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Wildlife Genomics and Genetic Diversity
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Wildlife Genomics and Genetic Diversity

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

Deadline for manuscript submissions: closed (15 March 2024) | Viewed by 15055

Special Issue Editor

Dr. Wenping Zhang

E-Mail Website
Guest Editor
Key Laboratory of Monitoring Biological Diversity in Minshan Mountain of National Park of Giant Pandas, College of Life Science & Biotechnology, Mianyang Normal University, Mianyang 621000, China
Interests: genetic diversity; genome; population genetics; metagenome; evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Biodiversity is a key component of ecosystems, responsible for driving variation in ecosystem productivity, stability and resilience. The ecological consequences of genetic diversity, therefore, lie at the core of efforts to understand the links between biodiversity and ecosystem function. The nature of genomics and genetic diversity in wildlife has always been the basic problem of evolutionary genetics, as well as gene flow, population depression, population growth, and so on. However, despite its cardinal role in evolutionary theory and application, the maintenance of genetic diversity remains largely enigmatic, notwithstanding the dramatic discoveries of molecular biology, which revealed the abundant genetic diversity in nature. Moreover, it is not clear how widely the ecological effects of genetic diversity apply in wildlife and little is known about the relative importance of genetic diversity vs. other factors that influence the ecological processes of interest in wildlife.

Therefore, this Special Issue will focus on the genomics and genetic diversity of wildlife, including animals, plants, and microorganisms and will aim to fill these gaps in research by evaluating the following aspects: (1) the genomics and genetic diversity in wildlife through all kinds of molecular markers, (2) the mechanisms by which environment- and genetic-driven trait variation occur in wildlife, (3) the ecological and evolutionary consequences of genotypic diversity effects on interactions in wildlife, (4) the genetic diversity consequences among stress factors; (5) the linkages between the evolutionary forces that shape the expression of additive genetic variation and ecological genetic diversity effects.

Dr. Wenping Zhang
Guest Editor

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Keywords

  • animal
  • plant
  • microorganism
  • genome
  • metagenome
  • genetic diversity
  • genomics diversity
  • molecular marker
  • mitochondrial DNA
  • chloroplast DNA

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Published Papers (6 papers)

