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16 pages, 15373 KiB

Open AccessArticle

Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis

by Wei Xu, Jingzhe Tai, Ke He, Tangjun Xu, Gaoji Zhang, Boyu Xu and Hongyi Liu

Animals 2024, 14(11), 1598; https://doi.org/10.3390/ani14111598 - 29 May 2024

Viewed by 1116

Although the pencilfish is a globally popular economic fish in the aquarium market, its taxonomic classification could be further refined. In order to understand the taxonomy of species of the genus Nannostomus (Characiformes, Lebiasinidae) and their phylogenetic position within the order Characiformes, in [...] Read more.

Although the pencilfish is a globally popular economic fish in the aquarium market, its taxonomic classification could be further refined. In order to understand the taxonomy of species of the genus Nannostomus (Characiformes, Lebiasinidae) and their phylogenetic position within the order Characiformes, in this study, we characterized mitochondrial genomes (mitogenomes) from four Nannostomus species for the first time. The four mitogenomes exhibited the typical circular structure, with overall sizes varying from 16,661 bp to 16,690 bp. They contained 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 1 control region (CR). Nucleotide composition analysis suggested that the mitochondrial sequences were biased toward A and T. Bayesian inference and maximum likelihood analyses based on PCGs support the family Lebiasinidae classification, described using four Nannostomus species, clustering together with Lebiasina multimaculata from the same family. The results of this study support the current taxonomic classification of the family Lebiasinidae. Phylogenetic analysis also suggested that gene rearrangement would not significantly impact the phylogenetic relationships within the order Characiformes. These results might provide new data regarding the phylogeny and classification of the order Characiformes, thus providing a theoretical basis for the economic development of aquarium fish markets. Full article

(This article belongs to the Special Issue Genetic Resources in Livestock and Fish: Management and Conservation Strategies)

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9 pages, 1143 KiB

Open AccessCommunication

Sequencing and Analysis of the Complete Mitochondrial Genome of Lentipes ikeae

by Cheng-He Sun, Yang-Liang Gu, Da-Wei Liu, Hong-Wei Du and Chang-Hu Lu

Animals 2024, 14(6), 943; https://doi.org/10.3390/ani14060943 - 19 Mar 2024

Viewed by 1222

Abstract

We sequenced and analyzed the complete mitochondrial genome of Lentipes ikeae and explored the phylogenetic relationships among Sicydiinae based on mitochondrial genome sequences. The complete mitochondrial genome sequence of L. ikeae was determined using the Illumina HiSeq X Ten sequencing platform, and the [...] Read more.

We sequenced and analyzed the complete mitochondrial genome of Lentipes ikeae and explored the phylogenetic relationships among Sicydiinae based on mitochondrial genome sequences. The complete mitochondrial genome sequence of L. ikeae was determined using the Illumina HiSeq X Ten sequencing platform, and the gene structural characteristics and base composition were analyzed. Based on the mitochondrial genome sequences of 28 Sicydiinae species published in GenBank and mitochondrial protein-coding genes (PCGs), Acanthogobius flavimanus (Gobionellinae) was selected as an outgroup to construct phylogenetic trees of Sicydiinae using the maximum likelihood and Bayesian inference methods. The mitochondrial genome of L. ikeae (GenBank number: OP764680) has a total length of 16,498 bp and encodes 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a D-loop (control) region. Gene rearrangement is not observed. The mitochondrial genome of L. ikeae exhibits an AT preference, with AT skew > 0 and GC skew < 0 across the entire genome. The phylogenetic relationships of Sicydiinae based on 13 mitochondrial PCG sequences are Sicydium + (Stiphodon + (Sicyopus + Lentipes)) + Sicyopterus, indicating that Sicydium, Sicyopterus, Lentipes, and Stiphodon are all monophyletic groups. Full article

(This article belongs to the Special Issue Genetic Resources in Livestock and Fish: Management and Conservation Strategies)

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16 pages, 3031 KiB

Open AccessArticle

Characterization of the Complete Mitochondrial Genome of Schizothorax kozlovi (Cypriniformes, Cyprinidae, Schizothorax) and Insights into the Phylogenetic Relationships of Schizothorax

by Qiang Qin, Lin Chen, Fubin Zhang, Jianghaoyue Xu and Yu Zeng

Animals 2024, 14(5), 721; https://doi.org/10.3390/ani14050721 - 25 Feb 2024

Cited by 2 | Viewed by 1383

Abstract

Schizothorax kozlovi is an endemic and vulnerable fish species found in the upper Yangtze River in China. Over the past few years, the population resources of S. kozlovi have been nearly completely depleted owing to multiple contributing threats. While the complete mitochondrial genomes [...] Read more.

