Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution.

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 the 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.

lncRNA Sequencing of Antler Mesenchymal Tissue Revealed that the Regulatory Network of Antler Cell Proliferation and Differentiation.

Antlers have been widely studied due to their unique physiological characteristics, such as rapid growth, periodic shedding and regeneration. However, little is known about how antler growth is regulated by long non-coding RNA (lncRNA). The aim of the present study was to identify the lncRNAs expression profile and explore the function of lncRNAs during the antler growth. Herein, RNA-sequencing technology (RNA-seq) was performed on the three growth periods (early developmental period: EP, middle developmental period: MP, later developmental period: LP) of male sika deer (Cervus nippon) antler, 16 differentially expressed lncRNAs (DE lncRNAs) and 11 DE lncRNAs were identified in EP vs MP and MP vs LP related to cell proliferation and cell differentiation, respectively. Finally, lncRNAs-mRNAs co-expression networks were constructed based on the identified DE lncRNAs and their potential trans-target genes. The result reveals that lncRNAs may play diverse roles in different periods of antler growth. It provides a novel perspective for revealing the molecular mechanism of antler growth.

Analysis of genetic information from the antlers of Rangifer tarandus (reindeer) at the rapid growth stage.

Reindeer is the only deer species in which both males and females regularly grow antlers, providing an excellent model for studying the rapid growth and annual regeneration of antlers. The study of genetic information from reindeer is the basis for revealing the unique mechanism of antler growth. In the present study, we obtained 18.86 GB of clean reads, which were assembled to obtain 94,575 unigenes (average length: 704.69). Among these reads, 30,980 sequences were identified by searching a database of known proteins and then annotated with Gene Ontology (GO) terms, Clusters of Orthologous Groups (COG) classifications and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. All 7,480 simple sequence repeats (SSRs) were detected. A total of 84,435 and 82,226 high-quality single-nucleotide polymorphisms (SNPs) were identified in male and female reindeer, respectively. We identified 31 genes that were highly expressed in reindeer antlers. These genes regulate cell activities that are closely associated with the process of rapid tissue growth. Our results provide a basis for studying reindeer antlers and for further studying the molecular genetics, population genetics, and functional genomics of reindeer.

Origins of Chinese reindeer (Rangifer tarandus) based on mitochondrial DNA analyses.

The most southern population of reindeer (Rangifer tarandus) inhabits northeastern China, but the migration route and origin of this population have not been confirmed. The sequences of mitochondrial DNA control regions from domestic and wild herds from Eurasia and China were analysed. The results showed that the Chinese reindeer population originated independently from north-central Russian domestic herds, belonging to a large reindeer population that was present across Beringia during the last glacial period. Some studies have reported that the Chinese reindeer population is closely related to wild forest reindeer herds in Russia. Our results, however, indicate that wild forest reindeer herds of southeastern Russia contributed little or nothing to the Chinese reindeer herd gene pool. Chinese reindeer herds have a much greater genetic similarity to more northerly distributed tundra-type herds that inhabit open areas. The present findings will be essential for future conservation planning for Chinese reindeer.

DNA methylation and mRNA expression of COL6A3 in antler mesenchyme of female and male reindeer.

BACKGROUD: Reindeer is the only deer species that both male and female produce antlers, which provides a particularly interesting case in studying the differences between antlers of the two sexes. Alpha 3(VI) Collagen Gene (COL6A3), forms a microfibrillar network associated with the structural integrity and biomechanical properties, has been found to be one of the differentially expressed genes in antler mesenchyme of female and male reindeer. OBJECTIVE AND METHODS: The promoter sequence of reindeer COL6A3 gene was obtained using the cloning technology and analyzed by the bioinformatics methods. Bisulfite sequencing PCR (BSP) was used to detect the methylation status of the COL6A3 promoter in reindeer antler mesenchyme. Real-time quantitative PCR was used to detect COL6A3 expression in the antler mesenchyme of female and male reindeer. RESULTS: Sequence analysis revealed that the reindeer COL6A3 partial promoter sequence was 983 bp including the possible promoter region at + 105 bp to + 155 bp. Homology and phylogenetic analysis indicated that the COL6A3 promoter of reindeer had the closest genetic distance with Bos taurus, Capra hircus and Ovis aries. BSP results indicated that the methylation level of COL6A3 promoter in the female reindeer antler mesenchyme was significantly higher than in the male. Correlating with increased methylation status, we also found that COL6A3 mRNA expression in female reindeer antler mesenchyme was significantly lower than in the male. CONCLUSION: The higher methylation level of the COL6A3 gene in female reindeer antler mesenchyme coincides with decreased COL6A3 mRNA expression, thereby affecting the transposon silencing mechanism and possibly contributing to apparent differences of antlers in female and male reindeer.

Molecular cloning and expression analysis of annexin A2 gene in sika deer antler tip.

