A new sequencing method for detecting the full transcriptome in single cells is presented in this week's Nature Biotechnology. Most single-cell transcriptome sequencing methods amplify the termini of polyadenylated transcripts, capturing only a small fraction of the total cellular transcriptome and precluding the detection of many long non-coding, short non-coding, and non-polyadenylated protein-coding transcripts. To address this shortcoming, a group led by researchers from the Hubrecht Institute in the Netherlands developed an approach that captures both non-polyadenylated and polyadenylated transcripts across their length in single cells by fragmenting and tailing all RNA molecules subsequent to cell lysis. Called VASA-seq — short for vast transcriptome analysis of single cells by dA-tailing — the technique is high throughput, compatible with both plate-based formats and droplet microfluidics, and does not rely on commercial kits. "VASA-seq is a sensitive and scalable single-cell technology that uncovers a layer of biological information not attainable with technologies that rely on the current mRNA termini-centric view," its developers write.
The genomes of six viruses that infect Asgard archaea, prokaryotic microbes believed to be closely related to eukaryotes, are reported in Nature Microbiology this week. Asgard are found worldwide and genomic data suggest that they are descendants of the archaeal cell that gave rise to the first eukaryotic common ancestor. Viruses that infect these organisms, however, have not been described. In this week's study, scientists from the University of Texas at Austin use metagenome sequences recovered from deep-sea hydrothermal sediments to characterize six relatively large double-stranded DNA viral genomes that infected two Asgard archaeal phyla. Among their findings is that the viruses contain features of both prokaryotic and eukaryotic viruses, which is consistent with the evolutionary position of their hosts. "This description of Asgard-linked viruses advances our understanding of their molecular roles, host interactions, and genomic characteristics," the researchers write.
A genomic catalog of microbes found within glaciers of the Tibetan Plateau is published in this week's Nature Biotechnology, representing a first-of-its-kind tool that may help inform investigations into the potential health risks of glacier melting. The Tibetan Plateau is the source of several of the world's largest rivers and contains the largest area of low-latitude glaciers. In the study, a team led by Chinese Academy of Sciences investigators sequenced 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice, and cryoconite habitats to build the Tibetan Glacier Genome and Gene catalog. The resource contains 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla, as well as more than 25 million non-redundant protein-encoding genes. The catalog, the scientists write, may serve as a database and a platform for archiving, analyzing, and comparing glacier microbiomes at the genome and gene levels — a particularly timely resource as the glacier ecosystem is threatened by global warming. "This work fills a major knowledge gap in the understanding of microbial diversity and functions in glacier ecosystems and provides a resourceful toolkit for bioactive compound bioprospecting and regional health impact evaluation for glacier retreat," they conclude.