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Genome Biology Papers on RNA Sequence Variants, Sequencing Quality Control 2, Walnut Adaptation

A team from the Peter MacCallum Cancer Center, the University of Melbourne, and other centers in Australia describes a reference-free pipeline called MINTIE for focusing on splice variants, structural changes, and other variants in RNA sequence data. The strategy "combines the advantages of full de novo assembly with differential expression to identify unique variants in a case sample versus a set of controls," the researchers write, along with computational steps to dial down transcriptional noise and annotate and prioritize variants. After using MINTIE to find transcript fusions and other variants in simulated data, the authors compared it to other available approaches. From there, they applied MINTIE to RNA-seq profiles for pediatric acute lymphoblastic leukemia (ALL) and controls, uncovering previously undetected fusion or splice variants in potential ALL driver genes.

Members of the US Food and Drug Administration-led "Microarray and Sequencing Quality Control" (MAQC/SEQC) Consortium share perspectives from the SEQC2 phase of the project, which ran from 2016 to 2021 and aimed to benchmark, standardize, and come up with best practices around RNA sequencing approaches and applications that may benefit future precision medicine efforts. "The SEQC2 project is organized into six themes, each focusing on a different clinical application, including genome sequencing, cancer genomics, single-cell sequencing, circulating tumor DNA, epigenetics (eDNA methylation), and targeted RNA sequencing," the authors note, explaining that hundreds of investigators from academic, government, and industry labs "evaluated the performance of these difference [next-generation sequencing] applications and built consensus standards for their best-practice use in clinical settings."

Investigators at the Chinese Academy of Forestry's State Key Laboratory of Tree Genetics and Breeding and elsewhere explore genetic features behind walnut traits, adaptations, and evolution. Based on genome re-sequencing data for more than 800 Juglans regia and J. sigillata walnut accessions in China, Iran, and Pakistan, the team found that the common walnut J. regia likely split off from, but continued to hybridize with, its relatively wild sister taxa J. sigillata. The analysis also highlighted enhanced genetic diversity during the improvement process for common walnut trees, along with agronomic trait or adaptation-linked loci and improvement-related selective sweeps affecting more than 900 genes. "The largest genomic resource for walnuts to date has been generated and explored in this study," the authors report, "unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree."