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Diversity
Special Issues
Genome Sequence and Analysis for Animal Ecology and Evolution
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Genome Sequence and Analysis for Animal Ecology and Evolution

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

Deadline for manuscript submissions: closed (29 August 2024) | Viewed by 7135

Special Issue Editor

Prof. Dr. Hyun Park

E-Mail Website
Guest Editor
Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
Interests: biotechnology; genome sequencing; eDNA

Special Issue Information

Dear Colleagues,

The study of animal ecology and evolution has significantly benefited from recent advancements in genome sequencing technologies. With the ability to sequence and analyze entire genomes, researchers are able to investigate the genetic basis of adaptations, trace evolutionary history, and study the interactions between organisms and their environment. This Special Issue aims to showcase the latest research on genome sequence and analysis in animal ecology and evolution.

The Special Issue will feature original research articles, reviews, and perspectives on the latest developments in animal genome sequencing and analysis. We welcome contributions from researchers working on a variety of animal taxa, including vertebrates and invertebrates, and utilizing various sequencing and analysis approaches. This Special Issue aims to provide a comprehensive overview of the state of the art in animal genome sequencing and analysis for the study of ecology and evolution.

The Special Issue will cover a broad range of topics, including but not limited to:

  • De novo genome sequencing information of new species or improved re-sequencing information of known species.
  • Comparative genomics of animals from different environments and habitats, highlighting the genetic basis of adaptation to different ecological niches.
  • Phylogenetic analysis of animal genomes to understand the evolutionary relationships between species and the timing of major evolutionary events.
  • Genome-wide association studies and quantitative trait locus analysis to identify the genetic basis of complex traits in animals, such as disease resistance, behavior, and morphology.
  • Studies on the impact of environmental change on animal populations and their genomes, including the effects of climate change and habitat fragmentation.
  • Genomic approaches to conservation biology, including the identification of genetic markers for population monitoring and management.

Prof. Dr. Hyun Park
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 sequencing
  • comparative genomics
  • genome-wide association studies
  • transcriptomic
  • adaptation
  • phylogenetic analysis of animal genomes
  • ecology and evolution
  • diversity and speciation

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Published Papers (4 papers)

