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

• Published in: PeerJ (San Francisco, CA) Vol. 8; p. e9552
• Main Authors: Mehmood, Furrukh, Abdullah, Ubaid, Zartasha, Shahzadi, Iram, Ahmed, Ibrar, Waheed, Mohammad Tahir, Poczai, Peter, Mirza, Bushra
• Format: Journal Article
• Language: English
• Published: United States PeerJ. Ltd 23-07-2020; PeerJ, Inc; PeerJ Inc
• Subjects: Adaptation; Annotations; Biodiversity; Biogeography; Chloroplast genome; Chloroplasts; Codons; Comparative analysis; DNA biosynthesis; DNA replication; DNA-directed RNA polymerase; Environmental conditions; Evolutionary biology; Evolutionary genetics; Evolutionary Studies; Gene mutation; Genes; Genomes; Genomics; Hybridization; Inverted repeat; Molecular evolution; Mutation; Mutational hotspots; Natural selection; Nicotiana; Nucleotide sequence; Oligonucleotides; Ornamental plants; Photosynthesis; Phylogenetics; Phylogeny; Plant biochemistry; Plant Science; Polyploidy; Positive selection; Proteins; Range extension; RNA editing; Solanaceae; Spacer region; Speciation; Species; Substitution and InDels; Substitutions; Taxonomy; Tobacco; Transfer RNA; Substitution and InDels; Nicotiana; Mutational hotspots; Chloroplast genome; Positive selection; Substitutions
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.9552

Species of the genus
(Solanaceae), commonly referred to as tobacco plants, are often cultivated as non-food crops and garden ornamentals. In addition to the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species:
and
. De novo assembled tobacco plastid genomes had the typical quadripartite structure, consisting of a pair of inverted repeat (IR) regions (25,323-25,369 bp each) separated by a large single-copy (LSC) region (86,510-86,716 bp) and a small single-copy (SSC) region (18,441-18,555 bp). Comparative analyses of
plastid genomes with currently available Solanaceae genome sequences showed similar GC and gene content, codon usage, simple sequence and oligonucleotide repeats, RNA editing sites, and substitutions. We identified 20 highly polymorphic regions, mostly belonging to intergenic spacer regions (IGS), which could be suitable for the development of robust and cost-effective markers for inferring the phylogeny of the genus
and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid
was the common ancestor of
and
, and the later species is more closely related to
. Relaxed molecular clock analyses estimated the speciation event between
and
appeared 0.56 Ma (HPD 0.65-0.46). Biogeographical analysis supported a south-to-north range expansion and diversification for
and related species, where
and
evolved in North/Central Peru, while
developed in Southern Peru and separated from
which adapted to the Southern coastal climatic regimes. We further inspected selective pressure on protein-coding genes among tobacco species to determine if this adaptation process affected the evolution of plastid genes. These analyses indicate that four genes involved in different plastid functions, including DNA replication (
A) and photosynthesis (
B,
D and
), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations in these genes might have contributed to better survival and superior adaptations during the evolutionary history of tobacco species.