| Abalone is known as the first of the "Eight Treasures of Seafood" because of its rich nutrition.In the past 30 years,the abalone farming industries in China have been booming,and China has become the top abalone farming and consuming country in the world.After nearly 20 years of southward domestication,the temperate species Pacific abalone has successfully adapted to the high-temperature environment in southern China.Benefiting from the success of south forward domestication of Pacific abalone Haliotis discus hannai,southern China,especially Fujian province has gradually become the main abalone farming area in China even in the world.The rapid southward domestication of Pacific abalone provided a good model for studying the adaptation potential of marine animals in response to high temperature.Therefore,a comprehensive analysis of the molecular mechanism of rapid adaptation to high temperature in abalone will not only genetically improve the thermal tolerance of abalone to reduce economic losses,also provide insights into how marine animals respond to global warming.However,the massive mortality of abalone due to high temperature in summer is still a major problem for the abalone farming industry in southern China.Crossbreeding is widely applied in shellfish breeding,as an effective genetic improvement method.In our group,we crossed Pacific abalone with green abalone H.fulgens to produce hybrid "lvpan" abalone with thermal tolerance and growth,greatly reducing summer mortality events.It is essential to uncover the molecular mechanism of heterosis for thermal tolerance of hybrid abalone.It will not only be helpful to the breeding of thermal-tolerant abalone species,but also could provide theoretical guidance for the sustainable development of the abalone farming industry.In this study,we focused on the molecular mechanism of high-temperature tolerance in abalone.Then we investigate the molecular mechanism underlying the rapid adaptation of abalone to high temperature and heterosis for thermal tolerance in hybrid abalone by a intergration of genomics,transcriptomics,population genetics,and methylation genomics.(1)De novo sequencing assembly of four abalone speciesWe used a combination of second-generation and third-generation highthroughput sequencing,and further combined genetic linkage map and Hi-C sequencing technologies to first report the high-quality chromosomal-scale genomes for four species of abalone,including Pacific abalone,small abalone(H.diversicolor),giant abalone(H.gigantea)and green abalone(H.fulgens)(Scaffold N50:54～74 Mb,BUSCO scope.88%-95.5%,reads mapping rate>98%),which are better than other published abalone genomes.These genome data lay a good foundation for the subsequent molecular biology research and genetic breeding of abalone.(2)Comparative genomic study of four abalone speciesBased on the phylogenetic analysis of the reported genomes of abalones,the time of the two species divergence events in the genus Haliotis were estimated.Firstly,the divergence time of the two main branches of the genus Haliotis was about 121.3 Mya,while later,the abalone species of the North Pacific branch further diverged at about 52.7 Mya,which was relatively later than the divergence time of the other branch(73.8 Mya).By comparative genomic approaches,two significant TE insertion events were identified in all four abalone species,presumably related to the abalone species divergence and the biodiversity outbreak of the genus Abalone.Meanwhile,the results of macro-synteny analysis exhibited substantial fragmental rearrangement among the four abalone species,suggesting that genomic rearrangement may have occurred in abalone ancestors prior to differentiation.Together,TE burst and genomic rearrangement may be potential factors driving the biodiversity explosion and adaptive evolution of the genus Haliotis.(3)Plasticity divergence of Pacific abalone between the northern China population and the southward domesticated populationConducting temperature tolerance assessment and common garden experiments,we found that the two populations showed significant phenotypic plasticity differences in response to high-and low-temperature stresses.Further combined with transcriptomics and DNA methylation,the study revealed that the two populations showed significant differences in transcriptional plasticity in response to hightemperature stress,which contributed to the rapid adaptation of the abalone to high temperature.The functional results of DEGs and DMGs indicated that the southern population might repair damage and rapidly restore normal body function by efficiently regulating the expression of genes related to energy metabolism and immune response.The results showed that the southward domesticated population could repair damage and quickly restore normal body function.The domesticated population may adopt a more efficient regulation of energy metabolism and immune response-related gene expression to adapt to a high-temperature environment.(4)Population genetics analysis for the western Pacific Ocean populations of Pacific abaloneWe performed systematical population genetic analysis based on the wholegenome sequencing of five representative populations in the western Pacific Ocean of the Pacific abalone.This study found that the five groups significantly clustered into five categories,which were consistent with their geographic distribution.Integrating the analysis of population structure and gene flow,we can conclude that the Pacific abalone is probably originated from southern Japan.Furthermore,a selective sweep analysis was done between the northern China population and the southward domesticated population.The results showed that the selected genes were mainly involved in apoptosis,energy metabolism,immunity,and transmembrane transportrelated progress,probably resulting from rapid adaptation to high temperature in the southward domesticated population.(5)De novo sequencing assembly and chromosome rearrangement of heterozygous diploid green abaloneIn this study,whole-genome de novo sequencing was conducted to assemble the genome of hybrid abalone,with a very high heterozygosity rate(2.67%).Combining Pacbio SMRT and Hi-C sequencing,two sets of haplotype chromosome-scale genome of hybrid abalone were finally obtained by haplotype typing,with a genome size of 2.59 Gb,containing 36 chromosomes and Scaffold N50 of 70.6 Mb.Integrating the chromatin interaction analysis and macro-synteny analysis between the hybrid abalone and its parents,it suggested that the interspecific hybridization led to chromosomal rearrangement in the hybrid abalone.During the rearrangement process in the hybrid abalone genome,large-scale chromosomal rearrangement may occur in the F’subgenome while the D’ subgenome serves as a template,suggesting that the subgenome dominance effect exists.(6)Molecular analysis of the thermal tolerance heterosis of the hybrid abaloneA 218-day gradient thermoregulation experiment ranging from 22 to 28℃ was conducted on Pacific abalone,green abalone,and hybrid abalone.It showed that the optimal growth water temperature of Pacific abalone,green abalone,and hybrid abalone were 16～24 ℃,22～28 ℃,and 18～26 ℃,respectively,and that the hybrid abalone had the significant advantages of heat tolerance heterosis.By resequencing the hybrid abalone population and analyzing the structural variation,we found that a large scale of structural variations occurred in the hybrid abalone relative to its parental populations.Most of the homologous genes with highimpact structural variations were identified,and functional enrichment analysis showed that these genes were mainly involved in energy metabolism-related pathways.Transcriptome analysis revealed that non-additive expressed genes were widely identified in the hybrid abalone after acute temperature stress.The non-additive genes were all over-expressed in response to the high temperature.Further functional analysis showed that these genes were mainly involved in energy metabolism and immunerelated pathways.Together,our study suggested that the non-additive expressed genes might play vital roles in response to the high-temperature stress,and probably serve as potential factors in the thermal tolerance heterosis of the hybrid abalone. |
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