The complete chloroplast genome of the miracle treeNeolamarckia cadambaand 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.

Chloroplast genomes of Rubiaceae: Comparative genomics and molecular phylogeny in subfamily Ixoroideae

“…Given that Coffea arabica could not be used as outgroup in the phylogeny, we decided to use the annotated genomes of Antirhea chinensis [35], Mitragyna speciosa [33] and Neolamarckia cadamba [34] belonging to the Cinchonoideae subfamily as reference genomes and outgroup taxa for the cp genome analyses. The alignments of the complete chloroplast genome sequences of the 28 studied Rubiaceae were visualized using mVISTA [53] in order to show global interspecific variation and variation within the tribes.…”

“…(S1 Table) Data obtained for other Rubiaceae such as Hedyotis ovata [36] and Paralasianthus hainanensis (as Saprosma merrillii; [37]) from the Rubioideae subfamily and Antirhea chinensis [35] PLOS ONE from the Cinchonoideae subfamily indicate a quadripartite structure and a total of 114 genes (eight duplicated genes counted once and eight genes missing in Rubiaceae, see below) of which 80 are unique protein-coding genes. For Neolamarckia cadamba (Cinchonoideae), [34] revealed a total of 130 genes, 79 of which are protein-coding. Data obtained from GenBank for three Rubioideae (accession numbers NC_036970 for Galium mollugo, NC_028009 for…”

“…Morinda officinalis and NC_028614 for Gynochtodes nanlenginsis) and from literature for two Cinchonoideae [34,35] permitted us to determine their plastid features ( [60], Geraniaceae [61], Pinaceae [62], Cactaceae [63], Arecaceae [64] and Passifloraceae [65]. Within the Ixoroideae, the chloroplast assembly of three species showed a tripartite genome structure.…”

“…Plastid genomes features of three taxa from the Rubioideae and three taxa from the Cinchonoideae subfamilies. Estimations were done from data extracted from [33,34,35,59] or calculated from data extracted from GenBank for Morinda officinalis (NC_028009) and Gynochtodes nanlingensis (NC_028614).…”

“…[33], Neolamarckia cadamba (Roxb.) Bosser [34] Nuclear genomic raw data can be assembled into short contigs and used to mine Single Nucleotide Polymorphisms (SNPs) to study the genetic diversity within and between populations and species [40], the evolution of traits of interest [19] or the dynamics of transposable elements [41]. Methodologies based upon short read sequencing such as Genotyping-By-Sequencing (GBS) using a reference genome, permit to define sets of nuclear SNPs for high numbers of genotypes (convenient for multiples of 96 well-plates) as was done for Coffea species [19].…”