genome is anchored into 15 chromosomes, with 99.2% gene completeness and a high LTR assembly index (LAI) score of 21.73, indicative of a complete, high-quality assembly. Annotation reveals the presence of 20,380 protein-coding genes, with 78.52% of the genome composed of repetitive sequences, predominantly long terminal repeat retrotransposons (LTR-RT). Phylogenetic analysis identified evolutionary relationships between A. amnicola and representative species in the Araceae and other plant families. This study provides the first reference genome sequence for the neotropical genus Anthurium and insights into Araceae evolution, benefiting the floriculture industry and evolutionary studies.

Synthetic Biology in Natural Product Biosynthesis

Synthetic biology has played an important role in the renaissance of natural products research during the post-genomics era. The development and integration of new tools have transformed the workflow of natural product discovery and engineering, generating multidisciplinary interest in the field. In this review, we summarize recent developments in natural product biosynthesis from three different aspects. First, advances in bioinformatics, experimental, and analytical tools to identify natural products associated with predicted biosynthetic gene clusters (BGCs) will be covered. This will be followed by an extensive review on the heterologous expression of natural products in bacterial, fungal and plant organisms. The native host-independent paradigm to natural product identification, pathway characterization, and enzyme discovery is where synthetic biology has played the most prominent role. Lastly, strategies to engineer biosynthetic pathways for structural diversification and complexity generation will be discussed, including recent advances in assembly-line megasynthase engineering, precursor-directed structural modification, and combinatorial biosynthesis.

Whole Genome Sequence of the gut commensal protist Tritrichomonas musculus isolated from laboratory mice

Tritrichomonas musculus is a commensal protist colonizing the large intestine of laboratory mice. Parasite colonization reshapes the gut microbiome and modulates mucosal immunity. This parasite is refractory to axenic culture. In order to facilitate functional genomic investigations we assembled a 193.49 Mbp high quality reference genome from FACS-purified parasites recovered from monocolonized mice using an integrated approach that combined long-read (PacBio and Oxford Nanopore) sequencing technologies for the draft genome assembly. The genome assembled into 756 contigs and RNA-Seq data was used to support the gene models for 46,131 annotated genes. Of these, 24,215 genes had an InterPro, Enzyme Commission and/or a Gene Ontology annotation. BUSCO analyses established that 53% of the genome annotations matched with available BUSCO genes in the eukaryote_odb10 database. This high quality reference genome will serve as a valuable resource to develop a metabolic and genetic model to grow T. musculus axenically and study genes relevant to its biology, life cycle transmission, and pathogenesis.

Genomic characteristics, virulence potential, antimicrobial resistance profiles, and phylogenetic insights into Nocardia cyriacigeorgica

BACKGROUND

Nocardia cyriacigeorgica, an opportunistic pathogen, is increasingly implicated in human infections. This pathogen predominantly causes pulmonary infections, leading to acute, subacute, or chronic necrotizing suppurative lesions, in severe cases, may progress to disseminated infections. Effective clinical diagnosis, prevention, and treatment strategies require a thorough understanding of its biological characteristics and pathogenic mechanisms. However, despite the rising incidence of nocardial diseases, research on the pathogenicity of N. cyriacigeorgica remains limited, primarily focusing on case reports and epidemiological studies. This study aimed to provide a comprehensive analysis of the genomic features, phylogenetic relationships, antimicrobial resistance profiles, and candidate virulence factors of N. cyriacigeorgica strains to inform future investigations into its pathogenesis.

METHODS

Whole-genome sequencing was conducted on five N. cyriacigeorgica strains isolated from patients with pulmonary infection at our hospital. This analysis utilized a combination of second-generation Illumina HiSeq and third-generation PacBio sequencing technologies. Additionally, publicly available genomic data from 58 strains in the National Center Biotechnology Information database were integrated, resulting in a dataset of 63 genomes. These genomes were subjected to comparative genomic analyses, including phylogenetic reconstruction, pan-genome evaluation, and gene distribution assessments.

RESULTS

Phylogenetic analysis identified five major clades within N. cyriacigeorgica. ANI analysis further subdivided clade B into five distinct subgroups. Pan-genome analysis revealed clade-specific orthogroups in the distribution of genes assigned to Clusters of Orthologous Groups, with clade A containing the highest number of clade-specific gene families. Comparative genomic analysis uncovered several potential pathogenic genes implicated in host cell invasion, phagosomal maturation arrest, and intracellular survival within macrophages, which were conserved across all analyzed strains. Notable differences in the distribution of enterobactin-encoding genes were observed among the clades. The mce3C gene also displayed variable distributions across clades; however, no correlation was established between its presence and strain source. Among the 63 strains, 27 were found to harbor both mce3C and mce4F genes, which were categorized into five distinct patterns. Furthermore, antibiotic resistance genes, including VanSO, VanRO, erm(O)-Irm, srmB, ermH, bcl, bla1, and cmIR, demonstrated clade-specific distribution patterns. Notably, the genes erm(O)-Irm, srmB, and ermH were associated with the isolation origin of the strains.

