Zoological Research最新文献

{"title":"Disentangling the molecular mechanisms underlying yellow body coloration in a soft-shelled turtle.","authors":"Ju Zhang, Zi-Han Ding, Peng-Fei Wu, Wei-Guo Du, Yue-Qiang Guan, Xi-Feng Wang","doi":"10.24272/j.issn.2095-8137.2024.276","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.276","url":null,"abstract":"<p><p>While the functions of body coloration have been well characterized in many animal taxa, the molecular mechanisms governing its production remain poorly understood. This study investigated the genetic and biochemical basis of yellow body coloration in a mutant form of the Yongzhang golden soft-shelled turtle (YGT, <i>Pelodiscus sinensis</i>), which exhibit a striking yellow phenotype. Comparative pigment analysis revealed that YGTs have significantly lower melanin and higher carotenoid pigmentation compared to atrovirens wild-type turtles (AWTs), while pterin concentrations did not differ between the two groups. Functional validation experiments demonstrated that a single amino acid substitution (I481R) in tyrosinase-related protein 1 ( <i>tyrp1</i>) plays a pivotal role in the reduction of melanin production in YGTs. Expression of <i>tyrp1</i> from YGTs and AWTs in A375 cells, in which human <i>tyrp1</i> (h <i>tyrp1</i>) function was depleted by CRISPR-Cas9, led to a specific reduction in melanin production in cells expressing the YGT- <i>tyrp1</i> variant. Moreover, <i>bco1</i> and <i>bco2</i>, genes negatively associated with carotenoid content, showed reduced expression in YGTs, suggesting that yellow coloration is achieved through a reduction in melanin pigmentation combined with an accumulation of carotenoids. These findings elucidate the molecular basis of yellow body coloration in turtles and enhance our understanding of pigment regulation in vertebrates.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"379-387"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bilateral asymmetry in craniofacial structures and kinematics of feeding attacks in the scale-eating cichlid fish, <i>Perissodus</i> <i>microlepis</i>.","authors":"Xiaomeng Tian, Sooyeon Lee, Jan Tuckermann, Axel Meyer","doi":"10.24272/j.issn.2095-8137.2024.314","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.314","url":null,"abstract":"<p><p>Cichlid fishes are a textbook example for adaptive radiations, since they diversified into several hundred highly specialized species in each of three great East African lakes. Even scale-eating, an extremely specialized feeding mode, evolved independently multiple times in these radiations and in Lake Tanganyika alone, six endemic scale-eating species occupy this extremely specialized ecological niche. <i>Perissodus</i> <i>microlepis</i> went a step further, by evolving bilaterally asymmetrical heads with an intra-specific polymorphism where left- and right-headed morphs predominantly scrape scales from the opposite sides of their prey. While the bilateral asymmetry of scale-eating cichlids has been known, exactly which craniofacial features explain the laterality of the heads remained unclear. Here we aimed, by utilizing micro-computed tomography (μCT), to resolve this issue of how bilateral symmetry in the skeletal structure is broken in scale-eating <i>Perissodus</i>. Our 3D geometric morphometrics analysis clearly separated and identified the two groups of either left- or right-headed fish. In addition, we observed consistent asymmetric volume changes in the premaxilla, maxilla, and mandible of the craniofacial structures, where left-headed fish have larger jaw elements on the right side, and vice versa. The bimodality implies that the effect sizes of environmental factors might be minor while genetics might be responsible to a larger extent for the asymmetry observed in their head morphology. High-speed video analyses of attacks by asymmetrical morphotypes revealed that they utilize their asymmetrical mouth protrusion, as well as lateralized behavior, to re-orientate the gape towards the preferred side of their prey fish to more efficiently scrape scales.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"370-378"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alterations in the salivary gland microbiota of <i>Haemaphysalis longicornis</i> during tick-to-host transmission of severe fever with thrombocytopenia syndrome virus.","authors":"Jingjing Chen, Chuanfei Yuan, Qiong Xu, Yu Sun, Rui Zheng, Chenghong Zeng, Yan Wu, Zhen Zou, Qianfeng Xia","doi":"10.24272/j.issn.2095-8137.2024.332","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.332","url":null,"abstract":"<p><p><i>Haemaphysalis longicornis</i> serves as the primary tick vector for severe fever with thrombocytopenia syndrome virus (SFTSV), the etiological agent responsible for severe fever with thrombocytopenia syndrome (SFTS). Understanding alterations in tick salivary gland microbiota during SFTSV transmission to vertebrate hosts is essential for developing novel control strategies. However, microbial shifts in tick salivary glands during pathogen transmission to hosts have not been reported for any tick-borne pathogens. In this study, SFTSV transmission from <i>H. longicornis</i> to vertebrate hosts was confirmed using a tick-rabbit transmission model. Salivary gland microbiota profiling via 16S rRNA gene sequencing identified significant changes in bacterial composition associated with viral transmission. The relative abundance of three genera ( <i>Serratia</i>, <i>Bifidobacterium</i>, and <i>Akkermansia</i>) increased, whereas five genera <i>(Flavobacterium</i>, <i>Staphylococcus</i>, <i>Enhydrobacter</i>, <i>Massilia</i>, and <i>Stenotrophomonas</i>) decreased. Correlation network analysis revealed a negative association between <i>Akkermansia</i> and <i>Flavobacterium</i>. These findings demonstrated that SFTSV transmission alters the salivary gland microbiota of <i>H. longicornis</i>, providing insights for future functional studies and the development of targeted strategies for SFTS control.