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Research

14 pages, 2087 KiB  
Article
Insights for the Captive Management of South China Tigers Based on a Large-Scale Genetic Survey
by Wenping Zhang, Kaixiong Lin, Wenyuan Fu, Junjin Xie, Xueyang Fan, Mingchun Zhang, Hongxing Luo, Yuzhong Yin, Qiang Guo, He Huang, Tengteng Chen, Xipan Lin, Yaohua Yuan, Cheng Huang and Shizhang Du
Genes 2024, 15(4), 398; https://doi.org/10.3390/genes15040398 - 24 Mar 2024
Viewed by 1806
Abstract
There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from [...] Read more.
There is an urgent need to find a way to improve the genetic diversity of captive South China tiger (SCT, Panthera tigris amoyensis), the most critically endangered taxon of living tigers, facing inbreeding depression. The genomes showed that 13 hybrid SCTs from Meihuashan were divided into two groups; one group included three individuals who had a closer relationship with pureblood SCTs than another group. The three individuals shared more that 40% of their genome with pureblood SCTs and might be potential individuals for genetic rescuing in SCTs. A large-scale genetic survey based on 319 pureblood SCTs showed that the mean microsatellite inbreeding coefficient of pureblood SCTs decreased significantly from 0.1789 to 0.0600 (p = 0.000009) and the ratio of heterozygous loci increased significantly from 38.5% to 43.2% (p = 0.02) after one individual of the Chongqing line joined the Suzhou line and began to breed in the mid-1980s, which is a reason why the current SCTs keep a moderate level of microsatellite heterozygosity and nucleotide diversity. However, it is important to establish a back-up population based on the three individuals through introducing one pureblood SCT into the back-up population every year. The back-up population should be an important reserve in case the pureblood SCTs are in danger in the future. Full article
(This article belongs to the Special Issue Wildlife Genomics and Genetic Diversity)
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27 pages, 15501 KiB  
Article
Revisiting the Asian Buffalo Leech (Hirudinaria manillensis) Genome: Focus on Antithrombotic Genes and Their Corresponding Proteins
by Zichao Liu, Fang Zhao, Zuhao Huang, Qingmei Hu, Renyuan Meng, Yiquan Lin, Jianxia Qi and Gonghua Lin
Genes 2023, 14(11), 2068; https://doi.org/10.3390/genes14112068 - 12 Nov 2023
Cited by 7 | Viewed by 3024
Abstract
Leeches are well-known annelids due to their obligate blood-feeding habits. Some leech species secrete various biologically active substances which have important medical and pharmaceutical value in antithrombotic treatments. In this study, we provided a high-quality genome of the Asian buffalo leech (Hirudinaria [...] Read more.
Leeches are well-known annelids due to their obligate blood-feeding habits. Some leech species secrete various biologically active substances which have important medical and pharmaceutical value in antithrombotic treatments. In this study, we provided a high-quality genome of the Asian buffalo leech (Hirudinaria manillensis), based on which we performed a systematic identification of potential antithrombotic genes and their corresponding proteins. Combining automatic and manual prediction, we identified 21 antithrombotic gene families including fourteen coagulation inhibitors, three platelet aggregation inhibitors, three fibrinolysis enhancers, and one tissue penetration enhancer. A total of 72 antithrombotic genes, including two pseudogenes, were identified, including most of their corresponding proteins forming three or more disulfide bonds. Three protein families (LDTI, antistasin, and granulin) had internal tandem repeats containing 6, 10, and 12 conserved cysteines, respectively. We also measured the anticoagulant activities of the five identified hirudins (hirudin_Hman1 ~ hirudin_Hman5). The results showed that three (hirudin_Hman1, hirudin_Hman2, and hirudin_Hman5), but not the remaining two, exhibited anticoagulant activities. Our study provides the most comprehensive collection of antithrombotic biomacromolecules from a leech to date. These results will greatly facilitate the research and application of leech derivatives for medical and pharmaceutical purposes in the treatment of thrombotic diseases. Full article
(This article belongs to the Special Issue Wildlife Genomics and Genetic Diversity)
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11 pages, 1518 KiB  
Article
The Draft Genome of the “Golden Tide” Seaweed, Sargassum horneri: Characterization and Comparative Analysis
by Shengqin Wang and Mingjiang Wu
Genes 2023, 14(10), 1969; https://doi.org/10.3390/genes14101969 - 21 Oct 2023
Cited by 2 | Viewed by 2091
Abstract
Sargassum horneri, a prevalent species of brown algae found along the coast of the northwest Pacific Ocean, holds significant importance as a valuable source of bioactive compounds. However, its rapid growth can lead to the formation of a destructive “golden tide”, causing [...] Read more.
Sargassum horneri, a prevalent species of brown algae found along the coast of the northwest Pacific Ocean, holds significant importance as a valuable source of bioactive compounds. However, its rapid growth can lead to the formation of a destructive “golden tide”, causing severe damage to the local economy and coastal ecosystems. In this study, we carried out de novo whole-genome sequencing of S. horneri using next-generation sequencing to unravel the genetic information of this alga. By utilizing a reference-guided de novo assembly pipeline with a closely related species, we successfully established a final assembled genome with a total length of 385 Mb. Repetitive sequences made up approximately 30.6% of this genome. Among the identified putative genes, around 87.03% showed homology with entries in the NCBI non-redundant protein database, with Ectocarpus siliculosus being the most closely related species for approximately one-third of these genes. One gene encoding an alkaline phosphatase family protein was found to exhibit positive selection, which could give a clue for the formation of S. horneri golden tides. Additionally, we characterized putative genes involved in fucoidan biosynthesis metabolism, a significant pathway in S. horneri. This study represents the first genome-wide characterization of a S. horneri species, providing crucial insights for future investigations, such as ecological genomic analyses. Full article
