Analysis Of Genetic Characteristics Of Platycarya Longipes Based On Chloroplast Genome And Transcriptome

Platycarya longipes belongs to the Platycarya(Juglandaceae),is an important woody species in maintaining the stability of community structure of karst forests of eastern Asia.At present,the research on P.longipes mainly focuses on morphological identification,community structure,characteristics of physiological and ecological,but there are few reports on its phylogeny,population structure and genetic diversity.In this study,we used high-throughput sequencing technology,combined with bioinformatics and population genetics to complete the chloroplast genomics and transcriptome information analysis of P.longipes.Based on the chloroplast genome and transcriptome information,the phylogeny,population structure and genetic diversity of P.longipes were analyzed.Results were obtained as follows:(1)The P.longipes cp genome comprises a 158,459 bp quadripartite circular molecule,which includes a large single copy(LSC)region of 87,898 bp and a small single copy(SSC)region of 18,521 bp separated by a pair of inverted repeats(IRA and IRB)with 26,020 bp.The overall GC content of the complete cp genome is 36.16%,contains 113 unique genes.Additionally,we detected49 long repeat sequences and 66 simple sequence repeats(SSRs)in P.longipes cp genome;The Ka/Ks values of genes in P.longipes compared with its related species were calculated,results showed that most genes were selected by purification,and there is a higher Ka/Ks value in P.longipes and P.strobilacea;Phylogenetic analysis based on ML and BI methods of the Fagales order showed that P.longipes is most closely related to P.strobilacea,but the Platycarya differentiated into two species before seven million years ago.In addition,the genome divergence and SNP analysis both show that there are certain differences between the chloroplast genomes of P.longipes and P.strobilacea,which supports the classification of Platycarya into two different species..(2)Through amplification,sequencing,and comparison of two chloroplast gene fragments(mat K and rbc L)from 120 samples in 12 populations of P.longipes,the successfully amplified sample were spliced together to obtain a total of 99 sequences.A total of 25 chloroplast haplotypes and 51 mutation sites were detected,among them,27 mutation sites were detected in the mat K and 24 detected in the rbc L fragment.The total haplotype diversity(Hd)and nucleotide diversity(π)were 0.6081 and 0.00067 respectively in P.longipes.In addition,there are differences in population diversity under different carbonate rocks and landforms.The diversity of dolomite populations is slightly higher than that of limestone populations,and the populations of peak-cluster depression are higher than those of peak-forest and peak cluster.(3)The development of transcriptomics and EST-SSRs molecular markers can provide available gene resources for further study of the population genetic structure of P.longipes.A total of 45,483,390 raw reads were obtained by sequencing the transcriptome of P.longipes,and349,295 transcripts were assembled.After redundancy,163,083 unigenes were obtained,then compared and annotated in GO and other public databases.SSR detection was performed on Unigenes,33,304 EST-SSR loci were found in 28,448 unigenes,of which the most were mononucleotide(14,787,51.9%).This study systematically expounded the evolutionary relationship between P.longipes and P.strobilacea from the cp genome,revealed the phylogenetic relationship of Platycarya in Fagales.Clarified the population structure and genetic diversity of P.longipes population in Guizhou,it provides a theoretical basis for the protein,utilization and breeding of P.longipes population.