CONCLUSIONS

This study provides a comprehensive evaluation of the genomic characteristics, potential virulence factors, antimicrobial resistance genes, and phylogenetic relationships of N. cyriacigeorgica. The findings offer valuable insights into the mechanisms underlying intracellular survival, replication within macrophages, and pathogen-host interactions in N. cyriacigeorgica infections. These results establish a foundation for future research into the pathogenesis and clinical management of N. cyriacigeorgica.

The draft genome sequence of Diaporthe vaccinii, isolated from diseased cranberries

We report the assembly and annotation of the nuclear genome of Diaporthe vaccinii, a pathogenic fungus isolated from diseased cranberries in Quebec, Canada. The genome was sequenced with the Illumina paired-end sequencing technology, assembled into 67 Mbp across 588 contigs, with an N50 of 386 Kbp and 97.5% BUSCO completeness.

The comparative genomic analysis provides insight into the divergent inhibitory activity metabolites in pathogen-driven three Pseudomonas palleroniana strains against primary pathogens of Pseudostellaria heterophylla

Pseudostellaria heterophylla (Miq.) Pax ex Pax et Hoffm. is a member of the Caryophyllaceae family, in which dried tuberous root is the well-known traditional Chinese medicine (TCM) and a widespread food ingredient in Asia. In recent years, the large-scale cultivation of P. heterophylla has led to frequent infectious diseases caused by multiple pathogens. However, efficient and safe approaches for preventing and managing P. heterophylla diseases have become urgent for this high-quality industrial development. Herein, a culturable microbiome of diseased P. heterophylla rhizosphere soil was constructed, and the broad-spectrum antifungal activity of Pseudomonas was screened. Three P. palleroniana strains, B-BH16-1, B-JK4-1, and HP-YBB-1B, were isolated and identified with vigorous antifungal activity by confrontation method. We employed the PacBio RS II single-molecule real-time (SMRT) sequencing and Illumina sequencing methods to obtain the genome of these three isolates. Phylogenetic, synteny, and ANI analysis showed that the lineage between strain B-JK4-1 with B-BH16-1 or HY-YBB-1B was closer than that between strain B-BH16-1 with HP-YBB-1B. The comparative genome of strains B-BH16-1, B-JK4-1, and HP-YBB-1B showed marked differences in secondary metabolite biosynthesis genes among these three P. palleroniana strains. Strain B-BH16-1, B-JK4-1, and HP-YBB-1 produced tolaasin I/tolaasin F (23 genes), sessilin A (37 genes), and putisolvin (39 genes), respectively. CAZyme analysis showed that 126, 129, and 127 CAZymes were identified in strains B-BH16-1, B-JK4-1, and HP-YBB-1B genomes, which genes in auxiliary activities (AA), carbohydrate esterases (CE), and glycosyl transferases (GT) categories were different among these three strains. These results provide new insights into the divergent antifungal metabolites in pathogen-driven three P. palleroniana strains against primary pathogens of Pseudostellaria heterophylla.

Genome Sequence of Arthrobacter globiformis B-2979 Phage Raphaella

Bacteriophage Raphaella was isolated from a soil sample collected in Springfield, MO using Arthrobacter globiformis B2979-SEA . Raphaella has a genome of 51692 base pairs with a GC content of 62.6%, 96 putative protein encoding genes and one tRNA. It has been placed in the AY cluster of Actinobacteriophages based on gene content similarity.

Genome characteristics of cluster EA Microbacterium bacteriophages HungryHenry, CaptainRex, and ChikPic isolated from soil in Tennessee

Bacteriophages HungryHenry, CaptainRex, and ChikPic were isolated from soil collected in Tennessee using the bacterium Microbacterium foliorum . These bacteriophages have genomes that are 41,516 bp, 39,941 bp, and 40,333 bp in length and encode 62, 61, and 63 putative genes, respectively. Based on gene content similarity, all three bacteriophages are assigned to actinobacteriophage cluster EA (subclusters EA1, EA2 and EA5, respectively).

Genome Sequence of Gordonia rubripertincta Phage DoobyDoo of the DV Cluster

Novel bacteriophage DoobyDoo was isolated and characterized utilizing host Gordonia rubripertincta NRRL B-16540. DoobyDoo has a siphoviral morphology and a 66,343 bp genome with a GC content of 58.3%. The genome contains 97 protein coding genes, including an esterase gene that is distributed broadly across actinobacteriophages.

