Maximum parsimony based resolution of inter-species phylogenetic relationships in Citrus L. (Rutaceae) using ITS of rDNA

Mohamed Hamdy Amar; Ahmed H M Hassan; Manosh Kumar Biswas; Ehsan Dulloo; Zong-Zhou Xie; Wen-Wu Guo

doi:10.1080/13102818.2014.901665

Maximum parsimony based resolution of inter-species phylogenetic relationships in Citrus L. (Rutaceae) using ITS of rDNA

Biotechnol Biotechnol Equip. 2014 Jan 2;28(1):61-67. doi: 10.1080/13102818.2014.901665.

Authors

Mohamed Hamdy Amar¹, Ahmed H M Hassan², Manosh Kumar Biswas³, Ehsan Dulloo⁴, Zong-Zhou Xie³, Wen-Wu Guo³

Affiliations

¹ Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology (MOE) , Wuhan , China ; Desert Research Center, Egyptian Deserts Gene Bank , North Sinai , Egypt.
² Desert Research Center, Egyptian Deserts Gene Bank , North Sinai , Egypt.
³ Huazhong Agricultural University, Key Laboratory of Horticultural Plant Biology (MOE) , Wuhan , China.
⁴ Bioversity International , Rome , Italy.

Abstract

The present study aims to analyse phylogenetic relationships, using internal transcribed spacer sequence data of ribosomal DNA (rDNA), across 24 Citrus species and close relatives by the evaluation of several parameters such as nucleotide substitution (r), nucleotide diversity (π) and the estimated values of transition/transversion bias (R). The observed results indicated the presence of a wide divergence pattern of rDNA in subfamily Aurantioideae. Maximum parsimony (MP) analysis inferred divergence pattern in the Citrus genus. We observed seven strongly supported clades among the subfamily Aurantioideae. We postulate that the present investigation provides a more robust topology of Citrus and its close relatives, which can significantly prove as an additional support to resolve the phylogenetic relationships in Citrus genera. Therefore, sequences of noncoding regions should exhibit more phylogenetically informative sites than the coding regions do, which is in accordance with the present study.

Keywords: Aurantioideae; Citrus; ITS; Rutaceae; phylogenetic relationship; ribosomal DNA (rDNA).

Grants and funding

This work was financially supported by the National 863 project of China [grant number 2011AA100205]; the National Natural Science Foundation of China; and Bioversity International (Rome, Italy).