Complete Sequence and Analysis of Coconut Palm

• Published in: PloS one 2016-10, Vol.11 (10), p.e0163990
• Main Authors: Aljohi, Hasan Awad, Liu, Wanfei, Lin, Qiang, Zhao, Yuhui, Zeng, Jingyao, Alamer, Ali, Alanazi, Ibrahim O, Alawad, Abdullah O, Al-Sadi, Abdullah M, Hu, Songnian, Yu, Jun
• Format: Article
• Language: English
• Subjects: Analysis; Genomes; Genomics; RNA; RNA sequencing
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0163990

Coconut (Cocos nucifera L.), a member of the palm family (Arecaceae), is one of the most economically important crops in tropics, serving as an important source of food, drink, fuel, medicine, and construction material. Here we report an assembly of the coconut (C. nucifera, Oman local Tall cultivar) mitochondrial (mt) genome based on next-generation sequencing data. This genome, 678,653bp in length and 45.5% in GC content, encodes 72 proteins, 9 pseudogenes, 23 tRNAs, and 3 ribosomal RNAs. Within the assembly, we find that the chloroplast (cp) derived regions account for 5.07% of the total assembly length, including 13 proteins, 2 pseudogenes, and 11 tRNAs. The mt genome has a relatively large fraction of repeat content (17.26%), including both forward (tandem) and inverted (palindromic) repeats. Sequence variation analysis shows that the Ti/Tv ratio of the mt genome is lower as compared to that of the nuclear genome and neutral expectation. By combining public RNA-Seq data for coconut, we identify 734 RNA editing sites supported by at least two datasets. In summary, our data provides the second complete mt genome sequence in the family Arecaceae, essential for further investigations on mitochondrial biology of seed plants.