Abstract: INTRODUCTION: Aronia melanocarpa (Michx.) Ell. also known as black chokeberry, belongs to the Aronia genus (Rosaceae family). The genus Aronia Medik. includes A. arbutifolia (L.) Pers. or red chokeberry and A. prunifolia (Marshall) Rehder or purple chokeberry, both of which are found in the wild in North American and an additional cultivated taxon, A. mitschurinii (A.K. Skvortsov and Maitul.) or Mitschurin’s chokeberry, originating from Europe. However, the species boundaries and relationships between species of Aronia are not clear. Moreover, the taxonomic history of Aronia is complex, as species of this genus have formerly been placed in numerous genera, such as Mespilus, Pyrus, Adenorachis, Sorbus, and Photinia. In the present study, we first sequenced and characterized the complete cp genome of A. melanocarpa and compared its sequence features with those of the cp genomes from 13 species of the family Rosaceae. The aims of this study were: (1) to increase our understanding of the structural patterns of complete cp genome of A. melanocarpa, (2) to determine the cp genome derived phylogenetic relationships of A. melanocarpa with other Rosaceae species.  RATIONALE: The chloroplast (cp) is a core organelle in green plants with vital roles in photosynthesis and carbon fixation. Comparative analyses of cp genomes between different plant species reveal intra- and inter-species rearrangements that have occurred during evolution, such as IR contraction and expansion. Based on these characteristics, the cp genome has been wildly used for species identification, phylogenetic analysis, and exploring the genetic basis of environmental adaptation.   RESULTS: For the first time, the complete A. melanocarpa chloroplast (cp) genome was sequenced and analyzed. Chloroplast genomic DNA of A. melanocarpa was extracted and sequenced, analyzed, and compared with that from 13 other species in the Rosaceae family. The A. melanocarpa cp genome is 159 772 bp; has a total guanine-cytosine (GC) content of 36.6%, and exhibits a typical quadripartite structure with four separate regions, including a large single-copy (LSC) region of 87,810 bp and a small single-copy (SSC) region of 19 200 bp separated by two inverted repeats (IRa and IRb) regions of 26,381 bp each. A total of 132 unique genes were annotated, including 87 protein-coding genes, 37 tRNAs, and eight rRNAs, with 22 duplicates in the IR regions. In total, 76 simple sequence repeats (SSRs) and 50 long repeats were detected. Phylogenetic analysis indicated that A. melanocarpa is most closely related to A. arbutifolia and forms a sister clade to Cydonia oblonga with weak support.  CONCLUSION: In the present study, we analyzed the complete cp genome of A. melanocarpa by using Illumina high-throughput sequencing technology. The A. melanocarpa cp genome is 159 772 bp, and 132 genes were predicted, including 87 protein coding genes, 37 tRNAs, and eight rRNAs. A total of 76 SSRs and 50 long repeats were identified, which could be further used for the development of molecular markers. Highly variable regions such as trnK-rps16, rps16-trnQ, trnG-atpA, petN-psbM, trnT-psbD, psbZ-trnG, trnT-trnL, ndhC-trnV and accD-psaI were also detected in intergenic spaces, which might be useful for broad applications in genetic research studies as well as phylogenetic studies. Phylogenetic construction results strongly supported that A. melanocarpa was closest related to A. arbutifolia, followed by Cydonia oblonga with weak support. This newly available genomic data for A. melanocarpa will provide a basis for future research on the population genetics and phylogenomics and will benefit genus Aronia crossbreeding studies and utilization of the genus Aronia.

Key words: Aronia melanocarpa, chloroplast genome, structural variation, phylogenetic relationships