Complete Chloroplast Genome of Nicotiana otophora and its Comparison with Related Species

Abstract

Nicotiana otophora is a wild parental species of Nicotiana tabacum, an interspecific hybrid of Nicotiana tomentosiformis and Nicotiana sylvestris. However, N. otophora is least understood as an alternative paternal donor. Here, we compared the fully assembled chloroplast (cp) genome of N. otophora and with those of closely related species. The analysis showed a cp genome size of 156,073 bp and exhibited a typical quadripartite structure, which contains a pair of inverted repeats separated by small and large single copies, containing 163 representative genes, with 165 microsatellites distributed unevenly throughout the genome. Comparative analysis of a gene with known function across Nicotiana species revealed 76 protein-coding sequences, 20 tRNA sequences, and 3 rRNA sequence shared between the cp genomes. The analysis revealed that N. otophora is a sister species to N. tomentosiformis within the Nicotiana genus, and Atropha belladonna and Datura stramonium are their closest relatives. These findings provide a valuable analysis of the complete N. otophora cp genome, which can identify species, elucidate taxonomy, and reconstruct the phylogeny of genus Nicotiana.

Plastid genomics of Nicotiana (Solanaceae): insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)

“…When less genomic resources are available for revealing divergence hotspot regions, the oligonucleotide repeats might be utilized as a substitute for identifying polymorphic regions (Ahmed et al, 2012; Ahmad, 2014). The current study results of oligonucleotide repeats are similar to the previously reported results of Nicotiana species and other angiosperm plastome studies (Asaf et al, 2016; Yang et al, 2019). Thus, the presence of both the high divergence regions in IGS and oligonucleotide repeats suggest that these regions are suitable for the development of markers to demonstrate phylogenetics relationships.…”

“…Here, we detected that the mononucleotide repeats (A/T), and trinucleotide SSRs (ATT/TAA) were present in large amounts in all the species of Nicotiana , which may be a result of the A/T rich proportion of chloroplast genome. A similar result was also reported in Nicotiana otophora (Asaf et al, 2016). In all the species of Nicotiana , the LSC region contained a greater amount of SSRs in comparison to SSC and IR, which has also been demonstrated in other studies of angiosperm plastomes (Shahzadi et al, 2019; Mehmood et al, 2019).…”

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

“…Although cp genomes are highly conserved in terms of genomic structure and size, the IR/SC junction position change caused by expansion and contraction of the IR/SC boundary regions was usually considered as a primary mechanism in creating the length variation of the higher plant cp genomes (Kim and Lee, 2005; Asaf et al, 2016; Dong et al, 2016; Yang et al, 2016; Zhang et al, 2016). In this study, however, the IR/SC junction position change was not observed among the six cp genomes.…”

“…In Nicotiana otophora , all mono-nucleotides (100%) are composed of A/T (Asaf et al, 2016). In the five Epimedium cp genomes, mono-nucleotide SSRs were found to be the richest, up to 72.76%, and the mono-nucleotide A/T repeat units occupied 80.17% in the homopolymer SSRs.…”

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman

“…sacra and Azadirachta indica . Missing and ambiguous gene annotations were confirmed by comparative sequence analysis after a multiple sequence alignment and gene order comparison [43]. These regions were aligned using MAFFT (version 7.222) [44] with the default parameters.…”