Schizothorax kozlovi is an endemic and vulnerable fish species found in the upper Yangtze River in China. Over the past few years, the population resources of S. kozlovi have been nearly completely depleted owing to multiple contributing threats. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of S. kozlovi has still received little attention. In this study, we analyzed the characterization of the mitochondrial genome of S. kozlovi and investigated the phylogenetic relationships of Schizothorax. The complete mitochondrial genome of S. kozlovi was 16,585 bp in length, which contained thirty-seven genes (thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)) and two non-coding regions for the origin of light strand (OL) and the control region (CR). There were nine overlapping regions and seventeen intergenic spacers regions in the mitochondrial genome. The genome also showed a bias towards A + T content (55.01%) and had a positive AT-skew (0.08) and a negative GC-skew (−0.20). All the PCGs employed the ATG or GTG as the start codon and TAA, TAG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1 which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that the topologies of the phylogenetic tree divided the Schizothorax into four clades and did not support the classification of Schizothorax based on morphology. The phylogenetic status of S. kozlovi was closely related to that of S. chongi. The present study provides valuable genomic information for S. kozlovi and new insights in phylogenetic relationships of Schizothorax. These data could also offer fundamental references and guidelines for the management and conservation of S. kozlovi and other species of Schizothorax. Full article

(This article belongs to the Special Issue Genetic Resources in Livestock and Fish: Management and Conservation Strategies)

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13 pages, 9135 KiB

Open AccessCommunication

Comparative Transcriptome Analysis Reveals Sexually Dimorphic Gene Expression in the Gonads of Brachymystax tsinlingensis Li

by Ling Huang, Huan Ye, Huamei Yue, Xiaoqian Leng, Rui Ruan, Hao Du, Chuangju Li and Jinming Wu

Animals 2023, 13(23), 3690; https://doi.org/10.3390/ani13233690 - 29 Nov 2023

Cited by 1 | Viewed by 1139

Abstract

Brachymystax tsinlingensis Li is an endangered cold-water salmonid fish native to China. This study aimed to identify sex-related genes and biological pathways via gonadal transcriptome sequencing of B. tsinlingensis Li. A total of 167,904 unigenes were identified with an average length of 836 [...] Read more.

Brachymystax tsinlingensis Li is an endangered cold-water salmonid fish native to China. This study aimed to identify sex-related genes and biological pathways via gonadal transcriptome sequencing of B. tsinlingensis Li. A total of 167,904 unigenes were identified with an average length of 836 bp and an N50 of 1452 bp, of which 84,977 (50.61%) unigenes were successfully annotated in six major databases. Comparative transcriptome analysis identified 22,864 differentially expressed genes (DEGs), of which 17,231 were up-regulated (male-biased genes, mDEGs) and 5633 were down-regulated (female-biased genes, fDEGs). Several DEGs associated with gonadal development were found through Gene Ontology enrichment analysis, such as ccnb1, zp3, bmp15, dmrt1, and psmc3ip. Signaling pathways related to gonadal development were found to be enriched through analysis using the Kyoto Encyclopedia of Genes and Genomes Pathway database, such as genes involves in base excision repair, the notch signaling pathway, neuroactive ligand-receptor interaction, the VEGF signaling pathway, and the estrogen signaling pathway. In addition, mRNA expression levels of 19 DEGs were determined to validate the reliability of the transcriptomic data by quantitative real-time polymerase chain reaction. These results revealed genes and signaling pathways potentially involved in gonadal development in B. tsinlingensis Li and provided basic molecular data for future research on reproductive regulation and breeding of B. tsinlingensis Li. Full article

(This article belongs to the Special Issue Genetic Resources in Livestock and Fish: Management and Conservation Strategies)

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16 pages, 2170 KiB

Open AccessArticle

Genetic Diversity and Population Structure in Captive Populations of Formosan Sambar Deer (Rusa unicolor swinhoei)

by Hsiao-Mei Liang, Kuo-Tai Yang, Yu-Tzu Cheng, Shen-Chang Chang, Cheng-Yung Lin, Ming-Yang Tsai, Der-Yuh Lin and Kuo-Hsiang Hung

Animals 2023, 13(19), 3106; https://doi.org/10.3390/ani13193106 - 5 Oct 2023

Cited by 1 | Viewed by 1503

Abstract

Formosan sambar deer (Rusa unicolor swinhoei) are of great economic significance in Taiwan, resulting in a substantial increase in deer farming to meet the high demand for velvet antlers. Inbreeding depression and reduced genetic variability can lead to the deterioration of [...] Read more.

