Genome Length Research Articles

Complete Genome Sequences of Mycobacterium smegmatis Phages MelsMeow, Yorick, Virgeve, and Mikro.

ABSTRACTMycobacterium phages Mikro, Yorick, Virgeve, and MelsMeow were isolated from soil in Rock Hill, South Carolina. Mikro is a myovirus with a comparatively large genome of 157,166 bp. The remainder are siphoviruses with genome lengths ranging from 59,227 bp to 68,563 bp. All phages were isolated on Mycobacterium smegmatis.

Comparative Plastome Analyses of Ephedra przewalskii and E. monosperma (Ephedraceae)

Ephedra species were erect, branching shrubs found in desert or arid regions worldwide as the source of ephedrine alkaloids. In this study, the complete chloroplast genome of Ephedra przewalskii and E. monosperma on the Qinghai-Tibet Plateau were sequenced, assembled, and annotated. Compared with the other four published Ephedra species, the chloroplast genomes of Ephedra species were highly conservative, with a quadripartite structure. The length of the chloroplast genome was 109,569 bp in E. przewalskii with 36.6% GC and 109,604 bp in E. monosperma with 36.6% GC. We detected 118 genes in both Ephedra species, including 73 PCGs, 37 tRNA genes, and eight rRNA genes. Among them, the ndh family genes were lost, which could be used to study the phylogeny and genetic diversity of the genus Ephedra, combined with multiple highly variable intergenic spacer (IGS) regions. Codon usage preference of Ephedra species was weak. The ratio of non-synonymous substitutions and synonymous substitutions was low, showing that the PCGs of Ephedra may be under the pressure of purifying selection. ML and BI analysis showed similar phylogenetic topologies. Ephedra species clustered together in a well-supported monophyletic clade. E. przewalskii and E. monosperma were not gathered in one clade, consistent with the classification system by Flora of China. This study reveals differences in the chloroplast genomes of Ephedra, providing valuable and abundant data for the phylogenetic analysis and species identification of Ephedra.

36 Exploring the Statistical Nature of Independent Chromosome Segments

Abstract Independent chromosome segments for a population with Ne effective population size and L genome length can be approximately defined as 4NeL non-overlapping haplotypes of L/2 length derived from any Ne animals. The number of independent chromosome segments (Me) can be approximated as 4NeL. The genetic selection with a genomic relationship matrix (GRM) using such haplotypes approaches that with a GRM using the SNP markers. The objective of this study was to investigate the statistical nature of independent chromosome segments. Data were simulated using QMSim and contained a population of ten non-overlapping generations, each including 2,000 animals with Ne equal to 20, and a polygenic trait with a heritability of 0.6. The last three generations were genotyped, and each genome contained ten 1 M long chromosomes, for a total genome length of 10 M and 50,000 SNP. Chromosome segments of each animal were organized in non-overlapping haplotypes by the SNP code using in-house software written in Fortran. The effects of the hypothetical independent chromosome segments were estimated using a model that included an overall mean plus the segment effects. To analyze the behavior around Me, the number of segments chosen to estimate segment effects varied around 4NeL. Accuracies were calculated for animals in the last generation by cor (TBV, Zsŝ), where Zs ŝ is a vector of breeding values based on segments and TBV is a vector of the true breeding values outputted by QMSim. Accuracies of segment effects were compared with the true accuracy, i.e., cor (TBV,GEBV). The maximum accuracy of segment effects was 0.84, and the true accuracy was 0.96. The results suggest that 4NeL segments contain most of the additive information in the population. However, the accuracy of GBLUP is greater than that of the chromosome segment effects, suggesting that arranging chromosome segments based solely on the statistical nature is not enough to account for all the genetic variation.

