Screening Of Key Genes For Adaptation To Drought Environment In Camels

Raising ruminant livestock,such as cows and sheep,is a crucial economic activity in arid and semi-arid regions of China.However,climate change has caused multiple environmental challenges,such as extreme temperatures,photoperiod changes,and frequent drought events,which have disrupted the fragile ecosystems of these regions.These changes have resulted in adverse effects on the growth,reproduction,productivity,and natural immunity of livestock,leading to increased susceptibility to diseases,and even death,which cause significant economic losses to animal husbandry.Hence,the identification of vital genes contributed to animal drought adaptation is significant to animal husbandry in China.Ungulate animals,such as Bactrian camel(Camelus bactrianus)and Arabian camel(Camelus dromedarius)in Camelidae,as well as some ruminants of Hippotraginae as Addax(Addax nasomaculatus),Scimitar oryx(Oryx dammah),and Gemsbok(Oryx gazella)in Hippotraginae,have evolved unique adaptive features to cope with challenges such as the extreme temperatures,water scarcity,and limited food availability in desert environments.These features include being able to carry out normal life activities for 3-5 days without drinking water,efficient fat storage and utilization,and stress responses at extreme temperatures.With the advancement of sequencing technology,the genomes of ungulates with broad ecological adaptability have been decoded.In this study,we assembled a high-quality genome of domesticated Bactrian camel and used comparative genomics approach to identify genes related to the extreme desert environment adaptation of the Camelidae and Hippotraginae lineages.The main results are as follows:1.We assembled a high-quality chromosome-level genome of domesticated Bactrian camels using Pac Bio Hifi sequencing combined with Hi-C technology.The genome size was estimated to be 2.4 Gb,and the quality assessment yielded a Contig N50 and Scaffold N50 of58.8 Mb and 79.9 Mb,respectively.The genome completeness evaluation using BUSCO was96.1%,and repeat sequences accounted for 29.8% of the genome.A total of 28,877 genes were annotated using a combination of transcriptome-based prediction,de novo prediction,and homology-based prediction methods.2.Positive selection and rapid evolution analyses were conducted to identify convergent positive selected genes and convergent rapidly evolving genes contributed to desert adaptation between Camelidae and Hippotraginae lineages.A total of 1482 and 751 candidate positive selection genes as well as 2,823 and 1,846 candidate rapidly evolving genes were identified for the Camelidae and Hippotraginae lineages,respectively.Finally,399 shared rapidly evolving genes and 101 convergent positive selection genes were obtained,involving various aspects such as fat metabolism(e.g.LAMP1,ACAD9,DLIN1),glucose metabolism(e.g.RUVBL1),blood pressure regulation(e.g.RAMP1),water reabsorption(e.g.AVIL,HMGXB4),and immune stress response(e.g.EAF2).3.We performed KEGG(Kyoto Encyclopedia of Genes and Genomes)and GO(Gene Ontology)pathway enrichment analysis on positively selected genes and rapidly evolving genes in the Camelidae and Hippotraginae lineages,and identified convergent pathways related to desert adaptation.The positive selected genes of both lineages were significant enriched in 14 pathways,including metabolic pathways(hsa05231),olfactory transduction(hsa04740),smooth muscle contraction(hsa04270),and peroxisome(hsa04146).101 convergent positively selected genes were significantly enriched in 106 GO terms,and399 convergent rapidly evolving genes were annotated to 387 significant GO terms,mainly involving environmental stress response(e.g.GO:0002323,p = 0.008;GO:0009267,p =0.016),lipid metabolism(e.g.GO:0046460,p = 0.021;GO:0006635,p = 0.012),insulin regulation(e.g.GO:0061178,p = 0.026),kidney development(e.g.GO:0072001,p =0.040),ion transport(e.g.GO:0098656,p = 0.007),and heart development(e.g.GO:0055024,p = 0.044).4.We analyzed the transcriptome data of liver,kidney,and adipose tissues from human,mouse,cattle,goat,and camel,and identified differentially expressed genes among these species.A total of 857,570,and 603 differentially expressed genes were identified in the liver,kidney,and adipose tissues of camel and other species,among which 58 differentially expressed genes were under positive selection and rapid evolution pressure,including SIRT2,AP2A2,AKT2,CNOT3,PACS2,CAP1,STRIP1,PPP3 CB,LRP1,and ALDH2.In summary,we assembled a high-quality chromosome-level genome of the domestic Bactrian camel,and performed comparative genomic analysis on the Camelidae and Hippotraginae lineages living in arid desert environments to identify convergent positive selection and rapid evolution genes and pathways.By combining transcriptome data of camel tissues,we identified some adaptive genes and pathways that enable camels to cope with food and water scarcity,extreme temperatures,and other challenges in the extreme desert environment.By analyzing the genetic basis of convergent adaptation to desert environments in related species of ruminants,this study aims to provide a theoretical basis for screening candidate targets for breeding drought,and heat stress-tolerant ruminants,enhancing their resilience to climate change,and ultimately supporting more efficient and stable development of animal husbandry in arid and semi-arid regions.