Genome Sequence of Arthrobacter Phage Sourignavong

We report the genome sequence of phage Sourignavong isolated from soil in Oklahoma City, Oklahoma using Arthrobacter sp. ATCC 21022. The 15,625 bp genome contains 27 predicted protein coding genes, including two predicted endolysin enzyme genes. Sourignavong is assigned to actinobacteriophage cluster AN.

Genome Sequences of Cluster E Mycobacteriophages Xandras and BigBubba

Bacteriophages Xandras and BigBubba were isolated on Mycobacterium smegmatis mc 2 155 from enriched soil samples. Xandras' genome length is 75,179 bp with 144 predicted protein-coding genes and two tRNAs. BigBubba's genome length is 75,006 bp with 147 predicted protein-coding genes and two tRNAs. Each genome contains a cyclic oligonucleotide sequestering protein (CBASS antagonist).

Development of a lytic Ralstonia phage cocktail and evaluation of its control efficacy against tobacco bacterial wilt

Introduction

Bacterial wilt (BW) caused by Ralstonia pseudosolanacearum is a devastating soil-borne disease. Bacteriophages are important biocontrol resources that rapidly and specifically lyse host bacteria, showing good application potential in agricultural production.

Methods

This study isolated nine phages (YL1-YL9) and, using host range and pot experiments, identified two broader host range phages (YL1 and YL4) and two higher control efficacy phages (YL2 and YL3), which were combined to obtain five cocktails (BPC-1-BPC-5).

Results

Pot experiments showed that BPC-1 (YL3 and YL4) had the highest control efficacy (99.25%). Biological characterization revealed that these four phages had substantial thermal stability and pH tolerance. Whole genome sequencing and analysis showed that YL1, YL2, YL3, and YL4 belonged to the genus Gervaisevirus. AlphaFold 3 predictions of tail fiber protein II structures showed that YL1 differed significantly from the other phages. Amino acid sequence alignment revealed that the ORF66 (YL1) "tip domain" of contained a higher proportion of aromatic and positively charged amino acids. However, the surface of the ORF69 (YL4) "tip domain" exhibited more positively charged residues than ORF66 (YL2) and ORF70 (YL3). These characteristics are hypothesized to confer a broader host range to YL1 and YL4.

Discussion

This study demonstrates that phages assembling a broad host range and high control efficacy have better biocontrol potential, providing high-quality resources for the biological control of BW.

Chromosome-level genome assembly of the clam, Xishi tongue Coelomactra antiquata

Xishi tongue (Coelomactra antiquata), a commercially valuable marine bivalve, is distributed along the coastal waters of East Asia. In China, significant morphological and genetic differences have been observed between northern and southern populations. Overfishing and pollution have caused a severe decline in its natural populations, rendering the species endangered. In this study, we constructed the first chromosome-level genome of C. antiquata based on PacBio HiFi and Hi-C sequencing data. The assembled genome was 791.83 Mb in size, with the scaffold N50 of 44.05 Mb, and 99.79% of the sequences (790.13 Mb) were anchored to 19 chromosomes. A total of 24,592 protein-coding genes were predicted in the final assembly, of which 89.88% were functionally annotated. The BUSCO analysis revealed a genome completeness of 97.69%. The high-quality genome serves as a critical resource for advancing research on population genetics and germplasm conservation of this commercial shellfish, thereby facilitating sustainable management and conservation efforts.

Complete genome sequences of AZ Arthrobacter phages Wildwest and Sue2

This announcement reports the complete genome sequences of two bacteriophages isolated from soil samples using the host Arthrobacter atrocyaneus Strain NRRL B-2883. These findings enhance our understanding of AZ1 cluster phages, particularly Wildwest and Sue2, with their unique genomic features.

Genome sequence of bacteriophage PensacolaC28 isolated using Microbacterium sp. Casco Bay

Bacteriophage PensacolaC28 is a lytic phage isolated on Microbacterium sp. Casco Bay (NCMA B81), a marine bacterium originally cultured in South Portland, Maine, USA. PensacolaC28 was isolated from an environmental sample collected in Pensacola, Florida, USA. It is a singleton siphovirus with a 16,749 bp genome and contains 24 protein coding genes.

Complete genome sequence of fig leaf mottle-associated virus 2

The complete genome sequence of fig leaf mottle-associated virus 2 (FLMaV2), a positive-sense single-stranded RNA virus with a genome length of 16,925 nucleotides, was determined via RT-PCR and rapid amplification of cDNA ends (RACE). Its genome organization resembles those of little cherry virus 2 (LChV2) and yam asymptomatic virus 1 (YaV1), both of which are currently classified as members of the genus Ampelovirus but differ from typical ampeloviruses. Phylogenetic analysis based on amino acid sequences of the RNA-dependent RNA polymerase and coat protein of members of the family Closteroviridae showed that FLMaV2 clustered with LChV2 and YaV1. Because of their unusual genome organization, FLMaV2, LChV2, and YaV1 might represent a distinct genus within the family Closteroviridae.