Formosan sambar deer (Rusa unicolor swinhoei) are of great economic significance in Taiwan, resulting in a substantial increase in deer farming to meet the high demand for velvet antlers. Inbreeding depression and reduced genetic variability can lead to the deterioration of captive populations. In this study, 239 Formosan sambar deer were genotyped using 13 microsatellites to analyze their genetic diversity and population genetic structure. Our results indicate a high-resolution power of these microsatellites in individual discrimination and parentage analysis. However, captive populations exhibit a low level of genetic diversity, likely because of inbreeding and bottleneck effects. Both principal coordinate analysis (PCoA) and STRUCTURE analyses revealed two distinct and segregated genetic groups within the captive populations and indicated no clear population genetic structure among the captive populations. Introducing new genetic material from the wild through translocation offers a potential solution for mitigating the impact of inbreeding and enhancing genetic diversity. The comprehensive information obtained from these genetic analyses is crucial for the development of effective breeding strategies aimed at preserving and enhancing Formosan sambar deer populations. Full article

(This article belongs to the Special Issue Genetic Resources in Livestock and Fish: Management and Conservation Strategies)

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21 pages, 2667 KiB

Open AccessArticle

Environmental and Socio–Cultural Factors Impacting the Unique Gene Pool Pattern of Mae Hong-Son Chicken

by Wongsathit Wongloet, Worapong Singchat, Aingorn Chaiyes, Hina Ali, Surachai Piangporntip, Nattakan Ariyaraphong, Trifan Budi, Worawit Thienpreecha, Wannapa Wannakan, Autchariyapron Mungmee, Kittipong Jaisamut, Thanyapat Thong, Thitipong Panthum, Syed Farhan Ahmad, Artem Lisachov, Warong Suksavate, Narongrit Muangmai, Rattanaphon Chuenka, Mitsuo Nunome, Wiyada Chamchumroon, Kyudong Han, Aniroot Nuangmek, Yoichi Matsuda, Prateep Duengkae and Kornsorn Srikulnath Show full author list Hide full author list

Animals 2023, 13(12), 1949; https://doi.org/10.3390/ani13121949 - 10 Jun 2023

Cited by 5 | Viewed by 3259

Abstract

Understanding the genetic diversity of domestic chicken breeds under the impact of socio–cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son [...] Read more.

Understanding the genetic diversity of domestic chicken breeds under the impact of socio–cultural and ecological dynamics is vital for the conservation of natural resources. Mae Hong Son chicken is a local breed of North Thai domestic chicken widely distributed in Mae Hong Son Province, Thailand; however, its genetic characterization, origin, and diversity remain poorly understood. Here, we studied the socio–cultural, environmental, and genetic aspects of the Mae Hong Son chicken breed and investigated its diversity and allelic gene pool. We genotyped 28 microsatellite markers and analyzed mitochondrial D-loop sequencing data to evaluate genetic diversity and assessed spatial habitat suitability using maximum entropy modeling. Sequence diversity analysis revealed a total of 188 genotyped alleles, with overall nucleotide diversity of 0.014 ± 0.007, indicating that the Mae Hong Son chicken population is genetically highly diverse, with 35 (M1–M35) haplotypes clustered into haplogroups A, B, E, and F, mostly in the North ecotype. Allelic gene pool patterns showed a unique DNA fingerprint of the Mae Hong Son chicken, as compared to other breeds and red junglefowl. A genetic introgression of some parts of the gene pool of red junglefowl and other indigenous breeds was identified in the Mae Hong Son chicken, supporting the hypothesis of the origin of the Mae Hong Son chicken. During domestication in the past 200–300 years after the crossing of indigenous chickens and red junglefowl, the Mae Hong Son chicken has adapted to the highland environment and played a significant socio–cultural role in the Northern Thai community. The unique genetic fingerprint of the Mae Hong Son chicken, retaining a high level of genetic variability that includes a dynamic demographic and domestication history, as well as a range of ecological factors, might reshape the adaptation of this breed under selective pressure. Full article

