Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.

Objective: Parathyroid hormone like hormone (PTHLH), as an essential factor for bone growth, is involved in a variety of physiological processes. The aim of this study was to explore the role of PTHLH gene in the growth of antlers.Methods: The coding sequence (CDS) of PTHLH gene cDNA was obtained by cloning in sika deer (Cervus nippon), and the bioinformatics was analyzed. The quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the differences expression of PTHLH mRNA in different tissues of the antler tip at different growth periods (early period, EP; middle period, MP; late period, LP).Results: The CDS of PTHLH gene was 534 bp in length and encoded 177 amino acids. Predictive analysis results revealed that the PTHLH protein was a hydrophilic protein without transmembrane structure, with its secondary structure consisting mainly of random coil. The PTHLH protein of sika deer had the identity of 98.31%, 96.82%, 96.05%, and 94.92% with Cervus canadensis, Bos mutus, Oryx dammah and Budorcas taxicolor, which were highly conserved among the artiodactyls. The qRT-PCR results showed that PTHLH mRNA had a unique spatio-temporal expression pattern in antlers. In the dermis, precartilage, and cartilage tissues, the expression of PTHLH mRNA was extremely significantly higher in MP than in EP, LP (p<0.01). In the mesenchyme tissue, the expression of PTHLH mRNA in MP was significantly higher than that of EP (p<0.05), but extremely significantly lower than that of LP (p<0.01). The expression of PTHLH mRNA in antler tip tissues at all growth periods had approximately the same trend, that is, from distal to basal, it was first downregulated from the dermis to the mesenchyme and then continuously up-regulated to the cartilage tissue.Conclusion: PTHLH gene may promote the rapid growth of antler mainly through its extensive regulatory effect on the antler tip tissue.

The Asian elephant ( Elephas maximus ), a crucial flagship and umbrella species in forest ecosystems, possesses significant conservation value. However, it has been categorized as endangered due to several factors, including land use change, human disturbance, and climate change. To evaluate the genetic diversity of Chinese Asian elephant populations and provide a scientific basis for the establishment of the Asian Elephant National Park, microsatellite and mitochondrial DNA analyses were conducted on seven populations distributed across Yunnan Province, China. A total of 121 unique genotypes and five mitochondrial DNA (mtDNA) haplotypes were identified. The results revealed that all populations exhibited varying degrees of inbreeding, with the Mengla population showing the highest inbreeding levels. Significant genetic differentiation was observed between the Mengla and other populations. Interestingly, the Yexianggu population exhibits relatively high genetic diversity despite having undergone a population bottleneck and exhibited significant heterozygote excess. Nevertheless, the overall genetic diversity of Chinese Asian elephants remains relatively low compared to that of populations in other countries. To ensure the long‐term viability of the Nangunhe population, it is imperative to facilitate gene flow between this and other populations. Finally, based on geographic subdivision analysis, we propose that the seven Asian elephant populations should be considered as three conservation management units, namely unit 1 (Nangunhe), unit 2 (Mengla), and unit 3 (Yexianggu, Mengman, Puwen, Kongge, and Menga). This study provides a solid reference for the scientific conservation of the Asian elephant in the future.

The catfish genus Pseudecheneis consists of small freshwater catfish that live at the bottom of fast-flowing streams. The genetic information carried by extant freshwater fish can provide new insights into deciphering the evolutionary processes of rivers. However, existing studies often rely on limited molecular markers, which are insufficient to thoroughly resolve genetic information and complex evolutionary relationships. We have deciphered the first high-quality Telomere-to-Telomere (T2T) chromosome-level genome of Pseudecheneis, with a genome size of 574.82 Mb and a contig N50 of 22.76 Mb. A total of 19,787 protein-coding genes were annotated, of which 98.4% were successfully functionally annotated. This study provides important references for clarifying the phylogenetic relationships and evolutionary history of Pseudecheneis, and also offers valuable data support for exploring the interrelationships among structure, function, and adaptation.

As a morphologically diverse representative of the Glyptosterninae, Tremeuchiloglanis macrotrema is vital for resolving the subfamily’s phylogeny and biogeography. However, limited genomic resources currently restrict research into its functional biology and mechanisms of environmental adaptation. Herein, we constructed the first telomere-to-telomere (T2T) genome assembly of Tremeuchiloglanis macrotrema by integrating Illumina, PacBio, ONT ultra-long reads, and Hi-C data. The assembly represents the first T2T reference genome of Tremeuchiloglanis. The final genome size was 860.15 Mb, with the majority of sequences successfully anchored onto 26 chromosomes. This high-quality genome assembly and annotation provide a valuable resource for protecting the genetic diversity of Tremeuchiloglanis and studying the adaptation mechanisms of aquatic organisms in fast-flowing riverine habitats, and facilitating future classification and evolutionary research.

Plateau wetlands provide important wintering habitats for migratory waterbirds, making the assessment of environmental contamination relevant to their conservation. Characterizing potentially toxic elements in lake sediments provides a basis for identifying contamination patterns and prioritizing environmental monitoring in these habitats. Here, we assessed potentially toxic element contamination in surface sediments and potential ecological risks in three plateau lakes supporting wintering black-necked cranes (Grus nigricollis) in Shangri-La, Yunnan, China. In January 2025, 131 composite sediment samples (0–20 cm) were collected from Bitahai, Shudu, and Napahai lakes. Concentrations of Cu, Zn, Pb, As, Hg, and Cd were determined by inductively coupled plasma mass spectrometry. Contamination and potential ecological risks were evaluated using the geo-accumulation index (I_geo) and potential ecological risk index (PERI), respectively. Potential sources were investigated using EPA PMF 5.0. Sediments were generally unpolluted to slightly polluted. Mean PERI values were 65.2, 62.7, and 76.5, respectively, indicating low potential ecological risk, with Cd and Hg contributing most. PMF resolved four factors tentatively associated with traffic/domestic emissions, agricultural/combustion inputs, localized inputs, and natural/regional sources. These findings provide a baseline for sediment monitoring and environmental management of black-necked crane wintering habitats, with particular attention to Cd, Hg, and As.