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: closed (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

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 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 (4 papers)

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Research

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Open AccessArticle Genome-Wide Analysis of the PYL Gene Family and Identification of PYL Genes That Respond to Abiotic Stress in Brassica napus
Received: 15 January 2018 / Revised: 26 February 2018 / Accepted: 6 March 2018 / Published: 12 March 2018
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Abstract
Abscisic acid (ABA) is an endogenous phytohormone that plays important roles in the regulation of plant growth, development, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein is a core regulatory component of ABA signaling networks in plants. However, no details regarding this
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Abscisic acid (ABA) is an endogenous phytohormone that plays important roles in the regulation of plant growth, development, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein is a core regulatory component of ABA signaling networks in plants. However, no details regarding this family in Brassica napus are available. Here, 46 PYLs were identified in the B. napus genome. Based on phylogenetic analysis, BnPYR1 and BnPYL1-3 belong to subfamily I, BnPYL7-10 belong to subfamily II, and BnPYL4-6 and BnPYL11-13 belong to subfamily III. Analysis of BnPYL conserved motifs showed that every subfamily contained four common motifs. By predicting cis-elements in the promoters, we found that all BnPYL members contained hormone- and stress-related elements and that expression levels of most BnPYLs were relatively higher in seeds at the germination stage than those in other organs or at other developmental stages. Gene Ontology (GO) enrichment showed that BnPYL genes mainly participate in responses to stimuli. To identify crucial PYLs mediating the response to abiotic stress in B. napus, expression changes in 14 BnPYL genes were determined by quantitative real-time RT-PCR after drought, heat, and salinity treatments, and identified BnPYR1-3, BnPYL1-2, and BnPYL7-2 in respond to abiotic stresses. The findings of this study lay a foundation for further investigations of PYL genes in B. napus. Full article
(This article belongs to the Special Issue Estimating Phylogenies from Large Genomic Datasets)
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Open AccessArticle Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies
Received: 1 December 2017 / Revised: 30 January 2018 / Accepted: 16 February 2018 / Published: 28 February 2018
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Abstract
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both
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Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest. Full article
(This article belongs to the Special Issue Estimating Phylogenies from Large Genomic Datasets)
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Open AccessArticle Genome-Wide Identification and Structural Analysis of bZIP Transcription Factor Genes in Brassica napus
Genes 2017, 8(10), 288; https://doi.org/10.3390/genes8100288
Received: 3 September 2017 / Revised: 16 October 2017 / Accepted: 19 October 2017 / Published: 24 October 2017
Cited by 1 | 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
[...] Read more.
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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Review

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Open AccessReview Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets
Received: 1 December 2017 / Revised: 2 February 2018 / Accepted: 19 February 2018 / Published: 26 February 2018
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Abstract
Summary coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including
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Summary coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset—the ‘recombination ratchet’—is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d’etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful enough to infer the correct species tree for difficult phylogenetic problems in the anomaly zone, where concatenation is expected to fail because of ILS, then there should be a decreasing probability of inferring the correct species tree using longer loci with many intralocus recombination breakpoints (i.e., increased levels of concatenation). Full article
(This article belongs to the Special Issue Estimating Phylogenies from Large Genomic Datasets)
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