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This Week in Genome Biology: Sep 5, 2018

Researchers in Korea report on findings from a genome sequencing study of the wild flowering cherry tree species Prunus yedoensis, commonly known as the King cherry, that is found on Korea's Jeju Island. Using a combination of long- and short-read sequencing, the team came up with an almost 324 million base draft genome assembly for P. yedoensis that contained nearly 41,300 predicted protein-coding genes. Together with genome re-sequencing data for 16 more Prunus or P. yedoensis accessions, the genome indicated that the King cherry stems from a cross between the P. pendula f. ascendens and P. jamasakura species and is distinct from the hybrid Yoshino cherry.

A National Cancer Institute-led team takes a look at potential ties between lung cancer, tumor somatic mutations, and the microbial communities found in the lung. The researchers suspected "somatic mutations, together with cigarette smoke, generate a dysbiotic microbiota that is associated with lung carcinogenesis" — a hypothesis they examined with RNA sequencing and 16S ribosomal RNA gene sequencing on lung samples from 143 individuals with lung cancer and 33 without. Along with data from the Cancer Genome Atlas, the analysis highlights diminished microbial diversity in the tumor tissue. The authors also saw a rise in Acidovorax microbes in squamous cell carcinoma samples from smokers, particularly in cases involving TP53 gene mutations.

Researchers from the Hospital for Sick Children, University of Toronto, and the Ontario Institute for Cancer Research present findings from a transcriptomic analysis of the freshwater planarian, Schmidtea mediterranea, a model organism used in regeneration and stem cell biology research. The team brought together transcriptome sequence data for S. mediterranea representatives exposed to a range of growth conditions in the lab, leading to more than 36,000 high-confidence transcripts used for comparative genomics, functional annotation, and metabolic reconstruction analyses. The investigators also did single-cell RNA sequencing on 2,000 cells to get a sense of the spatial distribution for the planarian transcripts. 

The Scan

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.