Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae
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ORIGINAL ARTICLE
Chloroplast genome assembly of Handroanthus impetiginosus: comparative analysis and molecular evolution in Bignoniaceae Mariane B. Sobreiro1 · Lucas D. Vieira1 · Rhewter Nunes1 · Evandro Novaes2 · Eric Coissac3 · Orzenil B. Silva‑Junior4 · Dario Grattapaglia4 · Rosane Garcia Collevatti1 Received: 31 August 2020 / Accepted: 15 October 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract 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. Abstract 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. Keywords Branch-site selection · Codon usage · Comparative genomics · Plastome evolution · Positive selection · Substitution rate Abbreviations AICc Akaike Information Criterion corrected for small sample size FDR False Discovery Rate HMM Hidden Markov Model IR Inverted Repeat LSC Large Single Copy Communicated by Dorothea Bartels. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00425-020-03498-9) contains supplementary material, which is available to authorized users. * Rosane Garcia Collevatti [email protected] Extended author information available on the last page of the article
LRT Likelihood Ratio Test RSCU Relative Synonymous Codon Usage SSC Small Single Copy SSR Simple Sequence Repeats
Introduction Advances in high throughput and affordable cost
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