## 1 Introduction
### Gene Expansion of HMGR Gene Family in L. erythrorhizon  
Gene duplications and loss play a significant factor in plant evolution and plant fitness [41]. To further understand the evolution of the _HMGR_ gene family, we performed gene duplication and loss analysis in 19 representative plants from seven lineages using Notung software by reconciling gene phylogenetic trees and species taxonomy common trees (Figure 2A). Based on the number of variations found in _HMGR_ family genes at different evolutionary stages, _HMGR_ ancestral genes were duplicated prior the emergence of _Mesostigma viride_, but none were lost (Figure 2A). No genes were duplicated or lost in the lineage of the common ancestor of two Gymnospermae; however, 16 genes were duplicated in _Pinus tubiliformis_ after its divergence from _Cycas panzhiuensis_ (Figure 2A). Similarly, no genes were lost or duplicated in the lineage of the common ancestor of the four monocots and the six eudicots; but, three and seven genes, respectively, were duplicated after the divergence of the ancestors of the monocots and the eudicots (Figure 2A). Moreover, there was a wide range of _HMGR_ genes that were duplicated and lost during the evolution ofthe six eudicots plants. Among the eudicots plants, the _HMGR_ genes of _L. erythrorhizon_ experienced the most duplications (Figure 2A). To elucidate the expansion mechanisms of the _LerHMGR_ gene family in _L. erythrorhizon_, we analyzed the genomic location and duplication types of each _LerHMGR_. Then the synthetic blocks were identified in the entire _L. erythrorhizon_ genome, as well as between it and the _O. europaea_ and _S. indicium_ genomes. We also calculated the median synonymous substitution rates (Ks) of the syntenic fragments containing _LerHMGR_ genes (Table S3). In the results of the synteny analysis between the genomes of _L. erythrorhizon_, _O. europaea_, and _S. indicium_, _LerHMGR5_ was collinear with _OeuHMGR3_, while _LerHMGR7_ was collinear with _SinHMGR1_ (Figure 2B). It suggested that most _LerHMGRs_ were acquired through species-specific duplication events during plant evolution. The genomic location showed that these 11 _LerHMGRs_ were located on eight different contigs (Figure 2C). Four members (i.e., _LerHMGR2_, _LerHMGR4_, _LerHMGR8_, and _LerHMGR9_) might be derived from tandem duplications, as indicated by their genomic loci: _LerHMGR2_, _LerHMGR3_, and _LerHMGR4_ were closely located in the contig02634, while _LerHMGR8_ and _LerHMGR9_ were closely located in the contig03594 (Figure 2C, Table 1). Six members (i.e., _LerHMGR1_, _LerHMGR3_, _LerHMGR5_, _LerHMGR6_, _LerHMGR10_, and _LerHMGR11_) might be derived from WGD/segmental (Table 1). Contig03521 containing _LerHMGR1_, contig01638 containing _LerHMGR5_, and contig02593 containing _LerHMGR10_ exhibit synteny relationships with contig02634 containing _LerHMGR3_, contig01263 containing _LerHMGR6_, and contig02287 containing _LerHMGR11_, respectively (Figure 2D). Figure 2: Gene expansion, synteny analysis and genome location of _HMGRs_ in _L. erythrorhizon_. (**A**) Gene duplication and loss analysis of _HMGR_ family genes using Notung software in 19 representative plants. Gene duplications and losses are represented by the + and \(-\) numbers on each branch. The numbers in parentheses in (**A**) represent the number of _HMGR_ gene family members identified from different species. (**B**) Synteny blocks of _HMGRs_ between _L. erythrorhizon_ and _O. europaea_, _S. indicium_. (**C**) Location of _LerHMGRs_ in the genome of _L. erythrorhizon_. (**D**) Synteny blocks of six _LerHMGRs_. The red line represents the homologous _HMGRs_ between _L. erythrorhizon_ and _O. europaea_, _S. indicium_, and _L. erythrorhizon_. Furthermore, the Ks distribution was analyzed by calculating the Ks value of 8257 synteny gene pairs based on [PERSON]'s published _L. erythrorhizon_ genome data [42] (Table S4). It was found that there were two peaks (Ks = about 0.088 and 0.376), indicating that the _L.