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"459-468"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell sequencing analysis reveals the essential role of the m ⁶A reader YTHDF1 in retinal visual function by regulating TULP1 and DHX38 translation.","authors":"Xian-Jun Zhu, Xiao-Yan Jiang, Wen-Jing Liu, Yu-Di Fan, Guo Liu, Shun Yao, Kuan-Xiang Sun, Jun-Yao Chen, Bo Lei, Ye-Ming Yang","doi":"10.24272/j.issn.2095-8137.2024.399","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.399","url":null,"abstract":"<p><p>N6-methyladenosine (m ⁶A) modification of mRNA is a critical post-transcriptional regulatory mechanism that modulates mRNA metabolism and neuronal function. The m ⁶A reader YTHDF1 has been shown to enhance the translational efficiency of m ⁶A-modified mRNAs in the brain and is essential for learning and memory. However, its role in the mature retina remains unclear. Herein, we report a novel role of <i>Ythdf1</i> in the maintenance of retinal function using a genetic knockout model. Loss of <i>Ythdf1</i> resulted in impaired scotopic electroretinogram (ERG) responses and progressive retinal degeneration. Detailed analyses of rod photoreceptors confirmed substantial degenerative changes in the absence of ciliary defects. Single-cell RNA sequencing revealed comprehensive molecular alterations across all retinal cell types in <i>Ythdf1</i>-deficient retinas. Integrative analysis of methylated RNA immunoprecipitation (MeRIP) sequencing and RIP sequencing identified <i>Tulp1</i> and <i>Dhx38</i>, two inheritable retinal degeneration disease-associated gene homologs, as direct targets of YTHDF1 in the retina. Specifically, YTHDF1 recognized and bound m ⁶A-modified <i>Tulp1</i> and <i>Dhx38</i> mRNA at the coding sequence (CDS), enhancing their translational efficiency without altering mRNA levels. Collectively, these findings highlight the essential role of YTHDF1 in preserving visual function and reveal a novel regulatory mechanism of m ⁶A reader proteins in retinal degeneration, identifying potential therapeutic targets for severe retinopathies.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"429-445"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671604","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beneficial effects of probiotics on <i>Litopenaeus vannamei</i> growth and immune function via the recruitment of gut Rhodobacteraceae symbionts.","authors":"Hao-Nan Sha, Yang-Ming Lu, Ping-Ping Zhan, Jiong Chen, Qiong-Fen Qiu, Jin-Bo Xiong","doi":"10.24272/j.issn.2095-8137.2024.364","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.364","url":null,"abstract":"<p><p>Probiotic supplementation enhances the abundance of gut-associated Rhodobacteraceae species, critical symbionts contributing to the health and physiological fitness of <i>Litopenaeus vannamei</i>. Understanding the role of Rhodobacteraceae in shaping the shrimp gut microbiota is essential for optimizing probiotic application. This study investigated whether probiotics benefit shrimp health and fitness via the recruitment of Rhodobacteraceae commensals in the gut. Probiotic supplementation significantly enhanced feed conversion efficiency, digestive enzyme activity, and immune responses, thereby promoting shrimp growth. Additionally, probiotics induced pronounced shifts in gut microbial composition, enriched gut Rhodobacteraceae abundance, and reduced community variability, leading to a more stable gut microbiome. Network analysis revealed that the removal of Rhodobacteraceae nodes disrupted gut microbial connectivity more rapidly than the removal of non-Rhodobacteraceae nodes, indicating a disproportionate role of Rhodobacteraceae in maintaining network stability. Probiotic supplementation facilitated the migration of Rhodobacteraceae taxa from the aquatic environment to the shrimp gut while reinforcing deterministic selection in gut microbiota assembly. Transcriptomic analysis revealed that up-regulation of amino acid metabolism and NF-κB signaling pathways was positively correlated with Rhodobacteraceae abundance. These findings demonstrate that probiotic supplementation enriches key Rhodobacteraceae taxa, stabilizes gut microbial networks, and enhances host digestive and immune functions, ultimately improving shrimp growth performance. This study provides novel perspectives on the ecological and molecular mechanisms underlying the beneficial effects of probiotics on shrimp fitness.