Genome Sequences of the Arthrobacter globiformis Phage BillyTP (Cluster AY) and Gordonia rubripertincta Phage MAnor (Cluster CT)

Phages BillyTP (Cluster AY) and MAnor (Cluster CT) were isolated from soil using Arthrobacter globiformis B-2979 and Gordonia rubripertincta NRRL B-16540, respectively, as hosts. The genome of BillyTP is 53,003 base pairs (bp) and contains 96 putative genes, while the genome of MAnor is 48,333 bp encoding 73 putative genes. BillyTP and MAnor are assigned to actinobacteriophage clusters AY and CT, respectively, based on gene content similarity (GCS) of at least 35%.

Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium

Orchids constitute one of the most diverse families of angiosperms, yet their genome evolution and diversity remain unclear. Here we construct and analyse chromosome-scale de novo assembled genomes of 17 representative accessions spanning 12 sections in Dendrobium, one of the largest orchid genera. These accessions represent a broad spectrum of phenotypes, lineages and geographical distributions. We first construct haplotype-resolved genomes for a Dendrobium hybrid and uncover haplotypic variations and allelic imbalance in the heterozygous genome, demonstrating the significance of diverse ancestry. At Dendrobium genus-wide scale, we further elucidate phylogenetic relationships, evolutionary dynamics, entire gene repertoire, and the mechanisms of preserving ancient genetic variants and rapid recent genome evolution for habitat adaption. We also showcase distinctive evolutionary trajectories in MADS-box and PEBP families over 28 Ma. These results considerably contribute to unearthing the mystery of orchid origin, evolution and diversification, laying the foundation for efficient use of genetic diversity in breeding.

Novel drug targets for monkeypox: From viral to host proteins

Background

The ongoing threat of the monkeypox virus (MPXV) underscores the need for new antiviral treatments, yet drug targets and candidate therapies are limited.

Methods

Calculating the centrality, conservation, and immunogenicity of MPXV proteins in the network to identify viral drug targets. Constructing the MIP-human protein interaction network and identifying key human proteins as potential drug targets through network topology analysis.

Results

We constructed a comprehensive protein-protein interaction (PPI) network between MPXV and humans, using data from the P-HIPSTer database. This network included 113 viral proteins and 2 607 MPXV-interacting human proteins (MIPs). We identified three MPXV proteins (OPG054, OPG084, and OPG190) as key targets for antiviral drugs, as well as 95 critical MIPs (most interacting MIPs, MMIPs) within the MPXV-human PPI network. Further analysis revealed 31 MMIPs as potential targets for broad-spectrum antiviral agents, supported by their involvement in other viral interactions. Functional enrichment of MIPs indicated their roles in infection and immune-related pathways.

Conclusions

In total, we identified 112 drugs targeting MPXV proteins and 371 drugs targeting MMIPs, with fostamatinib, trilostane, and raloxifene being able to inhibit both viral and host proteins. This work provides critical insights into MPXV-human interactions and supports the development of targeted antiviral therapies.

The Complete Genome Sequences of Bacteriophages ASegato, DejaVu, Judebell, and RicoCaldo isolated using Microbacterium foliorum

We report the discovery and characterization of bacteriophages ASegato, DejaVu, Judebell, and RicoCaldo, isolated from grass samples collected in Quincy, Massachusetts, using Microbacterium foliorum B-24224 as the isolation host. Based on gene content similarity, these phages are assigned to actinobacteriophage clusters ED2, ED1, EG, and EK2 respectively.

Genome Sequences of three CT cluster Bacteriophages isolated in Durham, North Carolina on Gordonia rubripertincta

PotPie, HippoPololi and BillDoor are bacteriophages with siphoviral morphologies that were isolated from soil in North Carolina using Gordonia rubripertincta . The three phages are all grouped in the CT cluster, with genomes of 48182 bp, 45423 bp, and 44875 bp, respectively, and are predicted to be lytic.

Complete genome sequence of bacteriophage Godfather isolated from Microbacterium foliorum

Microbacteriophage Godfather was collected from a soil sample in Stephenville, Texas. The 17,452-bp double-stranded genome contains 24 protein-coding genes. The genome shares >99% nucleotide sequence identity with cluster EE microbacteriophages Scamander, Danno, Kojax4, and Burgy.

Genome sequences of three temperate actinobacteriophages from clusters FA and AS

Three novel temperate siphoviruses, Juno112, KHumphrey, and ChuckDuck, were isolated from soil at Stevenson University using the bacterium Arthrobacter globiformis B-2979. Based on gene content similarity, Juno112 and KHumphrey are assigned to actinobacteriophage cluster AS3 and ChuckDuck to cluster FA. All three phages encode tyrosine recombinases, with ChuckDuck encoding two.