Comparative genomic analysis reveals the origin and global distribution of melon necrotic virus isolates

The melon necrotic spot virus (MNSV) is the family member of Tombusviridae and genus member of Gammacarmovirus. It can be widely found from almost everywhere across the globe, infecting host plants like rockmelon, cucumber, muskmelon and watermelon. In this study, we attempted to search for country-specific genome markers of MNSV via the comparison of several genome characteristics across isolates from different countries such as South Korea, China, India, Japan, Netherlands, Canada, Australia, Brazil, USA and Spain. As a result, we discovered that the whole genome length and GC content can be used to preliminarily distinguish South Korea, Japan and Australia MNSV isolates. Besides, single nucleotide polymorphism (SNP) markers and protein profiles (RNA-dependent RNA polymerase (RdRp) and coat protein (CP)) can further differentiate Japan and South Korea MNSV isolates and identify two Japan isolates that are postulated to have South Korea origin. The motif and phylogenetic analysis revealed the previously described divergent group from USA and Australia regions. Interestingly, the RdRp and CP protein models for all isolates are identical and this is a strong indication of the high MNSV functional conservation. In short, the information yielded from this study will in turn aid in future virulence-SNP association studies essential for cost-effective biological control of this virus via genetic engineering in order to reduce harvest loss.

Properties of a Novel Salmonella Phage L66 and Its Application Based on Electrochemical Sensor-Combined AuNPs to Detect Salmonella.

Salmonella is widespread in nature and poses a significant threat to human health and safety. Phage is considered as a new tool for the control of food-borne pathogens. In this study, Salmonella phage L66 (phage L66) was isolated from sewage by using Salmonella Typhimurium ATCC 14028 as the host bacterium, and its basic properties were obtained by biological and bioinformatics analysis. Phage L66 had a broad host spectrum, with an optimal infection complex of 0.1 and an optimal adsorption rate of 90.06%. It also exhibited thermal stability between 30 °C~60 °C and pH stability pH from 3 to 12, and the average lysis amount was 46 PFU/cell. The genome sequence analysis showed that the genome length of phage L66 was 157,675 bp and the average GC content was 46.13%. It was predicted to contain 209 genes, 97 of which were annotated with known functions based on the evolutionary analysis, and phage L66 was attributed to the Kuttervirus genus. Subsequently, an electrochemical sensor using phage L66 as a recognition factor was developed and the working electrode GDE-AuNPs-MPA-Phage L66 was prepared by layer-by-layer assembly for the detection of Salmonella. The slope of the impedance was 0.9985 within the scope from 20 to 2 × 107 CFU/mL of bacterial concentration. The minimum detection limit of the method was 13 CFU/mL, and the average spiked recovery rate was 102.3% with a relative standard deviation of 5.16%. The specificity and stability of this sensor were excellent, and it can be applied for the rapid detection of Salmonella in various foods. It provides a phage-based electrochemical biosensor for the detection of pathogenic bacteria.

Comparative analysis of two genomes of Chlamydia pecorum isolates from an Alpine chamois and a water buffalo

BackgroundTo date, whole genome sequencing has been performed mainly for isolates of Chlamydia trachomatis, C. pneumoniae, C. psittaci and C. abortus, but only a few isolates of C. pecorum have been entirely sequenced and this makes it difficult to understand its diversity and population structure. In this study the genome of two C. pecorum strains isolated from the lung of an Alpine chamois affected with pneumonia (isolate PV7855) and the brain of a water buffalo affected with meningoencephalomyelitis (isolate PV6959), were completely sequenced with MiSeq system (Illumina) and analyzed in their most polymorphic regions.ResultsThe genome length and GC content of the two isolates were found to be consistent with other C. pecorum isolates and the gene content of polymorphic membrane proteins and plasticity zone was found to be very similar. Some differences were observed in the phospholipase genes for both isolates and in the number of genes in the plasticity zone, such as the presence of some hypothetical proteins in PV6959, not present in any other genomes analyzed in this study. Interestingly, PV6959 possesses an extra pmp and has an incomplete tryptophan biosynthesis operon. Plasmids were detected in both isolates.ConclusionsGenome sequencing of the two C. pecorum strains did not reveal differences in length and GC content despite the origin from different animal species with different clinical disease. In the plasticity zone, the differences in the genes pattern might be related to the onset of specific symptoms or infection of specific hosts. The absence of a tryptophan biosynthesis pathway in PV6959 may suggest a strict relationship between C. pecorum and its host.

The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi.

