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

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Mehmood , F , Abdullah , Ubaid , Z , Shahzadi , I , Ahmed , I , Waheed , M T , Poczai , P & Mirza , B 2020 , ' Plastid genomics of Nicotiana (Solanaceae) : insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica) ' , PeerJ , vol. 8 , 9552 . https://doi.org/10.7717/peerj.9552

Title: Plastid genomics of Nicotiana (Solanaceae) : insights into molecular evolution, positive selection and the origin of the maternal genome of Aztec tobacco (Nicotiana rustica)
Author: Mehmood, Furrukh; Abdullah; Ubaid, Zartasha; Shahzadi, Iram; Ahmed, Ibrar; Waheed, Mohammad Tahir; Poczai, Péter; Mirza, Bushra
Contributor organization: Botany
Embryophylo
Finnish Museum of Natural History
Date: 2020-07-23
Language: eng
Number of pages: 30
Belongs to series: PeerJ
ISSN: 2167-8359
DOI: https://doi.org/10.7717/peerj.9552
URI: http://hdl.handle.net/10138/318010
Abstract: The genus Nicotiana of the family Solanaceae, commonly referred to as tobacco plants, are a group cultivated as garden ornamentals. Besides their use in the worldwide production of tobacco leaves, they are also used as evolutionary model systems due to their complex development history, which is tangled by polyploidy and hybridization. Here, we assembled the plastid genomes of five tobacco species, namely N. knightiana, N. rustica, N. paniculata, N. obtusifolia and N. glauca. De novo assembled tobacco plastid genomes showed typical quadripartite structure, consisting of a pair of inverted repeats (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 Nicotiana plastid genomes showed similar GC content, gene content, codon usage, simple sequence repeats, oligonucleotide repeats, RNA editing sites and substitutions with currently available Solanaceae genomes sequences. We identified twenty highly polymorphic regions mostly belonging to intergenic spacer regions (IGS), which could be appropriate for the development of robust and cost-effective markers to infer the phylogeny of genus Nicotiana and family Solanaceae. Our comparative plastid genome analysis revealed that the maternal parent of the tetraploid N. rustica was the common ancestor of N. paniculata and N. knightiana, and the later species is more closely related to N. rustica. The relaxed molecular clock analyses estimated that the speciation event between N. rustica and N. knightiana appeared 0.56 Ma (HPD 0.65–0.46). The biogeographical analysis showed a south-to-north range expansion and diversification for N. rustica and related species, where N. undulata and N. paniculata evolved in North/Central Peru, while N. rustica developed in Southern Peru and separated from N. knightiana, 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 indicated that four genes involved in different plastid functions, such as DNA replication (rpoA) and photosynthesis (atpB, ndhD and ndhF), came under positive selective pressure as a result of specific environmental conditions. Genetic mutations of the following genes might have contributed to the survival and better adaptation during the evolutionary history of tobacco species.
Subject: 1181 Ecology, evolutionary biology
11831 Plant biology
Nicotiana
chloroplast genome
substitution and InDels
mutational hotspots
substitutions
positive selection
COMPLETE NUCLEOTIDE-SEQUENCE
CHLOROPLAST GENOME
ALLOPOLYPLOID NICOTIANA
TRANSGENE CONTAINMENT
PHYLOGENETIC ANALYSIS
SUBSTITUTION RATES
PLANT
DNA
GENES
ORGANIZATION
Nicotiana
Chloroplast genome
Substitution and InDels
Mutational hotspots
Substitutions
Positive selection
COMPLETE NUCLEOTIDE-SEQUENCE
CHLOROPLAST GENOME
ALLOPOLYPLOID NICOTIANA
TRANSGENE CONTAINMENT
PHYLOGENETIC ANALYSIS
SUBSTITUTION RATES
PLANT
DNA
GENES
ORGANIZATION
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion
Funder: Itä-Suomen yliopisto
Jyväskylän yliopisto
Uudenmaan liitto
Jyväskylän yliopisto
Grant number:




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