Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae

• Published in: Planta Vol. 252; no. 5; p. 91
• Main Authors: Sobreiro, Mariane B., Vieira, Lucas D., Nunes, Rhewter, Novaes, Evandro, Coissac, Eric, Silva-Junior, Orzenil B., Grattapaglia, Dario, Collevatti, Rosane Garcia
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.11.2020; Springer Nature B.V; Springer Verlag
• Subjects: Agriculture; Anemopaegma; Assembly; Bignoniaceae; Bignoniaceae - classification; Bignoniaceae - genetics; Biochemistry, Molecular Biology; Biomedical and Life Sciences; Boundaries; chloroplast genome; Chloroplasts; Comparative analysis; Conserved sequence; Contraction; DNA-directed RNA polymerase; Dry forests; Ecology; Evolution, Molecular; Evolutionary genetics; Forestry; Gene sequencing; Genes; genetic variation; genome assembly; Genome, Chloroplast - genetics; Genomes; Genomics; Handroanthus impetiginosus; Inverted repeat; Life Sciences; Microsatellite Repeats - genetics; Molecular evolution; Negative selection; Neotropics; Nucleotides; Original Article; Phylogeny; Plant Sciences; Positive selection; Simple sequence repeats; Site selection; Tabebuia - classification; Tabebuia - genetics; Woody plants; Comparative genomics; Substitution rate; Branch-site selection; Plastome evolution; Positive selection; Codon usage
• ISSN: 0032-0935; 1432-2048; 1432-2048
• DOI: 10.1007/s00425-020-03498-9

Main conclusion Bignoniaceae species have conserved chloroplast structure, with hotspots of nucleotide diversity. Several genes are under positive selection, and can be targets for evolutionary studies. Bignoniaceae is one of the most species-rich family of woody plants in Neotropical seasonally dry forests. Here we report the assembly of Handroanthus impetiginosus chloroplast genome and evolutionary comparative analyses of ten Bignoniaceae species representing the genera for which whole-genome chloroplast sequences were available. The chloroplast genome of H. impetiginosus is 159,462 bp in size and has a similar structure compared to the other nine species. The total number of genes was slightly variable amongst the Bignoniaceae, ranging from 124 in H. impetiginosus to 144 in Anemopaegma acutifolium . The inverted repeat (IR) size was variable, ranging from 24,657 bp ( Tecomaria capensis ) to 40,481 bp ( A. acutifolium ), due to the contraction and retraction at its boundaries. However, gene boundaries were very similar among the ten species. We found 98 forward and palindromic dispersed repeats, and 85 simple sequence repeats (SSRs). In general, chloroplast sequences were highly conserved, with few nucleotide diversity hotspots in the genes accD , clpP , rpoA , ycf1 , ycf2 . The phylogenetic analysis based on 77 coding genes was highly consistent with Angiosperm Phylogeny Group (APG) IV. Our results also indicate that most genes are under negative selection or neutral evolution. We found no evidence of branch-site selection, implying that H. impetiginosus is not evolving faster than the other species analyzed, notwithstanding we found site positive selection signal in several genes. These genes can provide targets for evolutionary studies in Bignoniaceae and Lamiales species.