(This article belongs to the Special Issue Genetic Resources in Livestock and Fish: Management and Conservation Strategies)

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13 pages, 3433 KiB

Open AccessArticle

Karyotypic and Molecular Analysis of Pterygoplichthys pardalis (Castelnau 1855) from the Lower Amazon River

by Alcimara dos Santos Guimarães, Luan Aércio Melo Maciel, Mendelshon Fujiie Belém de Souza and Luís Reginaldo Ribeiro Rodrigues

Animals 2023, 13(9), 1533; https://doi.org/10.3390/ani13091533 - 3 May 2023

Viewed by 2116

Abstract

Pterygoplichthys pardalis is an armored catfish native to South America and an important resource for the ornamental fish industry. Recently, several exotic populations have been introduced into rivers on five continents. Despite its commercial and environmental importance, P. pardalis is poorly studied from [...] Read more.

Pterygoplichthys pardalis is an armored catfish native to South America and an important resource for the ornamental fish industry. Recently, several exotic populations have been introduced into rivers on five continents. Despite its commercial and environmental importance, P. pardalis is poorly studied from a genetic perspective. In this study, we analyzed the karyotype of P. pardalis from the Amazon River and molecular variations in the mitochondrial gene Cytochrome oxidase I (COI) between native and exotic populations. The karyotype presented diploid number 2n = 52 and NF = 100 without cytogenetic variation between males and females. Nucleolus organizer regions (Ag-NOR) in the distal region of the long arm of pair 12 coincided with the 18S hybridization signal, whereas 5S was syntenic to this chromosome but localized in the short arm. The constitutive heterochromatin was restricted in the distal regions of pairs 4, 12, 25, and 26. Telomeric probes showed only distal hybridization signals. The karyotype of P. pardalis diverged from that of its congeners, and COI molecular variation revealed four haplotypes. The Philippine population revealed the greatest diversity with three haplotypes, while haplotype H1 was the most abundant and observed in both native and exotic populations. This new genetic data contributes to species management and provides useful information from an aquaculture perspective. Full article

(This article belongs to the Special Issue Genetic Resources in Livestock and Fish: Management and Conservation Strategies)

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14 pages, 602 KiB

Open AccessArticle

Genetic Parameters and Genotype × Diet Interaction for Body Weight Performance and Fat in Gilthead Seabream

by Stavroula Oikonomou, Zoi Kazlari, Dimitrios Loukovitis, Arkadios Dimitroglou, Lefteris Kottaras, Konstantinos Tzokas, Dimitrios Barkas, Nikolaos Katribouzas, Leonidas Papaharisis and Dimitrios Chatziplis

Animals 2023, 13(1), 180; https://doi.org/10.3390/ani13010180 - 3 Jan 2023

Cited by 2 | Viewed by 2010

Abstract

There has been thorough research on the genotype by diet interaction and the extent of its impact on the genetic evaluation, using a partly replaced marine animal protein on the gilthead seabream. To do that, 8356 individuals were gathered from two batches and [...] Read more.

There has been thorough research on the genotype by diet interaction and the extent of its impact on the genetic evaluation, using a partly replaced marine animal protein on the gilthead seabream. To do that, 8356 individuals were gathered from two batches and followed different diets: a high-plant-protein diet containing 85% plant proteins and a standard commercial one containing 30% marine animal protein. During the experiment, body weight, growth and fat content were recorded. High heritability estimates were detected for the body weight performance and fat content. A small effect of genotype by diet interaction was detected in all phenotypes (presented as the genetic correlations from 0.95 to 0.97) but a medium-high ranking correlation between the breeding values for each trait was estimated (0.72–0.70). A higher expected response to selection for the body weight performance was detected using the standard commercial rather than the plant-based diet. Based on the findings, the establishment of a plant-based diet breeding strategy can be achieved provided the reduction of the cost of aquafeed is attained, though a lower genetic gain is expected. Full article

(This article belongs to the Special Issue Genetic Resources in Livestock and Fish: Management and Conservation Strategies)

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