In this paper, we report on the scaffold-level assembled genome for the federally endangered, California endemic crustacean Lepidurus packardi (the Vernal Pool Tadpole Shrimp). L. packardi is a key food source for other conserved California species including the California Tiger Salamander Ambystoma californiense. It faces significant habitat loss and fragmentation as vernal pools are threatened by urbanization, agricultural conversion, and climate change. This resource represents the first scaffold-level genome of any Lepidurus species. The assembled genome spans 108.6 Mbps, with 6 chromosome-length scaffolds comprising 71% of total genomic length and 444 total contigs. The BUSCO score for this genome is 97.3%, suggesting a high level of completeness. We produced a predicted gene set for this species trained on the Daphnia magna set of genes and predicted 17,650 genes. These tools can aid researchers in understanding the evolution and adaptive potential of alternative reproductive modes within this species.

Isolation, identification, and pathogenicity of a goose astrovirus causing fatal gout in goslings

Since November 2016, severe infectious diseases characterized by gout and kidney swelling and caused by goose astrovirus (GoAstV) have affected goslings in major goose-producing areas in China. In 2021, a similar serious infectious disease broke out in commercial goose farms in Heilongjiang Province, China. In this study, strain HLJ2021 was successfully isolated from goose embryos. Electron microscopy showed that the viral particles are spherical, with a diameter of about 28 nm. The complete genomic length of strain HLJ2021 is 7210 nt, and it encodes three viral proteins. A phylogenetic analysis showed that strain HLJ2021 belongs to GoAstV-2 (G2). Compared with the two original GoAstV strains, amino acid site 540Q of the strain HLJ2021 spike domain has a mutation that affects the protein structure. One potential recombination event occurred between strains HLJ2021 and AstV/HB01/Goose/0123/19, which led to the generation of recombinant strain AstV/HN03/Goose/0402/19. Strain HLJ2021 also showed strong pathogenicity in goslings. Goslings infected with GoAstV began to die at 48 h post-infection (hpi), with a mortality rate of 83.3% at 240 hpi. At autopsy, visceral urate deposits, severe renal hemorrhage and swelling, and urate in the ureter were observed in the dead goslings. These findings extend our understanding of the evolution of GoAstV, which causes gout. The isolated GoAstV strain HLJ2021 provides a potential resource for the development of biological products for the prevention of goose gout.

Whole-genome assembly and analysis of a medicinal fungus: Inonotus hispidus.

Inonotus hispidus (I. hispidus) is a medicinal macrofungus that plays a key role in anti-tumor and antioxidant functions. To further understand and enhance the value of I. hispidus, we performed whole-genome sequencing and an analysis of its strain for the first time. I. hispidus was sequenced using the Illumina NovaSeq high-throughput sequencing platform. The genome length was 35,688,031 bp and 30 contigs, with an average length of 1,189,601.03 bp. Moreover, database alignment annotated 402 CAZyme genes and 93 functional genes involved in regulating secondary metabolites in the I. hispidus genome to find the greatest number of genes involved in terpenes in that genome, thus providing a theoretical basis for its medicinal value. Finally, the phylogenetic analysis and comparative genomic analysis of single-copy orthologous protein genes from other fungi in the same family were conducted; it was found that I. hispidus and Sanghuangporus baumii have high homology. Our results can be used to screen candidate genes for the nutritional utilization of I. hispidus and the development of high-yielding and high-quality I. hispidus via genetic means.

Characterization of the complete chloroplast genome sequence of Isodon japonicus (N. Burman) H. Hara (Lamiaceae)

Isodon japonicus (N. Burman) H. Hara (family: Lamiaceae), is a traditional herbal plant from Henan Province, China. In this study, we sequenced the complete chloroplast genome of I. japonicus sampled from the Funiu Mountains, Henan Province, China. The total length of the chloroplast genome is 152,298 bp, and has a typical quadripartite structure, including a large single-copy region (LSC) of 83,184 bp, a small single-copy region (SSC) of 17,806 bp and a pair of inverted repeats of 25,654 bp. The chloroplast genome of I. japonicus consists of 133 genes, including 88 protein-coding genes, eight rRNA genes, and 37 tRNA genes. There are 34 tandem repeats and 50 simple sequence repeats (SSRs) in the chloroplast genome. The total guanine-cytosine (GC) content of the whole chloroplast genome is 37.6%. Phylogenetic analysis indicated that I. japonicus forms a clade with six other Isodon species and is closely associated with I. rubescens.