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Research

11 pages, 2064 KiB  
Article
Annotation and Characterization of the Zacco platypus Genome
by Sang-Eun Nam, Dae-Yeul Bae and Jae-Sung Rhee
Diversity 2024, 16(9), 529; https://doi.org/10.3390/d16090529 - 1 Sep 2024
Viewed by 546
Abstract
The pale chub Zacco platypus (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of [...] Read more.
The pale chub Zacco platypus (Cypriniformes; Xenocyprididae; Jordan & Evermann, 1902) is widely distributed across freshwater ecosystems in East Asia and has been recognized as a potential model fish species for ecotoxicology and environmental monitoring. Here, a high-quality de novo genome assembly of Z. platypus was constructed through the integration of a combination of long-read Pacific Bioscience (PacBio) sequencing, short-read Illumina sequencing, and Hi-C sequencing technologies. Z. platypus has the smallest genome size compared to other species belonging to the order Cypriniformes. The assembled genome encompasses 41.45% repeat sequences. As shown in other fish, a positive correlation was observed between genome size and the composition of transposable elements (TE) in the genome. Among TEs, a relatively higher rate of DNA transposon was observed, which is a common pattern in the members of the order Cypriniformes. Functional annotation was processed using four representative databases, identifying a core set of 12,907 genes shared among them. Orthologous gene family analysis revealed that Z. platypus has experienced more gene family contraction rather than expansion compared to other Cypriniformes species. Among the uniquely expanded gene families in Z. platypus, detoxification and stress-related gene families were identified, suggesting that this species could represent a promising model for ecotoxicology and environmental monitoring. Taken together, the Z. platypus genome assembly will provide valuable data for omics-based health assessments in aquatic ecosystems, offering further insights into the environmental and ecological facets within this species. Full article
(This article belongs to the Special Issue Genome Sequence and Analysis for Animal Ecology and Evolution)
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16 pages, 2044 KiB  
Article
Mining NCBI Sequence Read Archive Database: An Untapped Source of Organelle Genomes for Taxonomic and Comparative Genomics Research
by Vahap Eldem and Mehmet Ali Balcı
Diversity 2024, 16(2), 104; https://doi.org/10.3390/d16020104 - 6 Feb 2024
Cited by 1 | Viewed by 2281
Abstract
The NCBI SRA database is constantly expanding due to the large amount of genomic and transcriptomic data from various organisms generated by next-generation sequencing, and re-searchers worldwide regularly deposit new data into the database. This high-coverage genomic and transcriptomic information can be re-evaluated [...] Read more.
The NCBI SRA database is constantly expanding due to the large amount of genomic and transcriptomic data from various organisms generated by next-generation sequencing, and re-searchers worldwide regularly deposit new data into the database. This high-coverage genomic and transcriptomic information can be re-evaluated regardless of the original research subject. The database-deposited NGS data can offer valuable insights into the genomes of organelles, particularly for non-model organisms. Here, we developed an automated bioinformatics workflow called “OrgaMiner”, designed to unveil high-quality mitochondrial and chloroplast genomes by data mining the NCBI SRA database. OrgaMiner, a Python-based pipeline, automatically orchestrates various tools to extract, assemble, and annotate organelle genomes for non-model organisms without available organelle genome sequences but with data in the NCBI SRA. To test the usability and feasibility of the pipeline, “mollusca” was selected as a keyword, and 76 new mitochondrial genomes were de novo assembled and annotated automatically without writing one single code. The applicability of the pipeline can be expanded to identify organelles in diverse invertebrate, vertebrate, and plant species by simply specifying the taxonomic name. OrgaMiner provides an easy-to-use, end-to-end solution for biologists mainly working with taxonomy and population genetics. Full article
(This article belongs to the Special Issue Genome Sequence and Analysis for Animal Ecology and Evolution)
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12 pages, 1724 KiB  
Article
De Novo Genome Assembly of the Sea Star Patiria pectinifera (Muller & Troschel, 1842) Using Oxford Nanopore Technology and Illumina Platforms
by Jae-Sung Rhee, Sang-Eun Nam, Seung Jae Lee and Hyun Park
Diversity 2024, 16(2), 91; https://doi.org/10.3390/d16020091 - 31 Jan 2024
Viewed by 1833
Abstract
The sea star Patiria pectinifera (Asteroidea; Asterinidae; homotypic synonym: Asterina pectinifera; Muller & Troschel, 1842) is widely distributed in the coastal regions of the Seas of East Asia and the northern Pacific Ocean. Here, a de novo genome sequence of P. pectinifera [...] Read more.
The sea star Patiria pectinifera (Asteroidea; Asterinidae; homotypic synonym: Asterina pectinifera; Muller & Troschel, 1842) is widely distributed in the coastal regions of the Seas of East Asia and the northern Pacific Ocean. Here, a de novo genome sequence of P. pectinifera as a reference for fundamental and applied research was constructed by employing a combination of long-read Oxford Nanopore Technology (ONT) PromethION, short-read Illumina platforms, and 10 × Genomics. The draft genome of P. pectinifera, containing 13,848,344 and 156,878,348 contigs from ONT and Illumina platforms, respectively, was obtained. Assembly with CANU resulted in 2262 contigs with an N50 length of 367 kb. Finally, ARCS + LINKS assembly combined these contigs into 328 scaffolds, totaling 499 Mb with an N50 length of 2 Mbp. The estimated genome size by GenomeScope analysis was 461 Mb. BUSCO analysis indicated that 930 (97.5%) of the expected genes were found in the assembly, with 889 (93.2%) being single-copy and 41 (4.3%) duplicated after searching against the metazoan database. Annotation, utilizing sequences obtained from Illumina RNA-Seq and Pacific Biosciences Iso-Seq, led to the identification of 22,367 protein-coding genes. When examining the orthologous relationship of P. pectinifera against the scaffolds of the common sea star Patiria miniata, high contiguity was observed. Annotation of repeat elements highlighted an enrichment of 1,121,079 transposable elements, constituting 47% of the genome, suggesting their potential role in shaping the genome structure of P. pectinifera. This de novo genome assembly is expected to be a valuable resource for future studies, providing insight into the developmental, environmental, and ecological aspects of P. pectinifera biology. Full article
(This article belongs to the Special Issue Genome Sequence and Analysis for Animal Ecology and Evolution)
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11 pages, 8201 KiB  
Communication
The First Mitochondrial Genome of an Odonata Endemic to South America, Chalcopteryx rutilans (Rambur, 1842) (Odonata: Polythoridae), and Its Implications for the Phylogeny of the Zygoptera
by Leandro Juen, Ricardo Koroiva, Fernando Geraldo de Carvalho, Cristian Camilo Mendoza-Penagos, Joás da Silva Brito, Lenize Batista Calvão, Victor Rennan Santos Ferreira, Ândrea Ribeiro-dos-Santos, Caio S. Silva, Sávio Guerreiro, Giovanna C. Cavalcante, Leandro Magalhães, Jorge E. S. de Souza, Daniel H. F. Gomes, Luciano Fogaça de Assis Montag, Thaisa S. Michelan and Raphael Ligeiro
Diversity 2023, 15(8), 908; https://doi.org/10.3390/d15080908 - 1 Aug 2023
Cited by 1 | Viewed by 1817
Abstract
Chalcopteryx rutilans Rambur, 1842 (Polythoridae, Odonata) is a species widely distributed in central Amazonia. Due to its sensitivity to environmental changes, it is a bioindicator species used to evaluate the environmental conditions of streams in federally protected areas. By sequencing C. rutilans mitogenome, [...] Read more.
Chalcopteryx rutilans Rambur, 1842 (Polythoridae, Odonata) is a species widely distributed in central Amazonia. Due to its sensitivity to environmental changes, it is a bioindicator species used to evaluate the environmental conditions of streams in federally protected areas. By sequencing C. rutilans mitogenome, we report the first whole mitogenome from the Polythoridae family and the first from an Odonata species endemic to South America. The entire mitogenome has 15,653 bp and contains 13 protein-coding, 22 tRNA, and two rRNA genes. The nucleotide composition of the mitogenome is 42.7%, T: 25.5%, C: 19.4%, and G: 12.4%. The AT and GC skews of the mitogenome sequence were 0.249 and −0.220, respectively. C. rutilans was recovered as a sister to Pseudolestes mirabilis Kirby, 1900 (Pseudolestidae), demonstrating the absence of mitogenomes of species from multiple families in the current literature. Mitogenome data from this study will provide useful information for further studies on the phylogeny and conservation of Polythoridae. Full article
(This article belongs to the Special Issue Genome Sequence and Analysis for Animal Ecology and Evolution)
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