Sequencing of mitochondrial genome of Neolamarckia macrophylla uncovers divergent structure in genus Neolamarckia.

Neolamarckia macrophylla is one of two species in genus Neolamarckia of the Rubiaceae family and distributed only in Indonesia. The two species possess several common properties, including fast-growing, superiority of stem form for wood industry and potential medicinal value. However, compared with N. cadamba that has been extensively explored for industrial and pharmacological applications, little is known about N. macrophylla. Here we sequenced the mitochondrial genome of N. macrophylla, which was 289,793 bp in length and assembled into a single circular structure. The genome contained 36 protein-coding genes (PCGs), 19 tRNA and 3 rRNA genes, and was characterized by a high AT content (55.03%), low coding-site per site (13.39%), typical C-to-U RNA editing, and codon usage bias. Homologous sequences accounted for 39.13% of its length in alignment with the nuclear genome of N. cadamba, and 1.2% in alignment with the chloroplast genome of N. macrophylla. A comparative analysis indicated that N. macrophylla substantially differed from N. cadamba, with an alternative conformation besides a smaller mitochondrial genome size, higher gene density per site, and less protein- and tRNA-coding genes. Strong purifying selection was present in all PCGs between the two species. Phylogenetic analysis revealed that the two species were divergent at about 6.757 Mya. This study provides the first complete mitochondrial genome sequence of N. macrophylla, enriching the genomic resource of the Neolamarckia genus for future study. The overall findings confirmed divergent structure of mitochondrial genomes between the two species in genus Neolamarckia.