Phylogenetic Relationships of Citrus and Its Relatives Based on matK Gene Sequences

Tshering Penjor,Ryoji Matsumoto,Masashi Yamamoto,Yukio Nagano,Natsumi Matsumoto,Miki Uehara,Manami Ide,Randall P Niedz

doi:10.1371/journal.pone.0062574

Tshering Penjor, Ryoji Matsumoto + Show 6 more

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https://doi.org/10.1371/journal.pone.0062574

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Abstract

The genus Citrus includes mandarin, orange, lemon, grapefruit and lime, which have high economic and nutritional value. The family Rutaceae can be divided into 7 subfamilies, including Aurantioideae. The genus Citrus belongs to the subfamily Aurantioideae. In this study, we sequenced the chloroplast matK genes of 135 accessions from 22 genera of Aurantioideae and analyzed them phylogenetically. Our study includes many accessions that have not been examined in other studies. The subfamily Aurantioideae has been classified into 2 tribes, Clauseneae and Citreae, and our current molecular analysis clearly discriminate Citreae from Clauseneae by using only 1 chloroplast DNA sequence. Our study confirms previous observations on the molecular phylogeny of Aurantioideae in many aspects. However, we have provided novel information on these genetic relationships. For example, inconsistent with the previous observation, and consistent with our preliminary study using the chloroplast rbcL genes, our analysis showed that Feroniella oblata is not nested in Citrus species and is closely related with Feronia limonia. Furthermore, we have shown that Murraya paniculata is similar to Merrillia caloxylon and is dissimilar to Murraya koenigii. We found that “true citrus fruit trees” could be divided into 2 subclusters. One subcluster included Citrus, Fortunella, and Poncirus, while the other cluster included Microcitrus and Eremocitrus. Compared to previous studies, our current study is the most extensive phylogenetic study of Citrus species since it includes 93 accessions. The results indicate that Citrus species can be classified into 3 clusters: a citron cluster, a pummelo cluster, and a mandarin cluster. Although most mandarin accessions belonged to the mandarin cluster, we found some exceptions. We also obtained the information on the genetic background of various species of acid citrus grown in Japan. Because the genus Citrus contains many important accessions, we have comprehensively discussed the classification of this genus.

Highlights

The genus Citrus, which includes mandarin, orange, lemon, grapefruit and lime, has high economic and nutritional value
Because no indel was observed in the rbcL gene of this subfamily [25], we concluded that matK had a relatively fast mutation rate
Our analysis showed that Severinia buxifolia is most closely related to Atalantia bilocularis

Summary

Introduction

The genus Citrus, which includes mandarin, orange, lemon, grapefruit and lime, has high economic and nutritional value. The subtribe Citrinae, in the tribe Citreae, is distinct from all the other subtribes in the Aurantioideae because of the presence of pulp vesicles in the fruit In this subtribe, ‘‘true citrus fruit trees’’ are considered the most advanced genera based on morphological traits [1]. The genus Citrus belongs to the ‘‘true citrus fruit trees.’’ The characteristics of Citrus species include asexual reproduction, high mutation frequency, and cross compatibility between species. Because of these characteristics, there is great morphological and ecological diversity among Citrus species

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