Special Issue "Discoveries in Sequencing Data Analysis"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Bioinformatics".

Deadline for manuscript submissions: 20 May 2022.

Special Issue Editors

Dr. Yuanyan Xiong
E-Mail Website
Guest Editor
School of Life Sciences, Sun Yat Sen University, Guangzhou, China
Interests: bioinformatics; high-throughput sequencing
Dr. Mengbiao Guo
E-Mail
Guest Editor
School of Life Sciences, Sun Yat Sen University, Guangzhou, China
Interests: cancer biology; bioinformatics; multi-omics; autoimmune

Special Issue Information

Dear Colleagues,

High-throughput sequencing has been widely used in functional genomics studies and has revolutionized biological sciences. It enables researchers to perform a wide range of investigations and to study biological systems at an unprecedented level, as exemplified by large international research projects, including The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression project (GTEx), which provided comprehensive multi-omics sequencing datasets for research by scientists across the world. Analysis of sequencing data converts sequence information into meaningful knowledge and insights, which involves algorithm development, annotation or cataloguing information, multi-omics data integration, biomarker and drug target discovery, and disease diagnosis and drug response prediction. Whole transcriptome sequencing (RNA-seq), for example, provides sequence information about coding and multiple noncoding forms of RNA to assess variations and gene expression levels across the entire genome. Varied information can be obtained from RNA-seq, including gene expression levels, alternative splicing (AS), alternative polyadenylation (APA), gene fusion, and RNA editing. For genome or exome sequencing, nucleotide polymorphisms and structural variations, in addition to telomere variations, can be identified to uncover driver genomic events. Furthermore, single-cell RNA or DNA sequencing (scRNA- or scDNA-seq) has dramatically improved our understanding of biology in every aspect. Novel discoveries in sequencing data analysis are critical to pinpoint the key players in pathological conditions, especially for cancer and other age-related diseases.

The aim of this Special Issue is to provide a broad and up-to-date overview of “Discoveries in Sequencing Data Analysis” to elucidate new approaches analyzing sequencing data, integrating multi-omics data, discovering biological mechanisms, and developing novel treatments or therapies for diseases. Contributions in the form of research papers and reviews from experts in the field are needed to improve our understanding of relevant biological issues.

Dr. Yuanyan Xiong
Dr. Mengbiao Guo
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2000 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • sequencing data analysis
  • multi-omics data integration
  • biomarker identification
  • drug repurposing and drug response prediction
  • discoveries in immunology, cancer, and developmental biology

Published Papers (1 paper)

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Research

Article
Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis
Genes 2021, 12(12), 1944; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12121944 - 01 Dec 2021
Viewed by 244
Abstract
The peanut (Arachis hypogaea L.) is the leading oil and food crop among the legume family. Extensive duplicate gene pairs generated from recursive polyploidizations with high sequence similarity could result from gene conversion, caused by illegitimate DNA recombination. Here, through synteny-based comparisons [...] Read more.
The peanut (Arachis hypogaea L.) is the leading oil and food crop among the legume family. Extensive duplicate gene pairs generated from recursive polyploidizations with high sequence similarity could result from gene conversion, caused by illegitimate DNA recombination. Here, through synteny-based comparisons of two diploid and three tetraploid peanut genomes, we identified the duplicated genes generated from legume common tetraploidy (LCT) and peanut recent allo-tetraploidy (PRT) within genomes. In each peanut genome (or subgenomes), we inferred that 6.8–13.1% of LCT-related and 11.3–16.5% of PRT-related duplicates were affected by gene conversion, in which the LCT-related duplicates were the most affected by partial gene conversion, whereas the PRT-related duplicates were the most affected by whole gene conversion. Notably, we observed the conversion between duplicates as the long-lasting contribution of polyploidizations accelerated the divergence of different Arachis genomes. Moreover, we found that the converted duplicates are unevenly distributed across the chromosomes and are more often near the ends of the chromosomes in each genome. We also confirmed that well-preserved homoeologous chromosome regions may facilitate duplicates’ conversion. In addition, we found that these biological functions contain a higher number of preferentially converted genes, such as catalytic activity-related genes. We identified specific domains that are involved in converted genes, implying that conversions are associated with important traits of peanut growth and development. Full article
(This article belongs to the Special Issue Discoveries in Sequencing Data Analysis)
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