Resequencing Analyses of Five Sour Oranges (Citrus x aurantium)

Sour orange (Citrus x aurantium) is one of the most widely used rootstocks in commercial citrus orchards. ’Seville’ sour orange was identified as an F1 hybrid of pure mandarin (C. reticulata) and pummelo (C. maxima) parents in our previous study. To expand our knowledge about the origin of sour orange, four more sour orange types were resequenced using next-generation sequencing, including ‘Zhuluan’, ‘Goutou’, ‘Chinotto’ and ‘Standard’. The filtered reads were aligned to the genome of Clementine mandarin (C. x clementina cv. Clemenules v1.0 from Phytozome). A wide range of genetic variations were detected, including approximately 5 million single nucleotide polymorphisms and 1 million short insertions and deletions. Nucleotide diversity and admixture analyses showed that all sequenced sour orange, except ‘Zhuluan’, are F1 hybrids of pure mandarin and pummelo. Much more contribution of mandarin was detected in the genome of ‘Zhuluan’, especially in Scaffold_2 and Scaffold_4 of the Clementine mandarin genome. Phylogenetic analyses also showed a closer relationship among ‘Chinotto’, ‘Standard’ and ‘Seville’ sour oranges.