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Nature Papers Include Monotreme Genomes, Single-Cell Study of Gastric Adenocarcinoma, More

High-quality reference genomes for the platypus and echidna — two egg-laying mammals, or monotremes, of Australasia — are presented in Nature this week, providing insights into mammalian evolution. An international team led by scientists from the University of Copenhagen generated the platypus genome using a combination of single-molecule sequencing technology and physical mapping methods, assigning most of the sequences to a chromosome-scale assembly and markedly improving the genome continuity and gene annotation. A less-continuous assembly was also produced for the short-beaked echidna. In analyzing the genomes, the researchers were able to detect the ancestral and lineage-specific genomic changes shaping both monotreme and mammalian evolution. "The new genomes of both species will enable further insights into therian innovations and the biology and evolution of these extraordinary egg-laying mammals," the authors write.

In performing single-cell RNA sequencing of tumor cells from patients with gastric adenocarcinoma, a team of MD Anderson Cancer Center scientists have identified key contributors to intratumoral heterogeneity in cancer. As reported in Nature Medicine, the investigators sequenced peritoneal carcinomatosis (PC) cells from 15 patients to construct a map of over 45,000 PC cells, profile the transcriptome states of tumor cell populations, examine the intratumoral heterogeneity of malignant PC cells, and identify significant correlates with patient survival. They determine that diversity in tumor cell lineage/state compositions is a key contributor to intratumoral heterogeneity, as well as discover a 12-gene prognostic signature that may hold potential for stratifying patients for treatment.

A new method for improved metagenome binning and assembly is described in Nature Biotechnology this week. Metagenomic binning, the process of grouping metagenomic sequences by their organism of origin, is a key starting point for metagenomic studies, but the reconstruction of microbial species from metagenomics data remains challenging. To address this, researchers from the University of Copenhagen and collaborators developed a computational tool — called variational autoencoders for metagenomic binning, or VAMB — that uses deep variational autoencoders to encode sequence co-abundance and k-mer distribution information before clustering. The team shows that VAMB is able to integrate these two distinct data types without any previous knowledge of the datasets and can outperform existing state-of-the-art binners.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.