SLAF-seq of 111 Ammopiptanthus mongolicus Individuals
After SLAF library construction in 111 Ammopiptanthus mongolicus individuals, a total of 20.92 Gb of data containing 390.06 Mb reads were obtained, the GC content and Q30 value are 40.35% and 91.63%, respectively. While 957,624 SLAF tags were identified in Ammopiptanthus individuals, with an average coverage of 13.83 per samples. SLAF tags were mapped to the reference Ammopiptanthus genome using the BWA software, and 624,223 SLAF tags containing polymorphic SNPs were detected among the 111 Ammopiptanthus individuals (Table 3 and Fig 1). Of these SLAF tags containing polymorphic SNPs, 44.02% (274,782) were located on the 18 assembled chromosomes of the Ammopiptanthus reference genome, similar percentage (43.30%) of the total assembled genome sequence of Ammopiptanthus present in the chromosome assemblies (642.5 Mb of 1.535 Gb). The number of SLAF tags per chromosome ranged from 5,673 to 17,521.
Meanwhile, A total of 3,925,962 SNPs were identified among the 111 individuals of Ammopiptanthus, of which 1,261,501 SNPs were identified by both GATK and SAM tools and were subsequently used as SNP markers and the integrity of SNPs in the 111 accessions ranged from 80.66 to 97.66% (Fig 2). The raw data for the 111 Ammopiptanthus individuals SLAF-seq have been uploaded to the Sequence Reads Archive in National Center for Biotechnology Information. The number and distribution of the polymorphic SLAF tags on each chromosome are shown in Supplementary Table 1. Insertion and deletion (INDEL) polymorphisms, are abundant in the genomes of model organisms and are expected to be abundant in Ammopiptanthus as well. We used our computational pipeline to mine 296,977 INDELs from two independent Ammopiptanthus sets, ranging from 1 bp to 831 bp in length. Frameshift INDELs (INDEL length is not multiple of three bases) are under especially strong scrutiny as they generally result in a nonsense mutation and changes in amino acid sequences (Fig 3A). In our database, we discovered different INDELs which ranging in size from −80 to 12 base pairs. The overwhelming majority (95%) of the INDELs are short, and it has the rich distribution for in-frame INDELs (Fig 3B).
Genetic diversity and Genetic differentiation of population
Genetic diversity usually refers to the sum of genetic differentiation and variation among different individuals within a population or among different populations of a species [32, 33]. Results of genetic diversity showed that the genetic diversity of Ammopiptanthus mongolicus (he=0.32522, ho=0.31129) was higher than that of Ammopiptanthus nanus (he = 0.26143, ho = 0.25834) (Table 1). The population differentiation degree of Ammopiptanthus mongolicus was low (FST=0.1248) (Table 2), indicating that the population differentiattion was moderate and the variation mainly existed in the population. While the differentiation degree of Ammopiptanthus nanus population in Xinjiang was high (FST = 0.6989), indicating that Ammopiptanthus nanus population was highly differentiated and the variation mainly existed between populations. The variation of Ammopiptanthus mongolicus and Ammopiptanthus nanus exists between species, which is closely related to the geographical distance between the two species.
In this study, we also assumed that cpDNA variation was in a drift-migration equilibrium , and considerable differentiation of the whole-genome among the Ammopiptanthus populations growing in different geographically remote areas and therefore a high degree of genetic disunity between them are evidenced by the high pairwise genetic distances(FST, Table 2), as well as between the Ammopiptanthus mongolicus and Ammopiptanthus nanus groups (FST= 0.5813, P<0.0001).
Phylogenetic Relationships Based on SNP Data
Phylogenetic trees could reflect the evolutionary relationships of different individuals and groups, and which close relatives tend to gather together. So, In order to ascertain the divergence of 111 of Ammopiptanthus species during evolution, we performed the phylogenetic analysis, the results showed all species are clustered into five distinct branches (Fig 4), and that the majority of individuals can gather in the same group. The GS-MQ population is transplanting species out of five population (GS-MQ, GS-HSY, NX-HW, NX-BG and NMG-DQH population). The Ammopiptanthus nanus from Xinjiang province gathered together, while Ammopiptanthus nanus from Gansu province can not gather to a family group. Meanwhile, all Ammopiptanthus mongolicus gather to a big family group. The Ammopiptanthus mongolicus GS-HSY and NX-HW are clustered on a large branch, while the remaining communities in Ningxia gather on another branch. The majority of Ammopiptanthus mongolicus gathered together (Fig 4). Finally, all results indicated that NX-BG and NMG-DQH have the highest homology.
Population Structure and Linkage Disequilibrium Analysis
To ascertain the divergence of the NMG-DQH, NMG-ALBLG, NMG-AZQ, NMG-QLG, NMG-DKTST, NX-BG, NX-BDG, NX-BJT, NX-HW, GS-HSY, XJ-KS, XJ-AHQ, XJ -BX, XJ-WYS and GS-MQ groups during evolution, principal component, population structure analyses were performed. Additionally, the sequence diversity of the FD, SD and ND germplasms was evaluated. All of the analyses indicated that there are strong divergence between the different Ammopiptanthus groups.
A population structure analysis using the Admixture program and SNP data revealed that 111 Ammopiptanthus germplasms were mainly divided into three groups according to the cross-validation error rate (Fig 5). Of the three groups, group 1 comprised the most germplasms with 51 followed by group 2 (41 germplasms) and group 3 (19 germplasms). The Ammopiptanthus germplasms distributed in three groups, suggesting these Ammopiptanthus species were genetically diverse.
Meanwhile, Linkage disequilibrium (LD) analysis of these fifteen groups revealed that the distance of LD decay in the NX-HW and XJ-WHS group is longer than that in the other groups (Fig 6). The results indicated that Ammopiptanthus nanus had a more diverse genomic background.
The principal component analysis
In order to ascertain the divergence of fifteen population of Ammopiptanthus species during evolution, we performed the principal component analysis. The first three components explained 30.14% of the total genetic variation, of which the first two components contributed 64.67% (PC1) and 5.55% (PC2), The results showed that the NMG-DQH, NMG-ALBLG, NMG-AZQ, NMG-QLG, NMG-DKTST, NX-BG, NX-BDG, NX-BJT, NX-HW, GS-HSY, XJ-KS, XJ-AHQ, XJ -BX, XJ-WYS and GS-MQ collections were clearly distinguished (Fig 7), although existing some degrees of introgression in these groups. All results indicated that a strong divergence between different Ammopiptanthus groups.