The Chloroplast Genome,Population Genetic Diversity And Phylogeography Of Juniperus Sabina(Cupressaceae)

Juniperus sabina,a juniperus shrub of the Cupressaceae family,has the characteristics of strong germination,pruning resistance and sand burial.It is an excellent tree species for wind and sand fixation,soil and water conservation,and carbon sink.J.sabina presents an intermittent distribution pattern in arid and semi-arid regions in southern Europe,Central Asia and China.Research on the genetic diversity and phylogeography of natural populations helps to trace the historical causes of the existing distribution patterns,reveals the evolution of J.sabina,and clarify the impact of changes in geological history and climate on the species differentiation of J.sabina,and propose scientific and effective protection strategies.In this study,the structural characteristics of the chloroplast genome of J.sabina were first analyzed and the phylogenetic status of J.sabina in the genus Juniperus was reconstructed.Secondly,the genetic diversity,genetic structure,genetic differentiation and bottleneck effects of 11 natural populations of J.sabina were analysed based on SSR markers.Then,four cpDNA fragments(matK+petB-petD+trnL-trnF+trnS-trnG),a ITS fragment and a single copy nuclear gene(ABI3)were applied to reveal the relationship between haplotype lineages,estimate the differentiation time of each lineage,speculate the glacial refuge of J.sabina,clarify the cause and dynamic evolutionary history of the disperse geographical distribution of J.sabina,and explore the relationship between the evolutionary history of J.sabina,geological history and climate change events.Finally,the geographical distribution patterns of J.sabina in different periods were predicted based on the maximum entropy model(MaxEnt)and protection strategies were proposed for J.sabina based on the geographical distribution pattern of population genetic variation.According to the degree of genetic differentiation between populations,the geographical distribution pattern of different historical periods,and the main environmental constraints,protection strategies for J.sabina were proposed.The main findings were as follows:(1)The chloroplast genome of J.sabina consists of a large single copy region(91264 bp),a small single copy region(35952 bp)and two inverted repeat regions(261 bp).The genome was 127739 bp in length and contained 119 genes with 82 protein-coding genes,4 rRNA genes and 33 tRNA genes.J.sabina had similar genome size,gene composition and GC content with other Juniper plants.Phylogenetic analysis indicated that J.sabina is relatively close to J.bermudiana in the genus Juniperus,and the entire juniper branch is a monophyletic group.(2)J.sabina population had a high genetic diversity,with a trend of central population>eastern population>western population;the population of J.sabina has a moderate genetic differentiation,The 11 populations of J.sabina can be divided into 2 groups,including NMYQ,NMNL,NMTK and SXHS populations clustered as a group.The genetic variation of J.sabina mainly originated from individuals within the population,whereae the genetic variation between the populations was relatively small.(3)A total of 18 chloroplast haplotypes,38 ITS haplotypes and 25 single-copy nuclear gene haplotypes were defined in 11 natural populations.The ABI3 sequence indicated that the J.sabina population had a pedigree and geographic structure,and the genetic distance and geographic distance were positively correlated.(4)The differentiation time of the BEAST at the three molecular levels of cpDNA,ITS and ABI3 all speculated that J.sabina originated at least in the mid-Miocene tertiary period.The neutral test of cpDNA data and ITS data showed that J.sabina did not undergo a significant expansion process,and neither the neutral test nor the mismatch analysis of ABI3 fragment can reject the population expansion hypothesis.The population may occur after LGM at 19.37 ka BP.In general,J.sabina may be continuously distributed in the northern hemisphere in the Tertiary period,affected by the uplift of the Qinghai-Tibet Plateau,the Quaternary glacial period,and human activities.After the fragmentation of the habitat,the growth range is reduced to the mountain refuges.After the glacial period,some groups expanded in a small area near the refuge.Until now,most J.sabina populations are distributed in mountain valleys,seasonal rivers and sandy land with a lot of precipitation due to the increasing aridity.(5)Since the last glacial maximum,the total suitable area of J.sabina has shown a trend of first decreasing,then increasing and then decreasing,but the distribution area of the high and medium suitable areas has increased first and then decreased,and the current potential distribution area has reached the maximum.Annual precipitation(Biol2),precipitation of wettest month(Bio 13),elevation(Elev)and temperature annual range(Bio7)are the main environmental variables that limit the distribution of J.sabina.Compared with temperature,precipitation has a greater impact on the distribution pattern of J.sabina.(6)According to the geographical distribution pattern of J.sabina in different periods and the characteristics of haplotypes distribution,it is inferred that there are independent refuges in the Altai Mountains,Ili River Valley,Qilian Mountains,Helan Mountains,Yinshan Mountains and Hunshandake Sandy Land.The existing J.sabina population distributed in the Mu Us sandy land may be evolved from the remains of primitive vegetation in the Loess Plateau.(7)In order to conserve natural J.sabina germplasm resources reasonably and effectively,the population of J.sabina was divided into two distinct evolutionary units and 3 sub-regions according to the degree of genetic differentiation between the J.sabina populations,the geographical distribution pattern of different historical periods,and the main environmental constraints,corresponding germplasm resource protection strategies should be adopted respectively.