Complete Genome Sequence and Phylogenetic Analysis of a Goose Astrovirus Isolate in China

Astroviruses are considered the cause of gastroenteritis in humans and animals. Studies in recent years show avian astroviruses are also associated with duckling hepatitis, gosling gout, and chicken nephritis. In this study, a GAstV strain, designated as JS2019/China, was detected in dead goslings from a commercial goose farm in Jiangsu province of China. Viral strain was proliferated in goose embryos and sequence analysis showed the isolated strain had a classical structure arrangement and a series of conserved regions compared with other GAstVs. Sequence comparison and phylogenetic analysis of whole genome and ORF2 revealed that JS2019/China belongs to the GAstV group-1, which consists of most of the GAstV strains. Amino acid analysis indicated that some mutants might have an impact on viral protease capacity, such as V505I and K736E of ORF1a and T107I, F342S, and S606P of ORF2. Taken together, a novel GAstV strain was isolated and genomic analysis and protein polymorphism analysis indicated that some amino acid mutants might affect the viral virulence.

Characterization and Complete Genome Analysis of a Novel Escherichia Phage, vB_EcoM-RPN242

The novel Escherichia phage vB_EcoM-RPN242 was isolated using a strain of Escherichia coli host originated from a diarrheal piglet. The phage was able to form plaques on the E. coli lawn at 15−45ºC. Moreover, it was stable over a wide pH (4−10) and temperature (4−70ºC) range. The vB_EcoM-RPN242 genome was found to be a linear, double-stranded DNA consisting of 154,840 base pairs. There were 195 protein-encoding genes and 2 tRNAs detected in the genome, however no unfavorable gene was found. According to the overall nucleotide sequence comparison, the vB_EcoM-RPN242 possibly represents a new phage species in the genus Agtrevirus.

The Archaeal Transcription Termination Factor aCPSF1 is a Robust Phylogenetic Marker for Archaeal Taxonomy

Archaea represent a unique type of prokaryote, which inhabit in various environments including extreme environments, and so define the boundary of biosphere, and play pivotal ecological roles, particularly in extreme environments. Since their discovery over 40 years ago, environmental archaea have been widely investigated using the 16S rRNA sequence comparison, and the recently developed phylogenomic approach because the majority of archaea are recalcitrant to laboratory cultivation.

Selection of Moment Vectors in Protein Sequence Comparison Under Binary Representation

Similarity/dissimilarity study of protein and genome sequences remains a challenging task and selection of techniques and descriptors to be adopted, plays an important role in computational biology. Again, genome sequence comparison is always preferred to protein sequence comparison due the presence of 20 amino acids in protein sequence compared to only 4 nucleotides in genome sequence. So it is important to consider suitable representation that is both time and space efficient and also equally applicable to protein sequences of equal and unequal lengths. In the binary form of representation, Fourier transform of a protein sequence reduces to the transformation of 20 simple binary sequences in Fourier domain, where in each such sequence, Perseval’s Identity gives a very simple computable form of power spectrum. This gives rise to readily acceptable forms of moments of different degrees. Again such moments, when properly normalized, show a monotonically descending trend with the increase in the degrees of the moments. So it is better to stick to moments of smaller degrees only. In this paper, descriptors are taken as 20 component vectors, where each component corresponds to a general second order moment of one of the 20 simple binary sequences. Then distance matrices are obtained by using Euclidean distance as the distance measure between each pair of sequence. Phylogenetic trees are obtained from the distance matrices using UPGMA algorithm. In the present paper, the datasets used for similarity/dissimilarity study are 9 ND4, 16 ND5, 9 ND6, 24 TF proteins and 12 Baculovirus proteins. It is found that the phylogenetic trees produced by the present method are at par with those produced by the earlier methods adopted by other authors and also their known biological references. Further it takes less computational time and also it is equally applicable to sequences of equal and unequal lengths.

Effective sequence similarity detection with strobemers

k-mer-based methods are widely used in bioinformatics for various types of sequence comparisons. However, a single mutation will mutate k consecutive k-mers and make most k-mer-based applications for sequence comparison sensitive to variable mutation rates. Many techniques have been studied to overcome this sensitivity, for example, spaced k-mers and k-mer permutation techniques, but these techniques do not handle indels well. For indels, pairs or groups of small k-mers are commonly used, but these methods first produce k-mer matches, and only in a second step, a pairing or grouping of k-mers is performed. Such techniques produce many redundant k-mer matches owing to the size of k. Here, we propose strobemers as an alternative to k-mers for sequence comparison. Intuitively, strobemers consist of two or more linked shorter k-mers, where the combination of linked k-mers is decided by a hash function. We use simulated data to show that strobemers provide more evenly distributed sequence matches and are less sensitive to different mutation rates than k-mers and spaced k-mers. Strobemers also produce higher match coverage across sequences. We further implement a proof-of-concept sequence-matching tool StrobeMap and use synthetic and biological Oxford Nanopore sequencing data to show the utility of using strobemers for sequence comparison in different contexts such as sequence clustering and alignment scenarios.