Genomics in Biodiversity Conservation (Vertebrates and Invertebrates)

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Molecular Genetics".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 1957

Special Issue Editors


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Guest Editor
1. Ocean and Fisheries Development International Cooperation Institute, College of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
2. International Graduate Program of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea
Interests: biodiversity genomics; bioinformatics; conservation genetics

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Guest Editor
1. Department of Marine Biology, Pukyong National University, Busan 48513, Republic of Korea
2. Marine Integrated Biomedical Technology Center, National Key Research Institutes in Universities, Pukyong National University, Busan 48513, Republic of Korea
Interests: environmental DNA; metabarcoding; genetic resources
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Special Issue Information

Dear Colleagues,

In recent years, the application of genetics and genomics has significantly advanced conservation genetics, offering new tools with which to understand and preserve biodiversity in both vertebrates and invertebrates. Technological breakthroughs have made DNA sequencing faster and more cost-effective, allowing the accumulation of extensive genomic data critical for assessing genetic diversity within and between populations. Mitochondrial genomes have emerged as essential in this context due to their high mutation rates and maternal inheritance patterns, providing insights into population structure, phylogenetic relationships, and species identification. The unique gene arrangements found within mitogenomes are valuable for uncovering evolutionary processes and historical biogeography. These genomic signatures not only facilitate the study of genetic diversity, which is crucial for identifying vulnerable populations, but also aid in understanding how species adapt and evolve in response to environmental changes. However, these insights also underscore the complexity of conservation challenges, as genome plasticity, driven by factors such as transposable elements, can influence species resilience and adaptability, making it vital to integrate genetic data into conservation strategies for effective species management.

In this Special Issue, we propose a collection of works on the possible applications of genetics and genomics to biomolecules in the study of vertebrates and invertebrates.

Both research (in particular) and review articles proposing novelties or overviews, respectively, are welcome.

Dr. Shantanu Kundu
Prof. Dr. Hyun-Woo Kim
Guest Editors

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Keywords

  • genomics
  • mitochondrial genome
  • genetic diversity
  • phylogenetic analyses
  • conservation genetics
  • gene arrangements
  • evolution

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Published Papers (2 papers)

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Research

17 pages, 3590 KiB  
Article
Comparative Transcriptomic Analysis Provides Insight into Spatiotemporal Expression Patterns of Pivotal Genes During Critical Growth Stages in Min Pig Breed
by Miao Yu, Guandong Wu, Yang Chang, Jiancheng Cai, Chunan Wang, Dongjie Zhang and Chunzhu Xu
Biomolecules 2025, 15(2), 180; https://doi.org/10.3390/biom15020180 - 26 Jan 2025
Viewed by 706
Abstract
The growth and development of animals are dynamic processes characterized by fluctuations. Min pigs, a local breed renowned for their superior meat quality, present an intriguing yet poorly understood relationship between this quality and their growth and development patterns. To elucidate this relationship, [...] Read more.
The growth and development of animals are dynamic processes characterized by fluctuations. Min pigs, a local breed renowned for their superior meat quality, present an intriguing yet poorly understood relationship between this quality and their growth and development patterns. To elucidate this relationship, we employed a multi-faceted approach that included comparative transcriptomics, quantitative real-time PCR (qRT-PCR), selection pressure analysis of key genes, and three-dimensional protein structure simulations. Our findings revealed that 150 days (150 d) of age represented a pivotal turning point in the growth and development of Min pigs. Thirteen key genes exhibiting significant differential expression between early and late growth stages were identified. Notably, the CDK2 gene demonstrated specific high expression in the hind limb muscles and adipose tissues during the later growth stages. Comparative analysis with the African warthog revealed that while the CDK2 protein structure remained conserved, base mutations in upstream and downstream non-coding regions resulted in strong positive selection pressure on the CDK2 gene. These results suggest that CDK2 plays a crucial role in defining the spatiotemporal characteristics of meat development during the domestication of Min pigs. This study provides critical insights into the growth and development patterns of domestic pigs and offers a robust scientific foundation for improving meat quality traits through domestication. Full article
(This article belongs to the Special Issue Genomics in Biodiversity Conservation (Vertebrates and Invertebrates))
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13 pages, 3304 KiB  
Article
Complete Mitochondrial Genome of Niphon spinosus (Perciformes: Niphonidae): Genome Characterization and Phylogenetic Analysis
by Maheshkumar Prakash Patil, Jong-Oh Kim, Seung Hyun Yoo, Jiyoung Shin, Ji-Young Yang, Kyunghoi Kim and Gun-Do Kim
Biomolecules 2025, 15(1), 52; https://doi.org/10.3390/biom15010052 - 2 Jan 2025
Viewed by 855
Abstract
The species Niphon spinosus (Cuvier, 1829) is the only representative of the family Niphonidae and the genus Niphon, and its taxonomic history is complicated; it is still unclear in a phylogenetic sense. In this study, we report the complete mitochondrial genome of [...] Read more.
The species Niphon spinosus (Cuvier, 1829) is the only representative of the family Niphonidae and the genus Niphon, and its taxonomic history is complicated; it is still unclear in a phylogenetic sense. In this study, we report the complete mitochondrial genome of N. spinosus (OP391482), which was determined to be 16,503 bp long with biased A + T contents (53.8%) using next-generation technology. The typical set of 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one control region (D-loop) are included in the mitochondrial genome. The H-strand encoded 28 genes (14 tRNA, 2 rRNA, and 12 PCGs), and D-loop, whereas the L-strand encoded the remaining 9 genes (8 tRNA and ND6). Its nucleotide composition, gene arrangement, codon usage patterns, and tRNA secondary structures are identical with other members of the Percoidei suborder. Furthermore, we reconstructed phylogenetic trees based on the 13 PCGs. The resulting phylogenetic trees showed N. spinosus placing as a separate lineage within the family Niphonidae, its close relationship to Trachinus draco (Trachinidae), and the clustering of major subfamilies like Luciopercinae and Percinae of the Percoidei suborder. These findings will contribute to future studies on the evolutionary history, population genetics, molecular taxonomy, and phylogeny of N. spinosus and related species. Full article
(This article belongs to the Special Issue Genomics in Biodiversity Conservation (Vertebrates and Invertebrates))
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