The complete mitochondrial genome of Agriotes fuscicollis Miwa, 1928 (Coleoptera: Elateridae)

In this study, we sequenced the complete mitochondrial genome of Agriotes fuscicollis Miwa, 1928 (Coleoptera: Elateridae). The results showed that the length of complete mitochondrial genome was 15,866 bp with 26.8% GC content, containing 39.6% A, 33.5% T, 16.8% C, 10% G. There were 13 protein-coding genes (PCGs), 22 transfer RNA genes, and 2 ribosomal RNA genes. Phylogenetic analysis showed that A. fuscicollis was closely related to Cryptalaus larvatus, Cryptalaus yamato, Pyrophorus divergens and Ignelater luminosus. The complete mitogenome of A. fuscicollis would contribute to the study of the phylogeny and evolution of Elateridae.

Complete chloroplast genome sequence of Thalictrum viscosum W.T.Wang & S.H.Wang, 1979 (Ranunculaceae)

Thalictrum viscosum W.T.Wang & S.H.Wang, 1979 is a flowering plant species in family Ranunculaceae that is endemic to Yunnan province of China. To facilitate genetic study of T. viscosum, we de novo assembled and annotated the complete chloroplast (cp) genome of T. viscosum for the first time. The total length of the cp genome of T. viscosum was 155,984 bp, with a GC content of 38.4%. The T. viscosum cp genome had a typical quadripartite structure with a large single-copy region of 85,339 bp, a small single-copy region of 17,656 bp, and a pair of inverted repeat regions of 26,495 bp. The cp genome consisted of 133 genes, including 87 protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. We performed phylogenetic analysis of T. viscosum with the maximum-likelihood phylogenetic tree and indicated that T. viscosum was closely related to T. cirrhosum and T. foeniculaceum.

Phylogenetic analysis and complete chloroplast genome of Salix wilhelmsiana M.B.

Salix wilhelmsiana M.B. Bieberstein 1819 is a perennial woody plant with high economic and ecological value. In this study, we annotated the chloroplast (cp) genome of Salix wilhelmsiana M.B. The results showed that the length of the complete cp genome is 155,577 bp, which is typically composed of two single-copy regions (large single-copy (LSC) of 84,439 bp and small single-copy (SSC) of 16,221 bp) and a pair of IR regions of 27,457 bp with a quadripartite structure. The genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The GC content was 36.70%. Phylogenetic analysis based on cp genome sequences of 19 species from the Salicaceae family revealed that S. wilhelmsiana M.B. is closely related to S. viminalis var. gmelinii.

The complete chloroplast genome of Miliusa glochidioides (Annonaceae) and phylogenetic analysis

The chloroplast (cp) genome of Miliusa glochidioides has been fully sequenced. The cp genome of this species has a typical quadripartite structure comprised of four parts: a large single copy (LSC; 88,782 bp) region, a small single copy (SSC; 18,949 bp) region, and two inverted repeat (IR; 26,029 bp each) regions. The full length of the cp genome is 159,789 bp; its GC content is 36.7%, and it encodes a total of 129 genes including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among the protein-coding genes, nine (rps16, rpl2, rpl16, atpF, rpoC1, petB, petD, ndhA, and ndhB) contain one intron, and three (rps12, clpP, and ycf3) have two introns. A maximum-likelihood (ML) phylogenetic tree shows that M. glochidioides is a sister to Chieniodendron hainanense.

The complete mitochondrial genome of Priotyrannus closteroides Thomson, 1877 (Coleoptera: Cerambycidae)

Priotyrannus closteroides Thomson, 1877 (Coleoptera: Cerambycidae) is the trunk borer of orange trees. In this study, we sequenced and annotated the whole mitochondrial genome of P. closteroides. The results showed that the length of the complete mitochondrial genome is 15,854 bp with an overall GC content of 32.11%. The genome encodes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs). The relevant phylogenetic tree distinctly showed that P. closteroides is clustered with Dorysthenes paradoxus and Dorysthenes granulosus. This study provides a piece of valuable genomic information for the population genetics, evolution, and classification of P. closteroides.