Structural variation, selection, and diversification of the NPIP gene family from the human pangenome

The NPIP (nuclear pore interacting protein) gene family has expanded to high copy number in humans and African apes where it has been subject to an excess of amino acid replacement consistent with positive selection (1). Due to the limitations of short-read sequencing, NPIP human genetic diversity has been poorly understood. Using highly accurate assemblies generated from long-read sequencing as part of the human pangenome, we completely characterize 169 human haplotypes (4,665 NPIP paralogs and alleles). Of the 28 NPIP paralogs, just three (NPIPB2, B11, and B14) are fixed at a single copy, and only a single locus, B2, shows no structural variation. Four NPIP paralogs map to large segmental duplication blocks that mediate polymorphic inversions (355 kbp-1.6 Mbp) corresponding to microdeletions associated with developmental delay and autism. Haplotype-based tests of positive selection and selective sweeps identify two paralogs, B9 and B15, within the top percentile for both tests. Using full-length cDNA data from 101 tissue/cell types, we construct paralog-specific gene models and show that 56% (31/55 most abundant isoforms) have not been previously described in RefSeq. We define six distinct translation start sites and other protein structural features that distinguish paralogs, including a variable number tandem repeat that encodes a beta helix of variable size that emerged ~3.1 million years ago in human evolution. Among the 28 NPIP paralogs, we identify distinct tissue and developmental patterns of expression with only a few maintaining the ancestral testis-enriched expression. A subset of paralogs (NPIPA1, A5, A6-9, B3-5, and B12/B13) show increased brain expression. Our results suggest ongoing positive selection in the human population and rapid diversification of NPIP gene models.

Characteristics and biological mechanism of protein degradation by the black solider fly (Hermetia illucens L.) larvae gut strain Bacillus subtilis S4

The black solider fly larvae (BSFL) can efficiently convert nitrogen in organic waste into insect protein. Bacillus subtilis S4, an efficient protein-degrading bacterium from the BSFL gut, was isolated and identified to explore the mechanism of nutrient metabolism underlying BSFL nitrogen utilization. Results showed that B. subtilis S4 could effectively increase larval biomass in a bean stem bioconversion system. In vitro high-performance liquid chromatography analysis showed that B. subtilis S4 completely degraded casein into Val, Ile, Phe, Leu, Tyr, Lys, Gly, and Met. Various protease genes with secretion expression ability were annotated in B. subtilis S4. They included peptidoglycan DL - endopeptidase, aminopeptidase, extracellular metalloprotease, peptidoglycan endopeptidase, and peptidase M15. Therefore, the BSFL intestinal microbe B. subtilis S4 could effectively degrade protein and promote larval biomass accumulation, which could provide novel insights into the combined conversion of organic waste into proteins by microbes and insects.

Structural polymorphism and diversity of human segmental duplications

Segmental duplications (SDs) contribute significantly to human disease, evolution and diversity but have been difficult to resolve at the sequence level. We present a population genetics survey of SDs by analyzing 170 human genome assemblies (from 85 samples representing 38 Africans and 47 non-Africans) in which the majority of autosomal SDs are fully resolved using long-read sequence assembly. Excluding the acrocentric short arms and sex chromosomes, we identify 173.2 Mb of duplicated sequence (47.4 Mb not present in the telomere-to-telomere reference) distinguishing fixed from structurally polymorphic events. We find that intrachromosomal SDs are among the most variable, with rare events mapping near their progenitor sequences. African genomes harbor significantly more intrachromosomal SDs and are more likely to have recently duplicated gene families with higher copy numbers than non-African samples. Comparison to a resource of 563 million full-length isoform sequencing reads identifies 201 novel, potentially protein-coding genes corresponding to these copy number polymorphic SDs.

Lacrimispora sinapis sp. nov., isolated from pickled potherb mustard (Brassica juncea Coss.)

