The complete chloroplast genome of the miracle tree Neolamarckia cadamba and its comparison in Rubiaceae family

Abstract

Neolamarckia cadamba is a miracle tree species with considerable economic potential used as a timber wood and traditional medicine resource in South and Southeast Asia. To better understand the molecular basis of its chloroplast biology, we sequenced and characterised the complete chloroplast genome using Illumina pair-end sequencing. The analysis showed a chloroplast genome size of 154,999 bp in length, harbouring a pair of inverted repeats (IRs) of 25,634 bp separated by a large single copy (LSC) sequence of 85,880 bp and a small single copy (SSC) sequence of 17,851 bp. Of the 130 genes present, 96 were unique and 17 were duplicated in the IRs. The coding regions comprised 79 protein genes, 30 tRNA genes and 4 rRNA genes. In the protein-coding genes, nine genes contained one intron each, while another two genes comprised two introns. The overall GC content of the chloroplast genome was 37.6%. Simple sequence repeat (SSR) analysis revealed that most SSRs were A/T-rich, which contributed to the overall AT richness of the N. cadamba chloroplast genome. Additionally, fewer SSRs distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the chloroplast genome. A maximum likelihood phylogenetic analysis showed that N. cadamba was closely related to Morinda officinalis and Emmenopterys henryi, which belong to the Rubiaceae family. This complete chloroplast genome will offer valuable information for the development of highly variable DNA markers for future conservation, genetic engineering studies and variety selection of this miracle tree.

Keywords

• Neolamarckia cadamba
• chloroplast genome
• phylogenetic analysis
• conservation and variety selection