Complete genome sequence of a novel secovirid infecting cassava in the Americas

We report the complete genome sequence of a field isolate of a novel bipartite secovirid infecting cassava in Colombia, provisionally named "cassava torrado-like virus" (CsTLV). The genome sequence was obtained using Oxford Nanopore Technology, and the 5’ ends were confirmed by RACE. The RNA1 is 7252 nucleotides (nt) long, encoding a polyprotein of 2336 amino acids (aa) containing the typical “replication block”, conserved torradovirus motifs, and a Maf/Ham1 domain, which is not commonly found in viral genomes. The RNA2 is 4469 nt long and contains two overlapping ORFs encoding proteins of 226 and 1179 aa, showing the characteristic genome arrangement of members of the genus Torradovirus.

Metagenomic Analysis of Viral Diversity and a Novel Astroviruse of Forest Rodent

Background: Rodents are important virus reservoirs and natural hosts for multiple viruses. They are one of the wild animals that are extremely threatening to the spread of human viruses. Therefore, research on rodents carrying viruses and identifying new viruses that rodents carry is of great significance for preventing and controlling viral diseases.Methods: In this study, fecal samples from six species of forest rodents in Northeast China were sequenced using metagenomics, and an abundance of virome information was acquired.Results: Among the top 10 most abundant viral families, RNA virus include Orthomyxoviridae, Picornaviridae, Bunyaviridae and Arenaviridae, DNA virus include Herpesviridae, Insect virus include Nodaviridae and Baculoviridae, Plant virus Tombusviridae and Phage (Myoriviridae). Except for Myoviridae, there was no significant difference in the abundance of virus families in the feces of each rodent species. In addition, a new strain of astrovirus was discovered, with an ORF and genome arrangement comparable to other rodent astroviruses.The newly identified astrovirus had the highest similarity with the rodent astrovirus isolate, CHN/100.Conclusions: The data obtained in this study provided an overview of the viral community present in these rodent fecal samples, revealing some rodent-associated viruses closely related to known human or animal pathogens. Strengthening our understanding of unclassified viruses harbored by rodents present in the natural environment could provide scientific guidance for preventing and controlling new viral outbreaks that can spread via rodents.

Comparative Analysis of Chloroplast Genomes of Seven Chaetoceros Species Revealed Variation Hotspots and Speciation Time

Chaetoceros is a species-rich diatom genus with broad distribution and plays an important role in global carbon cycle and aquatic ecosystems. However, genomic information of Chaetoceros species is limited, hindering advanced researches on Chaetoceros biodiversity and their differential impact on ecology. In this study, we constructed full-length chloroplast genomes (cpDNAs) for seven Chaetoceros species, including C. costatus, C. curvisetus, C. laevisporus, C. muelleri, C. pseudo-curvisetus, C. socialis, and C. tenuissimus. All of these cpDNAs displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The sizes of these cpDNAs were similar, ranging from 116,421 to 119,034 bp in size, and these cpDNAs also displayed similar GC content, ranging from 30.26 to 32.10%. Despite extensive synteny conservation, discrete regions showed high variations. Divergence time estimation revealed that the common ancestor of Chaetoceros species, which formed a monophyletic clade at approximately 58 million years ago (Mya), split from Acanthoceras zachariasii at about 70 Mya. The availability of cpDNAs of multiple Chaetoceros species provided valuable reference sequences for studying evolutionary relationship among Chaetoceros species, as well as between Chaetoceros species and other diatom species.

Complete Mitochondrial Genomes of Babylonia Formosae and Babylonia Zeylanica (Neogastropoda: Babyloniidae) and Increased Sampling Give New Insights Into Neogastropoda Phylogeny

The phylogenetic relationships of Neogastropoda, a group of highly complex predatory marine snails, have been controversial. The two newly sequenced mitogenomes of Babylonia formosae and Babylonia zeylanica (Neogastropoda: Babyloniidae) are described. The mitogenomes of B. zeylanica and B. formosae were 16, 214 bp and 16, 181 bp in length, respectively. The mitogenomes of both species contain 13 PCGs, 22 tRNA genes, and 2 ribosomal RNA genes. The sequence of genes differed from the ancestral mitochondrial gene arrangement of Caenogastropoda mitogenomes. Also, 63 Neogastropoda species were analyzed for the genome organization of seventeen major lineage of Neogastropoda, five types of mitochondrial genome arrangement were identified. Bayesian Inference phylogenetic trees and Maximum likehood of Neogastropoda were established according to complete mitogenome. The monophyly of Neogastropoda families is strongly supported by this study, in contrast to previous molecular studies. Our results shed light on gene sequence distribution/arrangement characteristics of Neogastropoda mitogenomes, provide fundamental information for further phylogenetic studies on Neogastropoda.

