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Genes
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Genetic Improvement of Aquatic Species
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Genetic Improvement of Aquatic Species

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

Deadline for manuscript submissions: closed (25 May 2024) | Viewed by 8983

Special Issue Editor

Prof. Dr. Zhiqiang Han

E-Mail Website
Guest Editor
Fishery College, Zhejiang Ocean University, Zhoushan, China
Interests: population genetics; genomics; phylogenetics; transcriptomics; evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Aquatic species are of great importance for maintaining the ecological stability, function and services of marine and freshwater ecosystems, and for supplying food resources for human beings. Given the high biodiversity and diverse phenotypic and biological features, comparative genetics studies of wild and cultured aquatic species are widely performed for genetic diversity estimation, functional gene mining, gene expression analyses, among others, and can provide essential information for further genetic and selective breeding. The advancement of next-generation sequencing techniques and bioinformatics analytical methods largely facilitate the evolutionary and developmental biology of aquatic species by using multi-omics approaches, especially for species with high-quality reference genome sequences.

Research articles and reviews focusing on comparative genetics analyses of aquatic species, especially using high-throughput techniques including RNA-seq, genotyping-by-sequencing, RAD-seq, and whole-genome resequencing, will be appreciated, as well as manuscripts covering other genetic studies of aquatic species.

Prof. Dr. Zhiqiang Han
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. 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 2600 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

  • aquatic species
  • comparative genetics
  • genomics
  • transcriptomics
  • genetic diversity

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Published Papers (4 papers)

