Conservation Genomic Research Of Acanthochlamys Bracteata(velloziaceae)

Acanthochlamys bracteata P.C.Kao(2n = 2x = 40),a monocot plant which is the single species of the Velloziaceae(Pandanales)distributed in the Northern Hemisphere.Because of its small population,A.bracteata was listed as an endangered plant(category II)in China.And its distribution is fairly narrow,only in the hinterland of Hengduan Mountains in the east of Qinghai-Tibet Plateau(QTP).Previous phylogenetic studies have found that its divergence is earlier than the massive uplift of the QTP.However,how A.bracteata adapts to the harsh environment of QTP at high altitude,and how its tiny population would affect its current and future survival have not been studied yet.In this research,the above questions were tickled through highquality genome assembly of A.bracteata and resequencing of 21 individuals.We focused on the high-altitude adaptation mechanism,small population survival mechanism,and protection measures of A.bracteata in the future.The main findings are summarized as follows:(1)Based on Illumina,Nanopore and Hi-C sequencing data,a high-quality reference genome of A.bracteata was assembled,and the contig N50 was 8 Mb.After that,41 contigs were successfully anchored onto 20 chromosomes,with an anchoring rate of 99.51%.Based on ab initio prediction and homologous prediction,a total of23,144 protein-coding genes were annotated,among which 94.50% of the genes could be aligned to the homologous sequences in the protein database,indicating the high quality of genome annotation.(2)The phylogenetic analysis with nuclear and chloroplast genes both confirmed that A.bracteata was separated from other species of Velloziaceae in the late Mesozoic(69-81 Mya).This is much later than the time when the Indian plate was split from Gondwana in the Southern Hemisphere(140-180 Mya).Thus,the intercontinental discontinuous distribution pattern of Velloziaceae was likely caused by long-distance dispersal.(3)Based on comparative genomics analysis,it was revealed that A.bracteata shared the whole-genome duplication(WGD)event(τ)experienced by most monocots.Besides,an additional WGD event occurred in ～26 Mya alone.The occurrence of this duplication event coincided with the rapid uplift period of QTP,retaining genes mainly responding to cold,drought,salt,and hypoxia,which successfully helped A.bracteata adapt to the arid alpine environment.However,although it has experienced two rounds of WGDs,the genome(192 Mb)of A.bracteata is only 65% of its related species(Xerophyta viscosa,295.5 Mb)and smaller than most monocots on record.In this way,the ecological burden and the energy and nutrition requirements of A.bracteata living in the QTP may be lessened.(4)Based on PSMC analysis,the population history of A.bracteata and X.viscosa was reconstructed.The results showed that both species experienced rapid population contraction during the two glacial periods.However,the effective population size of A.bracteata was always lower than X.viscosa and kept shrinking continuously while the population of X.viscosa gradually recovered after that and maintained a high effective population size after the LGM.In addition,we found that the genetic relationship of individuals in each population was extremely close,with minimal genome difference.This indicated that within each population individuals primarily reproduce through asexual reproduction.(5)Comparing the genetic diversity indicators with more than 200 animals and plants,it was found that both the genome heterozygosity and the population nucleotide diversity of A.bracteata are in a very low state.In addition,the genetic load on the genome is very high,and the high inbreeding level in the population helps it efficiently eliminate the extremely harmful mutation.This way of purging was also detected and confirmed in other species by correlation analysis.To sum up,recent WGD event,smaller genome size and clonal reproduction have forged A.bracteata to survive in the harsh environment of QTP.However,a long-term small population leads to its extremely low genetic diversity and high genetic load.Efficient purging of extremely harmful mutations by high-level inbreeding ensures its survival as a small population.However,species with low genetic diversity can not cope with the complex environmental changes.Therefore,we should strengthen the gene exchange among different groups to increase the genetic diversity of the species,and conserve germplasm resources of A.bracteata in combination with in-situ conservation and ex-situ conservation to face possible situations in the future.This research not only enriches the genomics research of Velloziaceae,and reveals the highaltitude adaptation mechanism,endangered process,and small population survival mechanism of A.bracteata,but also provide a reference for the protection of other endangered alpine plants.