Identification of Novel Astroviruses in the Gastrointestinal Tract of Domestic Cats

Astroviruses, isolated from numerous avian and mammalian species including humans, are commonly associated with enteritis and encephalitis. Two astroviruses have previously been identified in cats, and while definitive evidence is lacking, an association with enteritis is suggested. Using metagenomic next-generation sequencing of viral nucleic acids from faecal samples, we identified two novel feline astroviruses termed Feline astrovirus 3 and 4. These viruses were isolated from healthy shelter-housed kittens (Feline astrovirus 3; 6448 bp) and from a kitten with diarrhoea that was co-infected with Feline parvovirus (Feline astrovirus 4, 6549 bp). Both novel astroviruses shared a genome arrangement of three open reading frames (ORFs) comparable to that of other astroviruses. Phylogenetic analysis of the concatenated ORFs, ORF1a, ORF1b and capsid protein revealed that both viruses were phylogenetically distinct from other feline astroviruses, although their precise evolutionary history could not be accurately determined due to a lack of resolution at key nodes. Large-scale molecular surveillance studies of healthy and diseased cats are needed to determine the pathogenicity of feline astroviruses as single virus infections or in co-infections with other enteric viruses.

A Single Chromosome Strain of S. cerevisiae Exhibits Diminished Ethanol Metabolism and Tolerance

This study characterized the growth, metabolism, and transcriptional profile of a S. cerevisiae strain with a single large chromosome that was constructed via successive chromosomal fusions. The single chromosome strain exhibited a longer lag phase, increased doubling time, and lower final biomass concentration compared with a wildtype strain when grown on YPD. These phenotypes were amplified when ethanol was added to the medium or used as the sole carbon source. RNAseq analysis showed diminished induction of genes involved in diauxic shift, ethanol metabolism, fatty-acid ß-oxidation, and methylglyoxal catabolism during growth on ethanol compared to the reference strain. Enzyme-constrained metabolic modeling predicted that decreased flux through these poorly induced enzymes results in diminished ATP formation and decreased biomass accumulation observed. Together, these observations suggest that switch-like control of carbon source dependent gene expression in S. cerevisiae requires genome arrangement into multiple chromosomes.

Complete Chloroplast Genomes and Comparative Analysis of Sequences Evolution among Seven Aristolochia (Aristolochiaceae) Medicinal Species

Aristolochiaceae, comprising about 600 species, is a unique plant family containing aristolochic acids (AAs). In this study, we sequenced seven species of Aristolochia, and retrieved eleven chloroplast (cp) genomes published for comparative genomics analysis and phylogenetic constructions. The results show that the cp genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The cp genomes range from 159,308 bp to 160,520 bp in length and have a similar GC content of 38.5%–38.9%. A total number of 113 genes were identified, including 79 protein-coding genes, 30 tRNAs and four rRNAs. Although genomic structure and size were highly conserved, the IR-SC boundary regions were variable between these seven cp genomes. The trnH-GUG genes, are one of major differences between the plastomes of the two subgenera Siphisia and Aristolochia. We analyzed the features of nucleotide substitutions, distribution of repeat sequences and simple sequences repeats (SSRs), positive selections in the cp genomes, and identified 16 hotspot regions for genomes divergence that could be utilized as potential markers for phylogeny reconstruction. Phylogenetic relationships of the family Aristolochiaceae inferred from the 18 cp genome sequences were consistent and robust, using maximum parsimony (MP), maximum likelihood (ML), and Bayesian analysis (BI) methods.

The complete mitochondrial genomes of two weevils, Eucryptorrhynchus chinensis and E. brandti: conserved genome arrangement in Curculionidae and deficiency of tRNA-Ile gene

The weevils Eucryptorrhynchus chinensis and Eucryptorrhynchus brandti (Coleoptera: Curculionidae), are two of the most important pests of the tree-of-heaven, Ailanthus altissima, which is found throughout China. In this study, the complete mitogenomes of the two weevils have been sequenced using Illumina HiSeqTM 2000. The mitogenomes of E. chinensis and E. brandti are 15,628bp and 15,597bp long with A+T contents of 77.7% and 76.6%, respectively. Both species have typical circular mitochondrial genomes that encode 36 genes. Except the deficiency of tRNA-Ile, the gene composition and order of E. chinensis and E. brandti are identical to the inferred ancestral gene arrangement of insects. In both mitochondrial genomes, the start codons for COI and ND1 are AAT and TTG, respectively. A5bp motif (TACTA) is detected in intergenic region between the tRNA-Ser (UCN) and ND1 genes. The ATP8/ATP6 and ND4L/ND4 gene pairs appear to overlap four or seven nucleotides (ATAA/ATGATAA) in different reading frames. The complete sequences of AT-rich region have two regions including tandem repeats. The study identifies useful genetic markers for studying the population genetics, molecular identification and phylogeographics of Eucryptorrhynchus weevils. The features of the mitochondrial genomes are expected to be valuable in