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Research

12 pages, 4128 KiB  
Article
Comparative Studies on Duplicated foxl2 Paralogs in Spotted Knifejaw Oplegnathus punctatus Show Functional Diversification
by Xinxin Du, Haiyang Yu, Yujue Wang, Jinxiang Liu and Quanqi Zhang
Genes 2023, 14(10), 1847; https://doi.org/10.3390/genes14101847 - 23 Sep 2023
Viewed by 1484
Abstract
As a member of the forkhead box L gene family, foxl2 plays a significant role in gonadal development and the regulation of reproduction. During the evolution of deuterostome, whole genome duplication (WGD)-enriched lineage diversifications and regulation mechanisms occurs. However, only limited research exists [...] Read more.
As a member of the forkhead box L gene family, foxl2 plays a significant role in gonadal development and the regulation of reproduction. During the evolution of deuterostome, whole genome duplication (WGD)-enriched lineage diversifications and regulation mechanisms occurs. However, only limited research exists on foxl2 duplication in teleost or other vertebrate species. In this study, two foxl2 paralogs, foxl2 and foxl2l, were identified in the transcriptome of spotted knifejaw (Oplegnathus punctatus), which had varying expressions in the gonads. The foxl2 was expressed higher in the ovary, while foxl2l was expressed higher in the testis. Phylogenetic reconstruction, synteny analysis, and the molecular evolution test confirmed that foxl2 and foxl2l likely originated from the first two WGD. The expression patterns test using qRT-PCR and ISH as well as motif scan analysis revealed evidence of potentially functional divergence between the foxl2 and foxl2l paralogs in spotted knifejaw. Our results indicate that foxl2 and foxl2l may originate from the first two WGD, be active in transcription, and have undergone functional divergence. These results shed new light on the evolutionary trajectories of foxl2 and foxl2l and highlights the need for further detailed functional analysis of these two duplicated paralogs. Full article
(This article belongs to the Special Issue Genetic Improvement of Aquatic Species)
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15 pages, 4904 KiB  
Article
Hsp70 Gene Family in Sebastiscus marmoratus: The Genome-Wide Identification and Transcriptome Analysis under Thermal Stress
by Xiaolu Han, Shihuai Jin, Chenyan Shou and Zhiqiang Han
Genes 2023, 14(9), 1779; https://doi.org/10.3390/genes14091779 - 9 Sep 2023
Cited by 7 | Viewed by 1885
Abstract
Heat shock protein 70 kDa (Hsp70) is a highly conserved heat stress protein that is important in biotic processes and responses to abiotic stress. Hsp70 genes may be important in Sebastiscus marmoratus, for it is a kind of nearshore reef fish, and habitat [...] Read more.
Heat shock protein 70 kDa (Hsp70) is a highly conserved heat stress protein that is important in biotic processes and responses to abiotic stress. Hsp70 genes may be important in Sebastiscus marmoratus, for it is a kind of nearshore reef fish, and habitat temperature change is more drastic during development. However, genome-wide identification and expression analysis in the Hsp70 gene family of S. marmoratus are still lacking. Here, a total of 15 Hsp70 genes in the genome of S. marmoratus are identified, and their expression patterns were investigated using transcriptomic data from thermal stress experiments. The expansion and gene duplication events of Hsp70 genes from the Hspa4, Hspa8, and Hspa12a subfamilies in S. marmoratus are revealed by phylogenetic analysis. qRT-PCR expression patterns demonstrated that seven Hsp70 genes were significantly up-regulated and none were significantly down-regulated after heat treatment. Only the hsp70 gene was significantly up-regulated after cold treatment. The selection test further showed a purifying selection on the duplicated gene pairs, suggesting that these genes underwent subfunctionalization. Our results add novel insight to aquaculture and biological research on S. marmoratus, providing important information on how Hsp70 genes are regulated in Scorpaeniformes under thermal stress. Full article
(This article belongs to the Special Issue Genetic Improvement of Aquatic Species)
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10 pages, 1983 KiB  
Article
A High-Quality Chromosome-Level Genome Assembly of a Snail Cipangopaludina cathayensis (Gastropoda: Viviparidae)
by Benhe Ma, Wu Jin, Huiyun Fu, Bing Sun, Su Yang, Xueyan Ma, Haibo Wen, Xiaoping Wu, Haihua Wang and Xiaojuan Cao
Genes 2023, 14(7), 1365; https://doi.org/10.3390/genes14071365 - 28 Jun 2023
Cited by 1 | Viewed by 2708
Abstract
Cipangopaludina cathayensis (Gastropoda: Prosobranchia; Mesogastropoda; Viviparidae) is widely distributed in the freshwater habitats of China. It is an economically important snail with high edible and medicinal value. However, the genomic resources and the reference genome of this snail are lacking. In this study, [...] Read more.
Cipangopaludina cathayensis (Gastropoda: Prosobranchia; Mesogastropoda; Viviparidae) is widely distributed in the freshwater habitats of China. It is an economically important snail with high edible and medicinal value. However, the genomic resources and the reference genome of this snail are lacking. In this study, we assembled the first chromosome-level genome of C. cathayensis. The preliminary assembly genome was 1.48 Gb in size, with a contig N50 size of 93.49 Mb. The assembled sequences were anchored to nine pseudochromosomes using Hi-C data. The final genome after Hi-C correction was 1.48 Gb, with a contig N50 of 98.49 Mb and scaffold N50 of 195.21 Mb. The anchored rate of the chromosome was 99.99%. A total of 22,702 protein-coding genes were predicted. Phylogenetic analyses indicated that C. cathayensis diverged with Bellamya purificata approximately 158.10 million years ago. There were 268 expanded and 505 contracted gene families in C. cathayensis when compared with its most recent common ancestor. Five putative genes under positive selection in C. cathayensis were identified (false discovery rate <0.05). These genome data provide a valuable resource for evolutionary studies of the family Viviparidae, and for the genetic improvement of C. cathayensis. Full article
(This article belongs to the Special Issue Genetic Improvement of Aquatic Species)
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23 pages, 3651 KiB  
Article
Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of Lepturacanthus savala
by Ren-Xie Wu, Ben-Ben Miao, Fang-Yuan Han, Su-Fang Niu, Yan-Shan Liang, Zhen-Bang Liang and Qing-Hua Wang
Genes 2023, 14(6), 1268; https://doi.org/10.3390/genes14061268 - 15 Jun 2023
Cited by 2 | Viewed by 2254
Abstract
Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. [...] Read more.
Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. savala genome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in the L. savala genome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms in L. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics of L. savala from a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies of L. savala and whole-genome analyses of other trichiurid fishes. Full article
(This article belongs to the Special Issue Genetic Improvement of Aquatic Species)
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