Intraspecific differentiation of Lindera obtusiloba as revealed by comparative plastomic and evolutionary analyses

Abstract

Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis-related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.

Keywords: Lindera obtusiloba; complete chloroplast genomes; intraspecific diversity; phylogenetic analysis; positive selection.

FIGURE 1

Samples location of the Lindera obtusiloba (a) and their gene maps of the complete chloroplast genome (b).

FIGURE 2

Number of repeats in the thirteen Lindera obtusiloba chloroplast genomes. (a) Total number of SSRs detected in each species. (b) Total number of the forward (F), palindrome (P), reverse (R), and complement (C) repeated elements detected in each species.

FIGURE 3

Sliding window analysis of the entire chloroplast genome of thirteen Lindera obtusiloba individuals (window length: 600 bp; step size: 200 bp). x‐axis: position of the midpoint of a window; y‐axis: nucleotide diversity of each window.

FIGURE 4

Visualization of genome alignment of the thirteen complete chloroplast genomes from Lindera obtusiloba. The cp genome of Lavandula latifolia is used as the reference. x‐axis indicates the sequence coordinates in the whole cp genome. y‐axis represents the similarity of the aligned regions, indicating percent identity to the reference genome (50–100%).

FIGURE 5

Phylogenetic tree reconstruction of ‘core’ Laureae using the maximum likelihood (ML) method based on complete chloroplast genome sequences. Only the ML tree is shown, because its topology is identical to that of the obtained BI tree.

FIGURE 6

Phylogenetic tree reconstruction and positive selection genes of Lindera obtusiloba using the maximum likelihood (ML) method based on 79 coding sequences. Genes were colored with blue background were identified by site model, Genes were colored with red background were identified by branch model with the Northern population of L. obtusiloba as the foreground branch. Amino acid differences were observed between the Northern and the Southern populations of L. obtusiloba for rpoC2 gene. *means p < 0.05 according selection analyses. **means p <0.01 according selection analyses.