Special Issue "Estimating Phylogenies from Large Genomic Datasets"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 30 November 2017

Special Issue Editors

Guest Editor
Dr. Charles Bell

Department of Biological Sciences, University of New Orleans, New Orleans, LA, USA
Website | E-Mail
Phone: 504.280.7040
Fax: 504.280.6121
Interests: diversification; divergence times; molecular clocks; RADseq; phylogeny; phylogenetics; phylogenomics
Guest Editor
Dr. Stephen A. Smith

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
Website | E-Mail
Interests: diversification; divergence times; molecular clocks; RADseq; phylogeny; phylogenetics; phylogenomics

Special Issue Information

Dear Colleagues,

With the explosion of new data from “next generation” sequencing technologies over the past decade, evolutionary biologists have been faced with a number of challenges in using this data for phylogenetic inference. The goal of this Special Issue is to provide a brief overview of recently proposed methods for phylogenetic inference, as well as novel techniques for the acquisition, curation, and implementation of large datasets. We are especially interested in a wide variety of studies (both theoretical and empirical), from overviews of recent software/techniques/pipelines that have been developed to infer phylogenies from large genomic datasets.

Dr. Charles Bell
Dr. Stephen A. Smith
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 1200 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

  • Genomics

  • Proteomics

  • Phylogenomics

  • Phylotranscriptomics

Published Papers (1 paper)

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Research

Open AccessArticle Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus
Genes 2017, 8(10), 288; doi:10.3390/genes8100288
Received: 3 September 2017 / Revised: 16 October 2017 / Accepted: 19 October 2017 / Published: 24 October 2017
PDF Full-text (23136 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed (Brassica napus). In this study, we identified 247
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The basic region/leucine zipper motif (bZIP) transcription factor family is one of the largest families of transcriptional regulators in plants. bZIP genes have been systematically characterized in some plants, but not in rapeseed (Brassica napus). In this study, we identified 247 BnbZIP genes in the rapeseed genome, which we classified into 10 subfamilies based on phylogenetic analysis of their deduced protein sequences. The BnbZIP genes were grouped into functional clades with Arabidopsis genes with similar putative functions, indicating functional conservation. Genome mapping analysis revealed that the BnbZIPs are distributed unevenly across all 19 chromosomes, and that some of these genes arose through whole-genome duplication and dispersed duplication events. All expression profiles of 247 bZIP genes were extracted from RNA-sequencing data obtained from 17 different B. napus ZS11 tissues with 42 various developmental stages. These genes exhibited different expression patterns in various tissues, revealing that these genes are differentially regulated. Our results provide a valuable foundation for functional dissection of the different BnbZIP homologs in B. napus and its parental lines and for molecular breeding studies of bZIP genes in B. napus. Full article
(This article belongs to the Special Issue Estimating Phylogenies from Large Genomic Datasets)
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