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Diversity
Special Issues
Generation of Genome-Wide Genetic Data and Evolutionary Analyses
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Generation of Genome-Wide Genetic Data and Evolutionary Analyses

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Phylogeny and Evolution".

Deadline for manuscript submissions: closed (1 September 2024) | Viewed by 12218

Special Issue Editors

Prof. Dr. Naoko Takezaki

E-Mail Website
Guest Editor
Life Science Research Center, Kagawa University, Kagawa 761-0793, Japan
Interests: molecular evolution; phylogeny construction; phylogenomics; divergence time estimation; vertebrate evolution
Special Issues, Collections and Topics in MDPI journals
Dr. Ben-Yang Liao

E-Mail Website
Co-Guest Editor
Institute of Population Health Sciences, National Health Research Institutes, Miaoli County 350, Taiwan
Interests: evolutionary Genomics; bioinformatics

Special Issue Information

Dear Colleagues,

We are pleased to announce a forthcoming Special Issue of Diversity (IF = 2.465, a full open access journal, ISSN 1424-2818) that focuses on generation of genome-wide genetic data and evolutionary analyses.

With advancement of sequencing technology, we can generate different types of large-scale genetic data in any organism of interest. Large-scale data in genomic and taxonomic coverage can be used for evolutionary analyses for investigating characteristics of evolutionary patterns of genomes and resolving phylogenetic relationships of species, populations, and genes. Use of unprecedented amounts of data was expected to provide fine-scale resolution. However, it also created challenges in compiling and analysing large-scale data. This Special Issue provides an exciting opportunity to showcase the studies that generate genome-wide data, elucidate evolutionary patterns using genome-wide data, and highlight the problems that arise from the use of large amounts of genetic data. In particular studies focusing the following topics are welcome.

  1. Generation of genomic and transcriptomic data as well as DNA methylome data of non-model organisms
  2. Generation of various -omics data such as epigenome data (DNA methylome, CHIP-seq based histone modification data), translatome, and interactome of model organisms
  3. Methodologies or tools for integrating, analysing and interpreting these -omics data
  4. Evolutionary analyses elucidating patterns of genome structures, e.g., large indels, transposable elements, and GC content and natural selection
  5. Methodologies or tools for analysing genome sequences and mining databases and interpreting them for the evolutionary analyses
  6. Phylogenetic analyses of species, populations, and genes/gene families
  7. Methodologies or tools for preparing the data and choosing samples and loci for phylogenetic analyses

Prof. Dr. Naoko Takezaki
Guest Editor

Dr. Ben-Yang Liao
Co-guest Editor

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 submissions that pass pre-check are 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. Diversity 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 2100 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

  • genome evolution
  • phylogenomics
  • genome-scale data
  • species evolution
  • bioinformatics

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Published Papers (4 papers)

