Genômica comparativa em Piper L.

Abstract

Piper L. is considered the second largest genus of Angiosperms and has species of high socioeconomic importance, including those that produce essential oils, such as Piper hispidinervum C.DC, Piper aduncum L. e Piper aff. hispidinervum C.DC. These species are involved in a taxonomic controversy because they have very similar morphological and cytogenetic traits. In order to identify higher resolution traits to define their taxonomic status, the aim was to carry out a comparative and phylogenetic analysis of the repetitive collection of DNA and the chloroplast genome between them. Genomic DNAs were sequenced on Illumina and repetitive sequence analyzes were performed on the RepeatExplorer pipeline. The species Piper nigrum L. was used as outgroup from nucleotide sequences available in the ENA bank. The similarity between the satellite sequences was determined by MAFFT in the UGENE software. Amino acid sequences of conserved protein domains of the Ty3-Gypsy superfamily were extracted, and phylogenetic relationships protected by the Neighbor-Joining method. Chloroplast genomes were assembled in NOVOPlasty, annotated via GeSeq-CHLOROBOX and Geneious Prime, and circular graphic maps obtained in OrganellarGenomeDRAW. The chloroplast genome sequences were identified with MAFFT, and the phylogenetic tree was built with 32 Piper species by the Maximum Likelihood method. The repetitive sample represented about 60% of the genome of P. hispidinervum, 62% of P. aduncum and P. aff. hispidinervum. Retrotransposons were the most abundant class, with the LTR order (52%) and the Ty3-Gypsy superfamily (49.8%) accounting for most of the repetitive revenue in P. hispidinervum, P. aduncum, and P. aff. hispidinervum. The EnSpm-CACATA family was absent in P. nigrum and was the most abundant transposon in the other species. On the other hand, the hAT and Mutator families were more abundant in P. nigrum and remained in lower capacities in the other species. DNA satellites were identified in all genomes and were classified into new families. Only the PafSat1 satellite was shared in all species, while the PadSat1 and PadSat2 satellites were exclusive to P. aduncum and PniSat1 and PniSat2 were exclusive to P. nigrum. The Ty3-Gypsy superfamily comprises six clades with common lineages of retrotransposition among Piper species. The chloroplast genome of these species has a quadripartite structure, formed by the small single copy region (SSC), inverted repeat regions (IRa and IRb) and the large single copy region (LSC). P. aduncum had a genome size of 161,719 bp, P. hispidinervum and P. aff. hispidinervum showed patterns of 161,287 and 161,257 bp, respectively, and all approved 129 genes, 88 protein-coding genes, 34 transfer RNA genes and seven ribosomal RNA genes. The repetitive collection and chloroplast genomes of P. hispidinervum and P. aff. hispidinervum were closer to each other and more distant from P. aduncum, supporting the hypothesis that P. hispidinervum is a distinct species from P. aduncum and P. aff. hispidinervum an ecotype of P. hispidinervum.