Comparative Analysis of Complete Chloroplast Genomes of Nine Species of Litsea (Lauraceae): Hypervariable Regions, Positive Selection, and Phylogenetic Relationships.

Litsea is a group of evergreen trees or shrubs in the laurel family, Lauraceae. Species of the genus are widely used for a wide range of medicinal and industrial aspects. At present, most studies related to the gene resources of Litsea are restricted to morphological analyses or features of individual genomes, and currently available studies of select molecular markers are insufficient. In this study, we assembled and annotated the complete chloroplast genomes of nine species in Litsea, carried out a series of comparative analyses, and reconstructed phylogenetic relationships within the genus. The genome length ranged from 152,051 to 152,747 bp and a total of 128 genes were identified. High consistency patterns of codon bias, repeats, divergent analysis, single nucleotide polymorphisms (SNP) and insertions and deletions (InDels) were discovered across the genus. Variations in gene length and the presence of the pseudogene ycf1Ψ, resulting from IR contraction and expansion, are reported. The hyper-variable gene rpl16 was identified for its exceptionally high Ka/Ks and Pi values, implying that those frequent mutations occurred as a result of positive selection. Phylogenetic relationships were recovered for the genus based on analyses of full chloroplast genomes and protein-coding genes. Overall, both genome sequences and potential molecular markers provided in this study enrich the available genomic resources for species of Litsea. Valuable genomic resources and divergent analysis are also provided for further research of the evolutionary patterns, molecular markers, and deeper phylogenetic relationships of Litsea.

Effects of Non-Virion Gene Expression Level and Viral Genome Length on the Replication and Pathogenicity of Viral Hemorrhagic Septicemia Virus.

Fish novirhabdoviruses, including viral hemorrhagic septicemia virus (VHSV), hirame rhabdovirus (HIRRV), and infectious hematopoietic necrosis virus (IHNV), harbor a unique non-virion (NV) gene that is crucial for efficient replication and pathogenicity. The effective levels and the function of the N-terminal region of the NV protein, however, remain poorly understood. In the present study, several recombinant VHSVs, which completely lack (rVHSV-ΔNV) or harbor an additional (rVHSV-dNV) NV gene, were generated using reverse genetics. To confirm the function of the N-terminal region of the NV protein, recombinant VHSVs with the NV gene that gradually mutated from the start codon (ATG) to the stop codon (TGA), expressed as N-terminally truncated NV proteins (rVHSV-NV1, -NV2, and -NV3), were generated. CPE progression and viral growth analyses showed that epithelioma papulosum cyprini (EPC) cells infected with rVHSV-ΔNV or rVHSV-NV3—which did not express NV protein—rarely showed CPE and viral replication as opposed to EPC cells infected with rVHSV-wild. Interestingly, regardless of the presence of two NV genes in the rVHSV-dNV genome, EPC cells infected with rVHSV-dNV or rVHSV-A-EGFP (control) failed to induce CPE and viral replication. In EPC cells infected with rVHSV-dNV or rVHSV-A-EGFP, which harbored a longer VHSV genome than the wild-type, Mx gene expression levels, which were detected by luciferase activity assay, were particularly high; Mx gene expression levels were higher in EPC cells infected with rVHSV-ΔNV, -NV2, or -NV3 than in those infected with rVHSV-wild or rVHSV-NV1. The total amount of NV transcript produced in EPC cells infected with rVHSV-wild was much higher than that in EPC cells infected with rVHSV-dNV. However, the expression levels of the NV gene per viral particle were significantly higher in EPC cells infected with rVHSV-dNV than in cells infected with rVHSV-wild. These results suggest that the NV protein is an essential component in the inhibition of host type-I interferon (IFN) and the induction of viral replication. Most importantly, viral genome length might affect viral replication efficiency to a greater extent than does NV gene expression. In in vivo pathogenicity experiments, the cumulative mortality rates of olive flounder fingerlings infected with rVHSV-dNV or rVHSV-wild were similar (60–70%), while those of fingerlings infected with rVHSV-A-EGFP were lower. Moreover, the virulence of rVHSV-ΔNV and rVHSV, both harboring a truncated NV gene (rVHSV-NV1, -NV2, and -NV3), was completely attenuated in the olive flounder. These results suggest that viral pathogenicity is affected by the viral replication rate and NV gene expression. In conclusion, the genome length and NV gene (particularly the N-terminal region) expression of VHSVs are closely associated with viral replication in host type-I IFN response and the viral pathogenicity.

