Zoological Research

1−2

Authors: Yong-Gang Yao,Yun Zhang

14−25

Authors: Jia-Fei Shen,  Qiu-Ming Chen,  Feng-Wei Zhang,  Quratulain Hanif,  Bi-Zhi Huang,  Ning-Bo Chen,  Kai-Xing Qu, Jing-Xi Zhan, Hong Chen, Yu Jiang, Chu-Zhao Lei

Cattle temperament is an interesting trait due to its correlation with production efficiency, labor safety, and animal welfare. To date, however, its genetic basis is not clearly understood. Here, we performed a genome-wide association study for a series of temperament traits in cattle, assessed with via open field and novel object tests, using autosomal single nucleotide polymorphisms (SNPs) derived from the whole-genome sequence. We identified 37 and 29 genome-wide significant loci in the open field and novel object tests, respectively. Gene set analysis revealed the most significant pathway was the neuroactive ligand-receptor interaction pathway, which may be essential for emotional control in cattle. Analysis of the expression levels of 18 tissue-specific genes based on transcriptomic data showed enrichment in the brain, with some candidate genes involved in psychiatric and neurodegenerative diseases in humans. Based on principal component analysis, the first principal component explained the largest variance in the open field and novel object test data, and the most significant loci were assigned to SORCS3 and SESTD1, respectively. Our findings should help facilitate cattle breeding for sound temperament by pyramiding favorable alleles to further improve cattle production.

30−32

Authors: Peng Yu, Li Zhou, Xiao-Li Yang, Liang-Liang Li, Hui Jin, Zhi Li, Zhong-Wei Wang, Xi-Yin Li, Xiao-Juan Zhang, Yang Wang, Jian-Fang Gui

Chedrinae fish, which belong to Danionidae, have important ornamental, economic, and scientific value. At present, however, their mitogenomic features are unclear and their phylogenetic relationships remain controversial. In this study, we presented five new Chedrinae mitochondrial genomes (mitogenomes) and analyzed the conserved and variable mitogenomic characteristics of 17 Chedrinae fish. The gene composition and arrangement and secondary structure of transfer RNAs (tRNAs) were highly conserved among the Chedrinae mitogenomes. However, the length of the control region and base composition were variable. Interestingly, the mitogenome of Barilius barila was unusual, with lower A+T content in the first codon of protein-coding genes (PCGs) (47.32% versus average of 54.47%) and distinct pattern of codons per thousand codons (CDspT). Three Chedrinae fish had a long tandem repeat (>291 bp) in the 5'-end of the control region, which may increase their adaptability. In addition, tRNA^Lys had notably larger DHU and TΨC loops than other tRNAs. The phylogenetic trees of the Chedrinae fish suggested that the Barilius genus was not a monophyletic group but could be divided into two main groups based on significant differences in A+T content. This study provides insights into the mitogenomic features and phylogenetic implications of Chedrinae fish, which should benefit their systematics and conservation.

40−51

Authors: Xiao-Yi Wang, Mao-Jun Zhong, Jian Zhang, Xing-Feng Si, Sheng-Nan Yang, Jian-Ping Jiang, Jun-Hua Hu

Mountain systems harbor an evolutionarily unique and exceptionally rich biodiversity, especially for amphibians. However, the associated elevational gradients and underlying mechanisms of amphibian diversity in most mountain systems remain poorly understood. Here, we explored amphibian phylogenetic and functional diversity along a 2 600 m elevational gradient on Mount Emei on the eastern margin of the Qinghai-Tibetan Plateau in southwestern China. We also assessed the relative importance of spatial (area) and environmental factors (temperature, precipitation, solar radiation, normalized difference vegetation index, and potential evapotranspiration) in shaping amphibian distribution and community structure. Results showed that the phylogenetic and functional diversities were unimodal with elevation, while the standardized effect size of phylogenetic and functional diversity increased linearly with elevation. Phylogenetic net relatedness, nearest taxon index, and functional net relatedness index all showed a positive to negative trend with elevation, indicating a shift from clustering to overdispersion and suggesting a potential change in key processes from environmental filtering to competitive exclusion. Overall, our results illustrate the importance of deterministic processes in structuring amphibian communities in subtropical mountains, with the dominant role potentially switching with elevation. This study provides insights into the underlying assembly mechanisms of mountain amphibians, integrating multidimensional diversity.

64−74

Authors: Lin Zhang, Shan-Shan Zhang, Kai-Fang Wang, Yi-Hui Li, Hui-Juan Xu, Kuan-Xiang Sun, Shi Ma, Hong-Mei Leng, Si-Zhu Chen, Wen-Jing Jia, Xian-Jun Zhu, Jie Li