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Research

15 pages, 8144 KiB  
Article
The Complete Mitogenomes of Two Species of Snakehead Fish (Perciformes: Channidae): Genome Characterization and Phylogenetic Analysis
by Tangjun Xu, Wenwen Zhang, Yao Li, Jiachen Wang, Yawen Bai and Hongyi Liu
Diversity 2024, 16(6), 346; https://doi.org/10.3390/d16060346 - 14 Jun 2024
Viewed by 980
Abstract
Channidae (snakehead fish) is a family of medium-to-large freshwater carnivorous fish and contain the genus, Channa. Here, the complete mitogenomes of two Channa fish were determined and comparatively analyzed with the mitogenomes of 16 other Channidae fish species. The two newly sequenced [...] Read more.
Channidae (snakehead fish) is a family of medium-to-large freshwater carnivorous fish and contain the genus, Channa. Here, the complete mitogenomes of two Channa fish were determined and comparatively analyzed with the mitogenomes of 16 other Channidae fish species. The two newly sequenced complete mitogenomes were circular DNA molecules with sizes of 16,953 bp (Channa burmanica; OP954106) and 16,897 bp (Channa aurantimaculata; OQ134162). The mitogenomes were composed of 37 genes and one D-loop region. Positive AT skews and negative GC skews were found in the mitogenomes. Most protein-coding genes (PCGs) started with the conventional start codon, ATG; however, the sequence of the stop codon was variable. There was no obvious difference in relative synonymous codon usage among the two mitogenomes, and the two species shared a similar number of codon usage of mitogenomic PCGs, which was also similar to the mean values for the other 15 species of Channa. All Ka/Ks values were <1; cox1 had the lowest value, and atp8 had the highest. All of the tRNAs were typical clover structures, except trnS1. Phylogenetic analysis showed that C. burmanica and C. aurantimaculata shared a close relationship and that they were also closely related to C. gachua. These findings enrich the gene database of Channidae species, clarify the mitochondrial genome structure of the two species, and provide basic data for invasive biological surveillance in the future. Full article
(This article belongs to the Special Issue Generation of Genome-Wide Genetic Data and Evolutionary Analyses)
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23 pages, 5797 KiB  
Article
Survival and Genome Evolution Signatures of Klebsiella pneumoniae Isolates Originated in Seven Species of Aquatic Animals
by Huiqiong Guan, Lu Xie and Lanming Chen
Diversity 2023, 15(4), 527; https://doi.org/10.3390/d15040527 - 6 Apr 2023
Cited by 2 | Viewed by 2545
Abstract
Klebsiella pneumoniae can cause life-threatening pneumonia in humans. The bacterium is also the causative agent of nosocomial infection diseases. In our recent research, we reported, for the first time, the presence of K. pneumoniae in fourteen species of aquatic animals sampled in Shanghai, [...] Read more.
Klebsiella pneumoniae can cause life-threatening pneumonia in humans. The bacterium is also the causative agent of nosocomial infection diseases. In our recent research, we reported, for the first time, the presence of K. pneumoniae in fourteen species of aquatic animals sampled in Shanghai, China. Here, we further investigated the bacterial survival and genome evolution traits. The results revealed that K. pneumoniae isolates (n = 7), recovered from 7 species of commonly consumed aquatic animals, had multiple antibiotic and heavy metal resistance profiles. The isolates were capable of growing vigorously at pH 4.5−7.5 and 0.5−1.0% NaCl in TSB medium at 37 °C. Draft genome sequences of the K. pneumoniae isolates were determined (5,256,522−5,857,823 bp, 56.35–57.81% GC contents), which carried many mobile genetic elements, including genomic islands (n = 87), prophages (n = 14), integrons (n = 4), and insertion sequences (n = 22), indicating possible active horizontal gene transfer during the genome evolution. Meanwhile, numerous strain-specific (n = 199−605) genes, antibiotic resistance (n = 20−35, e.g., β-lactamase) genes, and virulence (n = 43−59, e.g., enterobactin)-related genes, were also identified, demonstrating considerable genome variation in the K. pneumoniae isolates. Overall, the results of this study fill prior gaps in understanding the K. pneumoniae genomes derived from aquatic animals. Full article
(This article belongs to the Special Issue Generation of Genome-Wide Genetic Data and Evolutionary Analyses)
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20 pages, 8019 KiB  
Article
Comprehensive Genomic Analysis of G2-like Transcription Factor Genes and Their Role in Development and Abiotic Stresses in Arabidopsis
by Intikhab Alam, Xueting Wu, Qianxia Yu and Liangfa Ge
Diversity 2022, 14(3), 228; https://doi.org/10.3390/d14030228 - 20 Mar 2022
Cited by 12 | Viewed by 3972
Abstract
GOLDEN2-LIKE (GLK) transcription factors are a subfamily of GARP family transcription factors, which play an essential function in plant growth and development as well as stress response during abiotic and biotic stress conditions. This study reports GLK genes in the Arabidopsis thaliana genome [...] Read more.
GOLDEN2-LIKE (GLK) transcription factors are a subfamily of GARP family transcription factors, which play an essential function in plant growth and development as well as stress response during abiotic and biotic stress conditions. This study reports GLK genes in the Arabidopsis thaliana genome in-depth and identified 55 AtGLK genes in the Arabidopsis genome. Phylogenetic analyses resolved these GLK gene clusters into seven groups. A Ka/Ks ratios analysis indicated that they had experienced purifying selection. Many essential cis elements are present in the promoter regions of AtGLK genes associated with plant hormones, light, and stress. The expression profile from RNA-Seq data revealed that 29.1% of them had relatively high expression in all tested tissues or organs, indicating their crucial housekeeping function in plant growth and development. However, many other GLK members were selectively expressed in particular tissues or organs. In silico study of the transcriptional regulation of AtGLKs indicated that it is strongly regulated by cold, drought, osmotic, salt, and metal ion stressors. Our research provides essential information for the functional studies of each GLK gene in different species in the future. Full article
(This article belongs to the Special Issue Generation of Genome-Wide Genetic Data and Evolutionary Analyses)
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26 pages, 1549 KiB  
Article
Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
by Emily L. Gordon, Rebecca T. Kimball and Edward L. Braun
Diversity 2021, 13(11), 555; https://doi.org/10.3390/d13110555 - 1 Nov 2021
Cited by 3 | Viewed by 3780
Abstract
Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or [...] Read more.
Phylogenomic analyses have revolutionized the study of biodiversity, but they have revealed that estimated tree topologies can depend, at least in part, on the subset of the genome that is analyzed. For example, estimates of trees for avian orders differ if protein-coding or non-coding data are analyzed. The bird tree is a good study system because the historical signal for relationships among orders is very weak, which should permit subtle non-historical signals to be identified, while monophyly of orders is strongly corroborated, allowing identification of strong non-historical signals. Hydrophobic amino acids in mitochondrially-encoded proteins, which are expected to be found in transmembrane helices, have been hypothesized to be associated with non-historical signals. We tested this hypothesis by comparing the evolution of transmembrane helices and extramembrane segments of mitochondrial proteins from 420 bird species, sampled from most avian orders. We estimated amino acid exchangeabilities for both structural environments and assessed the performance of phylogenetic analysis using each data type. We compared those relative exchangeabilities with values calculated using a substitution matrix for transmembrane helices estimated using a variety of nuclear- and mitochondrially-encoded proteins, allowing us to compare the bird-specific mitochondrial models with a general model of transmembrane protein evolution. To complement our amino acid analyses, we examined the impact of protein structure on patterns of nucleotide evolution. Models of transmembrane and extramembrane sequence evolution for amino acids and nucleotides exhibited striking differences, but there was no evidence for strong topological data type effects. However, incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit. Thus, we believe that considering protein structure will improve analyses of mitogenomic data, both in birds and in other taxa. Full article
(This article belongs to the Special Issue Generation of Genome-Wide Genetic Data and Evolutionary Analyses)
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