OBJECTIVE: Molecular cloning and bioinformatics analysis of annexin A2 (ANXA2) gene in sika deer antler tip were conducted. The role of ANXA2 gene in the growth and development of the antler were analyzed initially. METHODS: The reverse transcriptase polymerase chain reaction (RT-PCR) was used to clone the cDNA sequence of the ANXA2 gene from antler tip of sika deer (Cervus Nippon hortulorum) and the bioinformatics methods were applied to analyze the amino acid sequence of Anxa2 protein. The mRNA expression levels of the ANXA2 gene in different growth stages were examined by real time reverse transcriptase polymerase chain reaction (real time RT-PCR). RESULTS: The nucleotide sequence analysis revealed an open reading frame of 1,020 bp encoding 339 amino acids long protein of calculated molecular weight 38.6 kDa and isoelectric point 6.09. Homologous sequence alignment and phylogenetic analysis indicated that the Anxa2 mature protein of sika deer had the closest genetic distance with Cervus elaphus and Bos mutus. Real time RT-PCR results showed that the gene had differential expression levels in different growth stages, and the expression level of the ANXA2 gene was the highest at metaphase (rapid growing period). CONCLUSION: ANXA2 gene may promote the cell proliferation, and the finding suggested Anxa2 as an important candidate for regulating the growth and development of deer antler.

Analysis on Genetic Diversity of Reindeer (Rangifer tarandus) in the Greater Khingan Mountains Using Microsatellite Markers.

Jian-Cheng Zhai, Wei-Shi Liu, Ya-Jie Yin, Yan-Ling Xia, and He-Ping Li (2017) The only population of reindeer (Rangifer tarandus) in China, herded extensively by the Ewenki people, is the most southern population in the world. Genetic diversity plays a key role in the survival of endangered reindeer. To systematically understand the genetic variability of reindeer in China, 163 individuals from 8 populations were analyzed using 11 microsatellite loci. A total of 85 alleles were detected and the average number of alleles per locus was 7.7. The observed heterozygosity and expected heterozygosity ranged from 0.3736 to 0.5299 and from 0.6491 to 0.7608. Hardy-Weinberg equilibrium analysis indicated that a de ciency of heterozygotes existed in all eight populations. Both the FST and AMOVA analyses showed a low level of genetic di erentiation among populations. UPGMA dendrogram revealed that population SYL formed one cluster, separating from the other populations. Then the GWQ and YSH populations formed another cluster and clustered with the BDX, BLJY, DML, DW and MLYS populations. Increasing the current exchange rate of reindeer among different populations and establishing natural reserve may be the e ective approaches to conserve the fragile reindeer populations in China.

[Mapping environmental vulnerability from ETM + data in the Yellow River Mouth Area].

The environmental vulnerability retrieval is important to support continuing data. The spatial distribution of regional environmental vulnerability was got through remote sensing retrieval. In view of soil and vegetation, the environmental vulnerability evaluation index system was built, and the environmental vulnerability of sampling points was calculated by the AHP-fuzzy method, then the correlation between the sampling points environmental vulnerability and ETM + spectral reflectance ratio including some kinds of conversion data was analyzed to determine the sensitive spectral parameters. Based on that, models of correlation analysis, traditional regression, BP neural network and support vector regression were taken to explain the quantitative relationship between the spectral reflectance and the environmental vulnerability. With this model, the environmental vulnerability distribution was retrieved in the Yellow River Mouth Area. The results showed that the correlation between the environmental vulnerability and the spring NDVI, the September NDVI and the spring brightness was better than others, so they were selected as the sensitive spectral parameters. The model precision result showed that in addition to the support vector model, the other model reached the significant level. While all the multi-variable regression was better than all one-variable regression, and the model accuracy of BP neural network was the best. This study will serve as a reliable theoretical reference for the large spatial scale environmental vulnerability estimation based on remote sensing data.

[Effects of LFA-1 costimulation on proliferation and IgG production of PBMCs from lupus nephritis patients].

AIM: To study the effect of lymphocyte function associated antigen-1(LFA-1) costimulation on proliferation and immunoglobin production of peripheral blood mononuclear cells(PBMCs) form lupus nephritis(LN) patients. METHODS: 29 LN patients were enrolled in this study, and 12 healthy persons served as control. PBMCs from LN patients and healthy persons were obtained by Ficoll density gradient centrifugation, and cell proliferation was detected by (3)H-TdR incorporation. IgG content in cultural supermatant was detected by ELISA. RESULTS: Stimulation of anti-CD3 mAb alone could enhance the proliferation and IgG production of PBMCs from 29 LN patients,while the effects on PBMCs from patients in active phase were stronger than those from the patients in the inactive phase (P<0.01). But anti-CD3 mAb had no influenence on PBMCs from healthy persons.The costimulation of anti-CD3 mAb and LFA-1 could increase proliferation and IgG production of PBMCs from LN patients and healthy persons. The effects of this costimulation decreased in turn from active and inactive LN patients to normal persons (P<0.01). The costimulant effects of LFA-1 was inhibited by anti-LFA-1 mAb. CONCLUSION: The effects of enhancing PBMC proliferation and IgG production by LFA-1 may be a mechanism of LN pathogenesis.