Adaptive Evolution Research Of Spiders Based On Genome

Adaptive evolution is a process of interaction between environmental changes and genetic variation in organisms.As a result,organisms are well adapted to the environment.Exploring the adaptive evolution of animals is to find the corresponding relationship between the external environmental changes and the changes of internal genetic material or metabolic pathway,so as to lay the foundation for predicting the changes of some organisms that may be caused by the existing environment,as well as the modification of other organisms with human’s purpose(such as artificial domestication).Spiders are ancient animals that have been evolving on earth for about 400 million years and provide basis for studying adaptive evolution.Spiders are cosmopolitan in distribution except Antarctica and can be found in almost all terrestrial living environments e.g.from coastal to inland,from plain to plateau,from underground to tree canopy,from leaf litter to rock crevices,and even under fresh water.In order to adapt to different environments,spiders have evolved different body shapes,colors,even different tissue and organ structures.Some are good at spinning webs,while others are good at hunting.Some are good at roaming on the surface,some are good at climbing,some are good at living in underground caves,and some are good at living underwater.The cause of such behavioral changes is due to the differential expression of different genes.With the advances in genome sequencing technology,more and more spider species genome has been sequenced,and due to the continuous progress of bioinformatics and genomics has opened a new era of adaptive evolution research.This study chooses two spider species Trichonephila antipodiana(Family Araneidae)and Argyroneta aquatica(Family Dictynidae)to obtain chromosome-level genome based on Pac Bio/Nanopore and Hi-C sequencing and resolved their adaptive evolution problems,like polyphagous adaptability and adaptation to water environment.The specific results are as follows:1.We present a chromosome-level genome of T.antipodiana constructed based on Pac Bio and Hi-C sequencing.Survey analysis based on illumina predicted a genome assembly size of 2.15 Gb.The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb.Hi-C scaffolding assigned 98.5% of the bases to 13pseudo-chromosomes,and BUSCO completeness analysis revealed that the assembly included 97.8% of the complete arthropod universal single-copy orthologs.We predicted 19,001 protein-coding genes with a mean number of 7.24 exons and 6.12 introns per gene,and mean exon and intron lengths of 247.46 bp and 3.73 kb,respectively.Furthermore,we found that a total of 18,303(96.33%)genes had at least one record in the Swiss Prot or Tr EMBL databases.Inter Pro Scan and Egg OG analyses identified the protein domains for 14,705(77.39%)genes,12,226 GO terms,9,465 KEGG ko terms,5,788 KEGG pathways,14,325 COG categories,and 3,183 Enzyme Codes.2.Polyphagy of T.antipodiana is highly related to the expansion of P450 gene family.For further analysis of the detoxification ability of T.antipodiana,we manually annotated the genes of detoxification-related enzymes(P450s,CCEs,GSTs,and ABCs).In the genome of T.antipodiana,we identified 167 CYP genes,comprising four major classes: CYP2(57 genes),mitochondrial P450(19),CYP3(43),and CYP4(48).The results indicate the remarkable expansion of CYP2 and CYP3 clade genes of T.antipodiana.We identified 48 CCE genes,among which the overwhelming majority(47)belongs to neuro/developmental class,and the remaining single gene belongs to the hormone/semiochemical class.We identified 22 GST genes,and phylogenetic analyses of the cytosolic revealed the five different classes of these genes named as,Delta/Epsilon(2 genes),Mu(15),Theta(1),Sigma(2),and Zeta(2),among which the Mu class is the largest and shows considerable expansion in T.antipodiana.And 47 ABC genes was found belonging to seven different classes: ABCA(10 genes),ABCB(12),ABCC(11),ABCD(3),ABCE(1),ABCF(3),and ABCG(7).We also analyzed the P450 genes expression in the T.antipodiana by RNA-Seq.Further analysis of the T.antipodiana genome architecture reveals an ancient whole-genome duplication event,based on 2 lines of evidence:(i)large-scale duplications from inter-chromosome synteny analysis and(ii)duplicated clusters of Hox genes located on chromosomes 8and 12,respectively.3.Chromosome-level genome sequencing of water spider constructed based on Nanopore and Hi-C sequencing.Survey analysis based on illumina predicted a genome assembly size of 721.78 Mb.The assembled genome is 753.77 Mb in size with a contig N50 of 2.44 Mb and a scaffold N50 of 67.27 Mb.Hi-C scaffolding assigned95.98% of the bases to 11 pseudo-chromosomes,and BUSCO completeness analysis revealed that the assembly included 97.7% of the complete arthropod universal single-copy orthologs.We predicted 17,632 protein-coding genes with a mean number of 7.53 exons and 6.31 introns per gene,mean exon and intron lengths of 313.2 bp and1.84 kb,respectively.Furthermore,we found that a total of 16,381(92.9%)genes had at least one record in the Swiss Prot or Tr EMBL databases.Inter Pro Scan and Egg OG analyses identified the protein domains for 15,973(90.59%)genes,9,475 GO terms,10,574 KEGG ko terms,6,509 KEGG pathways,14,384 COG categories,and 3,962 Enzyme Codes.4.Water spiders adapt to the underwater with hypoxic environment depending on Hemocyanin and HIF-1 signal pathway.Hemocyanin is the main functional protein for oxygen transport in water spider.There are seven hemocyanin genes in water spider,all of which belong to subunit types g that are tandem repeat genes distributed on chromosome 7,while the other a-f subunit types genes are lost.Compared with other non–aquatic spiders,the hemocyanin sequence in water spider changed greatly,that indicates these genes have special adaptability role to water environment.The hemocyanin protein combine to form multiple hexames 12-mer(2×6),which may have higher oxygen carrying capacity.The analysis of hypoxic tolerance factor genes,revealed that two HIF-1α and one HIF-β genes regulate downstream signaling pathways to adapt to long-term hypoxic conditions that is also supported by the transcriptome data.The lack of the Elongin C genes in the HIF-1 signal pathway may result in failure to synthesize the E3 ubiquitin ligase complex and ultimately leads to the failure to degrade the HIF-1α protein.It was also confirmed that HIF-1α gene expression was very high in the transcriptome of water spider.The position of expression was consistent with the downstream pathway,which further confirmed the regulatory role of HIF-1 signal pathway in its adaptation to underwater hypoxic environment.The downstream genes regulated by HIF-1 signaling pathway in water spider include i NOS,e NOS,Ang PT,FLT1,GLUT1,HK,PFKL,GAPDH,PGK1,Aldoa,e NO1 and Bcl2.The ultimate effect of these genes is in two directions.One is to enhance the transport of oxygen for underwater living;on the other hand,the reduction of oxygen consumption is embodied in promoting anaerobic metabolism,regulating cell proliferation and apoptosis.What’s more,gene families related to anaerobic metabolism,cell proliferation and apoptosis were also found to be expanded during KEGG enrichment analysis.The expression of the above listed genes continues to be enhanced,and the expansion of gene families helps water spiders to adapt the hypoxic environment underwater.In summary,high-quality chromosomes level of two spider species genomes were obtained and their adaptive evolution was analyzed by bioinformatics techniques that elucidates the polyphagy in T.antipodiana,which highly correlated with the expansion of the P450 gene family.The structural changes of hemocyanin and the continuous hypoxic control in the HIF-1 signal pathway contributes to the adaptability of the water spider to the extreme water environment.