Retinal angiogenesis is a critical process for normal retinal function. However, uncontrolled angiogenesis can lead to pathological neovascularization (NV), which is closely related to most irreversible blindness-causing retinal diseases. Understanding the molecular basis behind pathological NV is important for the treatment of related diseases. Twist-related protein 1 (TWIST1) is a well-known transcription factor and principal inducer of epithelial-mesenchymal transition (EMT) in many human cancers. Our previous study showed that Twist1 expression is elevated in pathological retinal NV. To date, however, the role of TWIST1 in retinal pathological angiogenesis remains to be elucidated. To study the role of TWIST1 in pathological retinal NV and identify specific molecular targets for antagonizing pathological NV, we generated an inducible vascular endothelial cell (EC)-specific Twist1 transgenic mouse model ( Tg-Twist1 iEC+ ). Whole-mount retinas from Tg-Twist1 iEC+ mice showed retarded vascular progression and increased vascular density in the front end of the growing retinal vasculature, as well as aneurysm-like pathological retinal NV. Furthermore, overexpression of Twist1 in the ECs promoted cell proliferation but disturbed cell polarity, thus leading to uncontrolled retinal angiogenesis. TWIST1 promoted pathological NV by activating the Wnt/β-catenin signaling pathway and inducing the expression of NV formation-related genes, thereby acting as a ‘valve’ in the regulation of pathological angiogenesis. This study identified the critical role of TWIST1 in retinal pathological NV, thus providing a potential therapeutic target for pathological NV.

78−80

Authors: Le Wang, Fei Sun, May Lee, Gen-Hua Yue

Understanding the genetic basis of phenotypes is of importance in evolutionary biology and for genetic improvement of economically valuable animals. The giant phenotype of the fighting fish, Betta splendens, provides a unique opportunity to explore the genetic architecture of overgrowth in body size. As such, we re-sequenced and analyzed the genomes of 54 fighting fish. Genome-wide FST and selective sweep analyses using 3 582 429 DNA variants revealed three genomic regions at chr1, chr9, and chr11 that were associated with the giant phenotype. With a total length of ~3.5 Mb, these regions showed high divergence between the giant and non-giant bettas. In contrast, no signature of selection was detected in the wild-type fish. Transcriptome analysis of brain and muscle samples from giant and normal bettas identified 14 candidate genes that were likely responsible for the giant phenotype. Overall, our data provide novel insights into the genetic basis of body size variation. The genome sequences, transcriptome sequences, DNA sequence variants, and candidate genes for body size provide valuable resources for further biological and evolutionary studies, as well as for rapid improvement in growth-related traits.

85−89

Authors: Wei-Cai Chen, Wan-Xiao Peng, You-Jun Liu, Zhong Huang, Xiao-Wen Liao, Yun-Ming Mo

A new species of the genus Occidozyga is reported from Southern Guangxi, China, based on morphological characters and molecular analyses. Morphological data revealed that the new species, Occidozyga shiwandashanensis sp. nov., differs from its congeners by a combination of the following characters: (1) medium body size (SVL 25.2−33.8 mm in males, 34.9−38.9 mm in females); (2) pale brown dorsum with irregular pale dark spots, especially on head; (3) creamy white ventral surface with brown spots on lateral margin and throat; (4) tongue fleshy, rounded, without notch, (5) tympanum hidden; (6) finger webbing absent and toe webbing full, but fourth toe not webbed to discs; (7) tips of fingers pointed, tips of toes rounded, slightly expanded into disc. The new species occurs on Mt. Shiwandashan and inhabits montane evergreen forests at 500−600 m above sea level.

95−97

Authors: Jin-Long Ren, Chaochao Yan, Zhong-Liang Peng, Jia-Tang Li

The Sichuan hot-spring snake (Thermophis zhaoermii) is a rare and endemic species found at high elevations in the Hengduan Mountains of China. Recent species-specific investigations showed that the Sichuan hot-spring snake is still restricted to geothermal zones at elevations higher than 3 000 m a.s.l. The species also remains at risk of extinction, with the effective population size showing continual decline over the past one million years based on coalescent inference from genome-level single nucleotide polymorphism (SNP) data. We propose several approaches for protecting Sichuan hot-spring snake populations and their habitat.

111−128

Authors: Ran Xu, Mariangela Iannello, Justin C. Havird, Liliana Milani, Fabrizio Ghiselli

In most eukaryotes, oxidative phosphorylation (OXPHOS) is the main energy production process and it involves both mitochondrial and nuclear genomes. The close interaction between the two genomes is critical for the coordinated function of the OXPHOS process. Some bivalves show doubly uniparental inheritance (DUI) of mitochondria, where two highly divergent mitochondrial genomes, one inherited through eggs (F-type) and the other through sperm (M-type), coexist in the same individual. However, it remains a puzzle how nuclear OXPHOS genes coordinate with two divergent mitochondrial genomes in DUI species. In this study, we compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of the DUI species Ruditapes philippinarum using sex- and tissue-specific transcriptomes. Mitochondrial and nuclear OXPHOS genes showed different transcription profiles. Strong co-transcription signal was observed within mitochondrial (separate for F- and M-type) and within nuclear OXPHOS genes but the signal was weak or absent between mitochondrial and nuclear OXPHOS genes, suggesting that the coordination between mitochondrial and nuclear OXPHOS subunits is not achieved transcriptionally. McDonald-Kreitman and frequency-spectrum based tests indicated that M-type OXPHOS genes deviated significantly from neutrality, and that F-type and M-type OXPHOS genes undergo different selection patterns. Codon usage analysis revealed that mutation bias and translational selection were the major factors affecting the codon usage bias in different OXPHOS genes, nevertheless, translational selection in mitochondrial OXPHOS genes appears to be less efficient than nuclear OXPHOS genes. Therefore, we speculate that the coordination between OXPHOS genes may involve post-transcriptional/translational regulation.