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"388-400"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA methylation confers a cerebellum-specific identity in non-human primates.","authors":"Xiao-Dong Liu, Chang-Cheng Ye, Yang Wang, Xiao-Song Zhang, Hui-Xian Wei, Lei-Jie Xie, Jia-Xiang Xie, Yan-Ru Xu, Li-Ying Zhong, Shi-Hua Li, Xiao-Jiang Li, Li Lin","doi":"10.24272/j.issn.2095-8137.2024.325","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.325","url":null,"abstract":"<p><p>Selective regulation of gene expression across distinct brain regions is crucial for establishing and maintaining subdivision identities. DNA methylation, a key regulator of gene transcription, modulates transcriptional activity through the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). While DNA methylation is hypothesized to play an essential role in shaping brain identity by influencing gene expression patterns, its direct contribution, especially in primates, remains largely unexplored. This study examined DNA methylation landscapes and transcriptional profiles across four brain regions, including the cortex, cerebellum, striatum, and hippocampus, using samples from 12 rhesus monkeys. The cerebellum exhibited distinct epigenetic and transcriptional signatures, with differentially methylated regions (DMRs) significantly enriched in metabolic pathways. Notably, genes harboring clustered differentially hydroxymethylated regions (DhMRs) overlapped with those implicated in schizophrenia. Moreover, 5mC located 1 kb upstream of the ATG start codon was correlated with gene expression and exhibited region-specific associations with 5hmC. These findings provide insights into the coordinated regulation of cerebellum-specific 5mC and 5hmC <b>,</b> highlighting their potential roles in defining cerebellar identity and contributing to neuropsychiatric diseases.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"414-428"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated single-cell transcriptomic map of pig kidney cells across various periods and anatomical sites.","authors":"Tian-Xiong Yao, Na Li, Lu-Sheng Huang","doi":"10.24272/j.issn.2095-8137.2024.335","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.335","url":null,"abstract":"<p><p>The kidney is essential for maintaining fluid, electrolyte, and metabolite homeostasis, and for regulating blood pressure. The pig serves as a valuable biomedical model for human renal physiology, offering insights across different physiological states. In this study, single-cell RNA sequencing was used to profile 138 469 cells from 12 pig kidney samples collected during the embryonic (E), fattening (F), and pregnancy (P) periods, identifying 29 cell types. Proximal tubule (PT) cells exhibited elevated expression of metabolism-related transcription factors (TFs), including <i>GPD1</i>, <i>ACAA1</i>, and <i>AGMAT</i>, with validation across multiple individuals, periods, and species. Fluorescence homologous double-labeling of paraffin sections further confirmed the expression of <i>ACAA1</i> and <i>AGMAT</i> in PT cells. Comparative analysis of pig and human kidneys revealed a high degree of similarity among corresponding cell types. Analysis of cell-type heterogeneity highlighted the diversity of thick ascending limb (TAL) cells, identifying a TAL subpopulation related to immune function. Additionally, the functional heterogeneity of kidney-resident macrophages (KRM) was explored across different anatomical sites. In the renal medulla, KRM were implicated in phagocytosis and leukocyte activation, whereas in the renal pelvis, they functioned as ligands, recruiting neutrophils with bactericidal activity to the renal pelvis to combat urinary tract infections.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"469-482"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Consistency, distinction, and potential metabolic crosstalk of nitrogen mobilization-related genes in silk production and silk gland biology.","authors":"Mei-Yan Yi, Xu Yang, Man Wang, Jing-Wei Chen, Jia-Hao Xiang, Li-Jun Xiang, Lan-Sa Qian, Dong-Bin Chen, Yong-Ping Huang, Xiao-Ling Tong, Zu-Lian Liu, Hui Xiang","doi":"10.24272/j.issn.2095-8137.2024.391","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.391","url":null,"abstract":"<p><p>The domesticated silkworm ( <i>Bombyx mori</i>) has evolved a highly efficient nitrogen utilization system to support silk production. The silk glands play a pleiotropic role in sequestering nitrogen resources for silk synthesis, mitigating aminoacidemia by assimilating free amino acids, and reallocating nitrogen during metamorphosis through programmed cell death. However, the specific functions of nitrogen metabolism-related genes in this process remain unclear. Using CRISPR/Cas9-based gene editing, mutations were generated in glutamine synthetase ( <i>GS</i>), glutamate synthetase ( <i>GOGAT</i>), asparagine synthetase ( <i>AS</i>), glutamate dehydrogenase ( <i>GDH</i>) and glutamate oxaloacetate transaminase 1 ( <i>GOT1</i>). Disruption of <i>GS</i>, <i>GOGAT</i>, and <i>AS</i> consistently reduced silkworm cocoon and pupal weight and significantly down-regulated silk protein gene transcription, whereas <i>GOT1</i> mutation had no such