(This article belongs to the Special Issue Wildlife Genomics and Genetic Diversity)
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8 pages, 870 KiB  
Communication
An Enhanced Method for the Use of Reptile Skin Sheds as a High-Quality DNA Source for Genome Sequencing
by Yeyizhou Fu, Yan Zhuang, Shu-Jin Luo and Xiao Xu
Genes 2023, 14(9), 1678; https://doi.org/10.3390/genes14091678 - 25 Aug 2023
Viewed by 2352
Abstract
With the emergence of high-throughput sequencing technology, a number of non-avian reptile species have been sequenced at the genome scale, shedding light on various scientific inquiries related to reptile ecology and evolution. However, the routine requirement of tissue or blood samples for genome [...] Read more.
With the emergence of high-throughput sequencing technology, a number of non-avian reptile species have been sequenced at the genome scale, shedding light on various scientific inquiries related to reptile ecology and evolution. However, the routine requirement of tissue or blood samples for genome sequencing often poses challenges in many elusive reptiles, hence limiting the application of high-throughput sequencing technologies to reptile studies. An alternative reptilian DNA resource suitable for genome sequencing is in urgent need. Here, we used the corn snake (Pantherophis guttatus) as a reptile model species to demonstrate that the shed skin is a high-quality DNA source for genome sequencing. Skin sheds provide a noninvasive type of sample that can be easily collected without restraining or harming the animal. Our findings suggest that shed skin from corn snakes yields DNA of sufficient quantity and quality that are comparable to tissue DNA extracts. Genome sequencing data analysis revealed that shed skin DNA is subject to bacteria contamination at variable levels, which is a major issue related to shed skin DNA and may be addressed by a modified DNA extraction method through introduction of a 30 min pre-digestion step. This study provides an enhanced method for the use of reptile shed skins as a high-quality DNA source for whole genome sequencing. Utilizing shed skin DNA enables researchers to overcome the limitations generally associated with obtaining traditional tissue or blood samples and promises to facilitate the application of genome sequencing in reptilian research. Full article
(This article belongs to the Special Issue Wildlife Genomics and Genetic Diversity)
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11 pages, 3731 KiB  
Article
Evolutionary Adaptation of Genes Involved in Galactose Derivatives Metabolism in Oil-Tea Specialized Andrena Species
by Gonghua Lin, Zuhao Huang, Bo He, Kai Jiang, Tianjuan Su and Fang Zhao
Genes 2023, 14(5), 1117; https://doi.org/10.3390/genes14051117 - 22 May 2023
Cited by 1 | Viewed by 2373
Abstract
Oil-tea (Camellia oleifera) is a woody oil crop whose nectar includes galactose derivatives that are toxic to honey bees. Interestingly, some mining bees of the genus Andrena can entirely live on the nectar (and pollen) of oil-tea and are able to [...] Read more.
Oil-tea (Camellia oleifera) is a woody oil crop whose nectar includes galactose derivatives that are toxic to honey bees. Interestingly, some mining bees of the genus Andrena can entirely live on the nectar (and pollen) of oil-tea and are able to metabolize these galactose derivatives. We present the first next-generation genomes for five and one Andrena species that are, respectively, specialized and non-specialized oil-tea pollinators and, combining these with the published genomes of six other Andrena species which did not visit oil-tea, we performed molecular evolution analyses on the genes involved in the metabolizing of galactose derivatives. The six genes (NAGA, NAGA-like, galM, galK, galT, and galE) involved in galactose derivatives metabolism were identified in the five oil-tea specialized species, but only five (with the exception of NAGA-like) were discovered in the other Andrena species. Molecular evolution analyses revealed that NAGA-like, galK, and galT in oil-tea specialized species appeared under positive selection. RNASeq analyses showed that NAGA-like, galK, and galT were significantly up-regulated in the specialized pollinator Andrena camellia compared to the non-specialized pollinator Andrena chekiangensis. Our study demonstrated that the genes NAGA-like, galK, and galT have played an important role in the evolutionary adaptation of the oil-tea specialized Andrena species. Full article
(This article belongs to the Special Issue Wildlife Genomics and Genetic Diversity)
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14 pages, 3738 KiB  
Article
Description of the Three Complete Mitochondrial Genomes of Sitta (S. himalayensis, S. nagaensis, and S. yunnanensis) and Phylogenetic Relationship (Aves: Sittidae)
by Qingmiao Yuan, Qiang Guo, Jing Cao, Xu Luo and Yubao Duan
Genes 2023, 14(3), 589; https://doi.org/10.3390/genes14030589 - 26 Feb 2023
Cited by 7 | Viewed by 1848
Abstract
Nuthatches (genus Sitta; family Sittidae) are a passerine genus with a predominantly Nearctic and Eurasian distribution. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced the complete mitochondrial genomes of three Sitta species (S. himalayensis [...] Read more.
Nuthatches (genus Sitta; family Sittidae) are a passerine genus with a predominantly Nearctic and Eurasian distribution. To understand the phylogenetic position of Sitta and phylogenetic relations within this genus, we sequenced the complete mitochondrial genomes of three Sitta species (S. himalayensis, S. nagaensis, and S. yunnanensis), which were 16,822–16,830 bp in length and consisted of 37 genes and a control region. This study recovered the same gene arrangement found in the mitogenomes of Gallus gallus, which is considered the typical ancestral avian gene order. All tRNAs were predicted to form the typical cloverleaf secondary structures. Bayesian inference and maximum likelihood phylogenetic analyses of sequences of 18 species obtained a well-supported topology. The family Sittidae is the sister group of Troglodytidae, and the genus Sitta can be divided into three major clades. We demonstrated the phylogenetic relationships within the genus Sitta (S. carolinensis + ((S. villosa + S. yunnanensis) + (S. himalayensis + (S. europaea + S. nagaensis)))). Full article
(This article belongs to the Special Issue Wildlife Genomics and Genetic Diversity)
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