Strain JR3T was isolated from Chinese pickled potherb mustard (Brassica juncea Coss.) purchased from a local market in Shanghai, China. A polyphasic approach including 16S rRNA gene sequence analysis, average nucleotide identity (ANI) analysis, digital DNA-DNA hybridization (dDDH), determination of G+C content and various phenotypic analyses was employed to characterize strain JR3T. The bacterium was rod-shaped, Gram-stain-positive, terminal round endospore-forming and catalase-positive. The strain could grow at a wide range of temperatures (20-45 °C) and pH values (6.0-8.0). Optimal growth of strain JR3T occurred at 35-40 °C and a pH value of 7.0. The strain exhibited growth at salt (NaCl) concentrations of up to 3% (w/v). The G+C content of the genomic DNA was 44.0 mol%. The major fatty acids were C16 : 0, C19 : 0 c9, 10, summed feature 10 (C18 : 1 c11/t9/t6) and C18 : 1 c9. 16S rRNA gene sequencing revealed that strain JR3T represents a member of the genus Lacrimispora, and it has higher sequence similarity with Lacrimispora amygdalina BR-10T (=DSM 12857T) (98.72%), Lacrimispora saccharolyticum WM1T (98.29%) and Lacrimispora xylanolytica sy1 (98.22%). The dDDH value for strain JR3T and phylogenetically related species within the genus Lacrimispora ranged from 17.7% to 29.9%. The ANI of strain JR3T with its closely related taxa was far lower than the threshold (95%-96%) used for species differentiation. Results of phylogenetic, physiological and phenotypic characterization confirmed that strain JR3T represented a novel species within the genus Lacrimispora, for which the name Lacrimispora sinapis sp. nov. is proposed. The type strain is JR3T=CCTCC AB 2024044T=LMG 33655T.

Plant Growth-Promoting Effect and Complete Genomic Sequence Analysis of the Beneficial Rhizosphere Streptomyces sp. GD-4 Isolated from Leymus secalinus

Plant growth-promoting rhizobacteria (PGPR) are beneficial bacteria residing in the rhizosphere and are capable of enhancing plant growth through various mechanisms. Streptomyces sp. GD-4 is a plant growth-promoting bacterium isolated from the rhizosphere soil of Leymus secalinus. To further elucidate the molecular mechanisms underlying the beneficial effects of the strain on plant growth, we evaluated the growth-promoting effects of Streptomyces sp. GD-4 on forage grasses and conducted comprehensive genome mining and comparative genomic analysis of the strain. Strain GD-4 effectively colonized the rhizosphere of three forages and significantly promoted the growth of both plant roots and leaves. Genome sequence functional annotation of GD-4 revealed lots of genes associated with nitrogen, phosphorus, and sulfur metabolism. Additionally, genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, and phosphate solubilization were annotated. Whole-genome analysis revealed that GD-4 may possess molecular mechanisms involved in soil nutrient cycling in rhizosphere soil and plant growth promotion. The bacteria also possess genes associated with adaptability to abiotic stress conditions, further supporting the ability of Streptomyces sp. GD-4 to colonize nutrient-poor soils. These findings provide a foundation for further research into soil remediation technologies in plateau regions.

A high-quality chromosome-scale genome assembly of the Cherokee rose (Rosa laevigata)

Rosa laevigata is an excellent rose germplasm, highly resistant to aphid, and immune to both rose black spot and powdery mildew disease. It is also a well-known edible plant with a long history of medicinal use in China, having the effects of improving kidney function, inhibiting arteriosclerosis, and reducing inflammation. In this study, we assembled a high-quality chromosome-scale genome for R. laevigata by combining Illumina, PacBio, and Hi-C data, which has a length of approximately 494.2 Mb with a scaffold N50 of 68.6 Mb. A total of 493.2 Mb (99.8%) of the draft genome sequences were anchored on seven pseudochromosomes and two gapless pseudochromosomes were included in the final genome assembly. A total of 37,117 protein-coding genes were predicted, 34,047 of which were functionally annotated. Repeat annotation revealed 659,558 (285.6 Mb) repeat elements, accounting for 57.8% of the genome. The chromosome-scale genome provides valuable information to facilitate comparative genomic analysis of rose family and will accelerate genome-guided breeding and germplasm improvement of both R. laevigata itself and modern roses.

Ligilactobacillus agilis W70: a probiotic with capacity to enhance ammonia assimilation in the rumen

Ruminants excrete both undigested and excess consumed nitrogen (N) through feces and urine, which results in the waste of feed protein and environmental pollution. This study aims to screen bacteria to identify strains with potential to improve nitrogen utilization in the rumen. In a tube screening test, when 30 mmol/L ammonium sulfate was added as the only nitrogen source in liquid medium, among 115 bacterial strains belonging to Bacillus and lactic-acid bacteria, 10 strains with the highest growth (OD600nm level) in comparison to the other evaluated strains were identified, and of these, Ligilactobacillus agilis W70 and Limosilactobacillus fermentum M50, had the highest ammonia nitrogen utilizing capabilities of ammonium sulfate (32.09 and 40.64%, respectively). A subsequent in vitro fermentation experiment was conducted with the diet consisting of 0.5 g TMR, 50 mL buffer solution, and 25 mL fresh rumen fluid per serum bottle which was incubated at 39°C for 24 h. The experiment consisted of 3 treatments, CTL, L. agilis W70 (1 × 109 cfu/mL), and L. fermentum M50 (1 × 109 cfu/mL), each treatment had 6 replicates, repeated across 3 batches. The addition of L. agilis W70 decreased NH3N (p < 0.01), the ratio of acetate to propionate (A:P) (p < 0.01), and increased the yields of microbial protein (MCP) (p < 0.01) and enzymatic activities of glutamate dehydrogenase (GDH) (p < 0.05) and glutamine synthetase (GS) (p < 0.05). Further genome analysis revealed that the L. agilis W70 harbors the glutamate dehydrogenase and glutamine synthetase-encoding genes gdhA and glnA that play key roles in ammonia utilization. This study identified L. agilis W70 as a strain which exhibits high NH3N utilization capability and enhances ammonia assimilation in vitro. The strain was further characterized to elucidate this ammonia assimilation potential. Further studies will be conducted to develop strain L. agilis W70 as a new feed additive to improve the nitrogen utilization efficiency in ruminant animals.