Genomic insights from Paraclostridium bifermentans HD0315_2: General features and pathogenic potential.

BackgroundParaclostridium bifermentans is the most diverse distributed species of Paraclostridium and can cause fatal human infections under rare conditions. However, its pathogenic mechanisms and adaptation ability behind infections remain unclear. Herein, we reported the complete genome sequence of P. bifermentans HD0315_2 isolated from the feces of a patient with Crohn's disease. Then, we performed genomic analyses to understand its pathogenic mechanisms and adaptation ability.ResultsThe de novo assembly revealed that the HD0315_2 strain carried a circular chromosome of 3.27 Mb and six circular plasmids (19.41 to 139.50 kb). The phylogenomic analysis assigned the HD0315_2 strain as P. bifermentans and reclassified some previously non-P. bifermentans strains into this clade. The general genomic features showed that this species harbored a flexible genomic pool characterized by variable genome length and multiple plasmids. Then, the HD0315_2 strain was predicted as a human pathogen with high probability, and Listeria LIPI-1 virulence proteins were identified on its genome. Besides, abundant antibiotics/metal/stress resistant genes, such as asrABCH, cat, mccF, macB, entS, albA, bcrA, and tetB, were carried by either the genome or the plasmids. Furthermore, we proposed that transposase-directed horizontal gene transfer was responsible for the distribution of multiple copies of the hin gene in the plasmids.ConclusionThe flexible genomic pool of P. bifermentans encodes abundant functions for antimicrobial or oxidative stress resistance, helping it successfully inhabit and adapt to diverse environments. Moreover, P. bifermentans HD0315_2 might infect hosts via a Listeria LIPI-1-like cycle, with the help of a plasmid expressing the Hin DNA invertase to evade host immune responses.

Complete mitochondrial genome of freshwater pearl mussel Lamellidens marginalis (Lamarck, 1819) and its phylogenetic relation within unionidae family.

Freshwater mussels play a key role in ecology and are often considered as ecological indicators. Conversely, these molluscs are one of the most threatened groups due to several anthropogenic factors. Knowledge of phylogenetic diversity would assist in formulating effective management and conservation measures. Lamellidens marginalis is one of the most widely used freshwater mussel for pearl production in India. The genomic resources for investigating its evolutionary relationship within the Unionidae family are lacking. In this study, the f-type mitochondrial genome of L. marginalis was sequenced using the Illumina sequencing platform. The length of the mitochondrial genome was 15,732bp consisting of 23 tRNAs, 2 rRNAs and 13 protein coding genes. The arrangement of genes was UF1 type and gene overlap was observed between trnG and nad1. Comparative analysis with other Unionidae species showed a high divergence rate in nad6 followed by nad2 atp8 and nad5. The phylogenetic tree supported monophyly of the Unioninae subfamily and L. marginalis (Parreysiinae) formed a sister branch to this subfamily. The divergence time of the Parreysiinae from its most recent common ancestor (MRCA) was placed in the Mesozoic era. This information will be useful for the understanding the evolutionary pattern of the species of Parreysiinae subfamily.

Genome Sequence Resource for Strains of Pseudomonas syringae Phylogroup 2b and P. viridiflava Phylogroup 7a Causing Bacterial Stem Blight of Alfalfa.

Genome Sequence Resource for Strains of Pseudomonas syringae Phylogroup 2b and P. viridiflava Phylogroup 7a Causing Bacterial Stem Blight of Alfalfa.