Nucleotide Diversities and Genetic Relationship in the Three Japanese Pine Species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis

Susumu Shiraishi,Suharyanto Suharyanto

doi:10.3390/d3010121

Abstract

The nucleotide diversities and genetic relationship in the three Japanese pine species, P. thunbergii, P. densiflora, and P. luchuensis, were measured using low-copy anchor loci in Pinaceae. The average nucleotide diversity among these three Japanese pines revealed that P. thunbergii was the highest (6.05 × 10−3), followed by P. densiflora (5.27 × 10−3) and P. luchuensis (5.02 × 10−3). In comparison to other conifer species, it was concluded that the pines possessed an intermediate level of nucleotide diversity. The Heat shock protein (HSP) gene in P. thunbergii, Phenylalanine tRNA synthetase, RuBP carboxylase, and Disease resistance response protein 206 genes in P. densiflora were significantly deviated from standard neutral models. Some of these genes were related to stress or pathogen/defense response. As the samples used in this study were collected from natural populations that showed specific characteristics of being resistant to pine wilt nematode, it was hypothesized that the initial selection was an important factor in discriminating the deviation from neutrality models. Phylogenetic reconstruction revealed that the three Japanese pines were split into two lineages corresponding to P. densiflora and P. thunbergii–P. luchuensis. The latter lineage was differentiated further into two clades; P. thunbergii and P. luchuensis. The result concludes that the three Japanese pines are closely related and P. thunbergii is genetically closer to P. luchuensis, than P. densiflora.

Highlights

Analyzing the amounts and patterns of nucleotide diversity within and between species is important to comprehend the mechanisms of evolution by which genetic diversity is maintained and the processes of genetic polymorphisms within species become transformed into genetic divergence between species [1]
We investigated the potential of fifteen conifer anchor loci to resolve nucleotide diversities and phylogenetic relationship among the three Japanese pine species of P. thunbergii, P. densiflora, and P. luchuensis
A total of 122 Single nucleotide polymorphisms (SNPs) in P. thunbergii; 140 SNPs in P. densiflora; and 115 SNPs in P. luchuensis were identified from the sequences, giving a frequency of one SNP per 48 bp, 42 bp, and 51 bp, respectively (Table 3)

Summary

Introduction

Analyzing the amounts and patterns of nucleotide diversity within and between species is important to comprehend the mechanisms of evolution by which genetic diversity is maintained and the processes of genetic polymorphisms within species become transformed into genetic divergence between species [1]. Such diversities are influenced by evolutionary processes, such as mutation, recombination, selection, and population structures. In several model species, such as Drosophila [4], Arabidopsis [5,6], and maize [7], studies of nucleotide diversities using SNPs have been conducted. There is a need to conduct investigations of the nucleotide diversity on higher plants which possess different life history traits from the annual selfing Arabidopsis and the annual outcrossing maize

Objectives

Methods

Results

Discussion

Conclusion