| Acer catalpifolium Rehd.(Sapindaceae,Acer),is a perennial deciduous broad-leaved tree species and is mainly distributed northwest edge of Chengdu plain,Sichuan province,China.This area is also known as the Rainy Zone of West China.Due to the constant population decline of A.catalpifolium and its narrow natural distribution,it has been listed in the second-class protection plant of China,and wild plants with small populations(WPESP)rescue and protection plan in 2009.Thus,A.catalpifolium is under high priority for urgent management intervention.Due to its lack of genomic and genetic information,the implementation of effective conservation strategies,conservation priorities,and adaptive evolution research is limited.Hence,we assembled a chromosomal-level genome of A.catalpifolium,chloroplast genome,and used SLAF genome sequencing technology to precede population genetics analysis to conduct a comprehensive interpretation in several aspects,including genome structure evolution,phylogenetic analysis and genetic mechanism of endangered A.catalpifolium.Thus,the main research results are as follows:A.catalpifolium genome overview: The genomes of A.catalpifolium were obtained by integrating Pac Bio Sequel data(～ 34.39Gb),Illumina data(～ 34.40Gb)and Hi-C sequencing data(～ 45.55Gb).The total length was 654.51Mb(scaffold N50 was 37.58Mb),86% could be located on 13 chromosomes.A total of 35,326protein-coding genes were annotated,and BUSCO assessment estimated ～93.3%genome completeness for the assembly.A.catalpifolium chloroplast genome sequence was obtained from the genome sequencing data.The total length of the chloroplast genome was 157,349 bp,the GC content was 37.9%,and contained 117 genes.Phylogenetic analysis and genomic evolution: Similar to Vitis vinifera,A.catalpifolium underwent only ancient whole-genome duplication(WGD)after angiosperm formation.Phylogenetic analysis showed that A.catalpifolium and A.yangbiense were separated about 6.9 million years ago.The chloroplast genomes of A.catalpifolium and nine related species were sequenced and assembled,and a total of48 chloroplast genomes of included previously published Acer species were compared and analyzed.Acer chloroplast genomes phylogenetic analysis showed that A.catalpifolium and A.miaotaiense had the closest phylogenetic relationship.Molecular basis of the Rainy Zone of West China environmental adaptability of A.catalpifolium: According to the unique climatic environment in the Rainy Zone of West China,we compared the genomics to detect an expanded number of the FRS-FRF gene family in A.catalpifolium,which involved in various shade avoidance responses.That may be related to the lack of light in the Rainy Zone of West China.The positive selection analysis of Acer species chloroplast genes showed that two genes(psa I and psb K)were positively selected,imply different light environment is a crucial selection pressure for Acer species.However,this may make A.catalpifolium to becoming specific taxa in this region and weaken the ability to various habitats.In addition,candidate genes of key enzymes in the lignin synthesis pathway of A.catalpifolium were identified.These genes might promote the high growth of A.catalpifolium stem and obtain more light resources in this region,but it has also led to more deforestation threats.Genetic mechanism of endangered A.catalpifolium: The efficient population size of A.catalpifolium began to decrease from 0.3 mya.This continuous decrease has occurred during the Last Glacial Maximum,but the rate of population decline did not increase significantly.However,in the relatively warm post-glacial period,the efficient population size did not recover,which may have resulted in the loss of much genetic diversity in A.catalpifolium.A total of 23 A.catalpifolium samples were used for SLAF genome sequencing technology to precede population genetics analysis.Results show that A.catalpifolium group expected heterozygosity(Exp＿Het)mean value was 0.106,that far lower than other maple species.Comparative genomic analysis revealed positive selection between the conserved domains of the NAC(No Apical Meristem)family in the A.catalpifolium genome.That plays essential roles in embryo,flower,vegetative growth,defence,and response to abiotic stresses.Deleterious mutations were identified in representative genes of these two gene families,which might harm their environmental adaptation in Acer species.In summary,A.catalpifolium endangered mainly due to the historical climate,that it’s population declines rapidly since the Quaternary period and has not increased after the glacial period.Population genetics analysis shows that A.catalpifolium genetic diversity critically endangered,and it is urgent to protect the WPESP species.During the evolution process,the A.catalpifolium genome has been adapted to the specific climatic conditions in the Rainy Zone of West China.Since its low population accumulated the harmful mutations,and due to the impact of genetic drift,its genetic diversity was seriously lost,which may lead to further population decline.In this study,we studied the nuclear genome,chloroplast genome,and population genetics to provide genetic information for the protection and population rejuvenation of the Acer genus and other endemic species in the Rainy Zone of West China. |