Isolation and Annotation of Arthrobacter globiformis Phage AWGoat

AWGoat, a lytic bacteriophage that infects Arthrobacter globiformis, was isolated from a goat pen in Charlotte, NC. Its genome is 65,496 bp long, with a GC content of 67.1%. Based on gene content similarity, AWGoat is assigned to actinobacteriophage cluster AP. It encodes a putative toxin from a broadly distributed toxin/antitoxin pair and an unusually large minor tail protein.

Complete Genome Sequences of Mycobacterium smegmatis Phages Dove and Issimir

We announce the discovery of two mycobacteriophages isolated from soil in Rock Hill, South Carolina. Phage Dove has a genome sequence length of 108,976bp, a siphovirus morphology, and a predicted temperate lifecycle. Phage Issimir has a genome sequence length of 155,564bp, a myovirus morphology, and a predicted lytic lifecycle.

Complete Genome Sequences of Two Arthrobacter Phages, assigned to clusters AT and AZ

Two bacteriophages, BeatusComedenti and Cyan, were isolated using Arthrobacter sp. and Arthrobacter globiformis , respectively. BeatusComedenti and Cyan, which contain 100 and 70 putative genes, are assigned to actinobacteriophage clusters AT and AZ1, respectively.

Expanding the Diversity of Actinobacterial Tectiviridae: A Novel Genus from Microbacterium

Six novel Microbacterium phages belonging to the Tectiviridae family were isolated using Microbacterium testaceum as a host. Phages MuffinTheCat, Badulia, DesireeRose, Bee17, SCoupsA, and LuzDeMundo were purified from environmental samples by students participating in the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program at Alliance University, New York. The phages have linear dsDNA genomes 15,438-15,636 bp with 112-120 bp inverted terminal repeats. Transmission electron microscopy (TEM) imaging analysis revealed that the six novel phages have six-sided icosahedral double-layered capsids with an internal lipid membrane that occasionally forms protruding nanotubules. Annotation analysis determined that the novel Microbacterium phages all have 32-34 protein-coding genes and no tRNAs. Like other Tectiviridae, the phage genomes are arranged into two segments and include three highly conserved family genes that encode a DNA polymerase, double jelly-roll major capsid protein, and packaging ATPase. Although the novel bacteriophages have 91.6 to 97.5% nucleotide sequence similarity to each other, they are at most 58% similar to previously characterized Tectiviridae genera. Consequently, these novel Microbacterium phages expand the diversity of the Tectiviridae family, and we propose they form the sixth genus, Zetatectivirus.

Genome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement

The allotetraploid wild grass Aegilops ventricosa (2n = 4x = 28, genome DvDvNvNv) has been recognized as an important germplasm resource for wheat improvement owing to its ability to tolerate biotic stresses. In particular, the 2NvS segment from Ae. ventricosa, as a stable and effective resistance source, has contributed greatly to wheat improvement. The 2NvS/2AS translocation is a prevalent chromosomal translocation between common wheat and wild relatives, ranking just behind the 1B/1R translocation in importance for modern wheat breeding. Here, we assembled a high-quality chromosome-level reference genome of Ae. ventricosa RM271 with a total length of 8.67 Gb. Phylogenomic analyses revealed that the progenitor of the Dv subgenome of Ae. ventricosa is Ae. tauschii ssp. tauschii (genome DD); by contrast, the progenitor of the D subgenome of bread wheat (Triticum aestivum L.) is Ae. tauschii ssp. strangulata (genome DD). The oldest polyploidization time of Ae. ventricosa occurred ∼0.7 mya. The Dv subgenome of Ae. ventricosa is less conserved than the D subgenome of bread wheat. Construction of a graph-based pangenome of 2AS/6NvL (originally known as 2NvS) segments from Ae. ventricosa and other genomes in the Triticeae enabled us to identify candidate resistance genes sourced from Ae. ventricosa. We identified 12 nonredundant introgressed segments from the Dv and Nv subgenomes using a large winter wheat collection representing the full diversity of the European wheat genetic pool, and 29.40% of European wheat varieties inherit at least one of these segments. The high-quality RM271 reference genome will provide a basis for cloning key genes, including the Yr17-Lr37-Sr38-Cre5 resistance gene cluster in Ae. ventricosa, and facilitate the full use of elite wild genetic resources to accelerate wheat improvement.

Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs

Pseudomonas aeruginosa has increasing clinical relevance and commonly occupies the cystic fibrosis (CF) airways. Its ability to colonize and persist in diverse niches is attributed to its large accessory genome, where prophages represent a common feature and may contribute to its fitness and persistence. We focused on the CF airways niche and used 197 longitudinal isolates from 12 patients persistently infected by P. aeruginosa. We computationally predicted intact prophages for each longitudinal group and scored their long-term persistence. We then confirmed prophage inducibility and mapped their location in the host chromosome with lysate sequencing. Using comparative genomics, we evaluated prophage genomic diversity, long-term persistence, and level of genomic maintenance. Our findings support previous findings that most P. aeruginosa genomes harbour prophages some of which can self-induce, and that a common CF-treating antibiotic, ciprofloxacin, can induce prophages. Induced prophage genomes displayed high diversity and even genomic novelty. Finally, all induced prophages persisted long-term with their genomes avoiding gene loss and degradation over 4 years of host replication in the stressful CF airways niche. This and our detection of phage genes, which contribute to host competitiveness and adaptation, lends support to our hypothesis that the vast majority of prophages detected as intact and inducible in this study facilitated their host fitness and persistence.

Genome Sequence of Gordonia terrae Bacteriophage Wheezy

Bacteriophage Wheezy, a lytic phage with siphoviral morphology isolated using the host Gordonia terrae 3612, has a genome of 67,021 base pairs and is 65.9% GC. The genome sequence of Wheezy aligns most closely with subcluster CR2 phages Tracker and NatB6. Annotation of the full-length genome sequence of Phage Wheezy revealed 92 protein-coding genes and no tRNA genes.

Genome Sequence of Three Siphoviruses in the EE, GA and EA5 Actinobacteriophage Clusters: Biscayne, Bush and GreenIvy

Bacteriophages Biscayne, Bush and GreenIvy were isolated from soil samples in Miami, FL using Microbacterium foliorum NRRL B-24224 as host. Transmission electron microscopy shows siphoviral morphologies for all three phages. Based on gene content similarity to other actinobacteriophages, they are assigned to the EE, GA and EA5 clusters, respectively.

Genome sequence of WestPM, a phage infecting Microbacterium foliorum isolated from beach environmental samples

Bacteriophage WestPM is a siphoviral-like phage infecting Microbacterium foliorum isolated from environmental samples collected on Pensacola Beach, FL. The genome of this phage is 39,693 bp long and contains 59 predicted protein-coding genes and zero tRNA genes. Based on gene content similarity, WestPM is grouped in the actinobacteriophage EA11 subcluster.

Complete Genome Sequence of the Cluster DJ Actinobacteriophage, Petito, isolated on the host Gordonia rubripertinca

Gordonia phage Petito is a newly discovered siphovirus that infects Gordonia rubripertincta NRRL B-16540. The double-stranded DNA genome of this phage is 60,447 bp long with 93 predicted protein-coding genes and no tRNAs. Petito is a Cluster DJ phage.

A Proteogenomic Approach for the Identification of Virulence Factors in Leishmania Parasites

Identifying new genes involved in virulence and drug resistance may hold the key to a better understanding of parasitic diseases. The proteogenomic profiling of various Leishmania species, the causative agents of leishmaniasis, has identified several novel genes, N- and C-terminal extensions of proteins, and corrections of existing gene models. Various virulence factors (VFs) responsible for leishmaniasis have been previously annotated through a proteogenomic approach, including the C-terminal extension of heat shock protein 70 (HSP70). Furthermore, the diversity of VFs across Leishmania donovani, L. infantum, L. major, and L. mexicana was determined using phylogenetic analysis. Moreover, protein-protein interaction networks (PPINs) of VFs with HSPs aid in making significant biological interpretations. Overall, an integrated omics approach involving proteogenomics was used to identify and study the relationship among VFs with other interacting proteins, including HSPs. This chapter provides a step-by-step guide to the identification of new genes in Leishmania using a proteogenomic approach and their functional assignment using a bioinformatics-based approach.

Genome Sequence of the Mycobacterium smegmatis Bacteriophage Eugenia

We report the discovery and genome sequence of mycobacteriophage Eugenia, isolated from soil samples collected in Akron, OH. Eugenia is a double-stranded DNA virus with a genome size of 69,139 bp, featuring 104 predicted protein-encoding genes, with 32 of these genes assigned putative functions.