effect. <i>GOGAT</i> mutants exhibited abnormally enlarged silk glands, whereas <i>GS</i> and <i>AS</i> mutants showed delayed programmed cell death in the silk glands. In contrast, <i>GOT1</i> mutants displayed normal silk gland morphology but were consistently smaller. Disruption of <i>GS</i>, <i>GOGAT</i>, and <i>AS</i> led to more extensive transcriptional changes, including altered expression of transcription factors in the silk glands, compared with <i>GOT1</i> mutants. Both <i>GS</i> and <i>GOGAT</i> mutants exhibited up-regulation of <i>AS</i> and <i>GDH</i>, while only <i>GOGAT</i> mutants displayed elevated AS enzymatic activity, suggesting that GOGAT may compete with AS for glutamine in the silk glands to support silk protein synthesis. <i>AS</i> mutants showed significantly elevated GOT activity and up-regulation of several metabolic pathways, indicating that AS may functionally interact with GOT in regulating both silk gland development and programmed cell death during metamorphosis.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"446-458"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pathogenic mechanisms of <i>Enterocytozoon hepatopenaei</i> through the parasite-gut microbiome-shrimp ( <i>Litopenaeus vannamei</i>) physiology axis.","authors":"Yang-Ming Lu, Jia-Qi Lu, Qi Zhao, Jiong Chen, Jin-Bo Xiong","doi":"10.24272/j.issn.2095-8137.2024.411","DOIUrl":"https://doi.org/10.24272/j.issn.2095-8137.2024.411","url":null,"abstract":"<p><p>The progressive impact of <i>Enterocytozoon hepatopenaei</i> (EHP) infection on gut microbial function in <i>Litopenaeus vannamei</i> remains poorly understood beyond static comparisons between healthy and infected individuals. To close this knowledge gap, metagenomic sequencing was used to characterize the gut microbiomes of normal, long, medium, and short-sized adult shrimp categorized by increasing severity of infection. EHP infection suppressed digestive activity while inducing immune responses compared with healthy shrimp. Increasing infection severity was associated with a gradual decline in gut α-diversity and an expansion of potential pathogens and virulence factors (VFs). In addition, dysbiosis in gut microbiota composition and function, as well as reduced network stability among differential species, intensified with infection severity. Accordingly, we identified 24 EHP-discriminatory species that contributed an overall 83.3% accuracy in diagnosing infection severity without false negatives. Functional pathway analysis revealed significant suppression of metabolic, degradative, and biosynthetic processes in EHP-infected shrimp compared with healthy controls. Among them, map00630 glyoxylate and dicarboxylate metabolism and map00280 valine, leucine and isoleucine degradation were consistently depleted in infected individuals, thereby impairing their digestive function and anti-inflammatory responses. Additionally, EHP infection diversified VFs directly affecting shrimp gut microbiome. These findings support a conceptual model linking EHP pathogenesis to the parasite-gut microbiome-shrimp physiology axis.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 2","pages":"401-413"},"PeriodicalIF":4.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143651559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transposable elements shape the landscape of heterozygous structural variation in a bird genome.","authors":"Bo-Ping Li, Na Kang, Zao-Xu Xu, Hao-Ran Luo, Shi-Yu Fan, Xiao-Han Ao, Xing Li, Ya-Peng Han, Xiao-Bin Ou, Luo-Hao Xu","doi":"10.24272/j.issn.2095-8137.2024.237","DOIUrl":"10.24272/j.issn.2095-8137.2024.237","url":null,"abstract":"<p><p>Avian genomes exhibit compact organization and remarkable chromosomal stability. However, the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorly explored. This study generated a diploid genome assembly for the golden pheasant ( <i>Chrysolophus pictus</i>), a species distinguished by the vibrant plumage of males. Each haploid genome assembly included complete chromosomal models, incorporating all microchromosomes. Analysis revealed extensive tandem amplification of immune-related genes across the smallest microchromosomes (dot chromosomes), with an average copy number of 54. Structural variation between the haploid genomes was primarily shaped by large insertions and deletions (indels), with minimal contributions from inversions or duplications. Approximately 28% of these large indels were associated with recent insertions of transposable elements, despite their typically low activity in bird genomes. Evidence for significant effects of transposable elements on gene expression was minimal. Evolutionary strata on the sex chromosomes were identified, along with a drastic rearrangement of the W chromosome. These analyses of the high-quality diploid genome of the golden pheasant provide valuable insights into the evolutionary patterns of structural variation in avian genomes.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"46 1","pages":"75-86"},"PeriodicalIF":4.0,"publicationDate":"2025-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11891004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143025387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}