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Background  Chloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in  Populus . Angiosperm chloroplast genomes are maternally inherited, but the chloroplast’ variation pattern of poplar at the single-base level during the transmission from mother to offspring remains unknown.    Results  Here, we constructed high-quality and almost complete chloroplast genomes for three poplar clones, ‘NL895’ and its parents, ‘I69’ and ‘I45’, from the short-read datasets using multi-pass sequencing (15–16 times per clone) and ultra-high coverage (at least 8500× per clone), with the four-step strategy of Simulation–Assembly–Merging–Correction. Each of the three resulting chloroplast assemblies contained contigs covering > 99% of  Populus trichocarpa  chloroplast DNA as a reference. A total of 401 variant loci were identified by a hybrid strategy of genome comparison-based and mapping-based single nucleotide polymorphism calling. The genotypes of 94 variant loci were different among the three poplar clones. However, only 1 of the 94 loci was a missense mutation, which was located in the exon region of  rpoC1  encoding the β’ subunit of plastid-encoded RNA polymerase. The genotype of the loci in NL895 and its female parent (I69) was different from that of its male parent (I45).    Conclusions  This research provides resources for further chloroplast genomic studies of a F 1  full-sibling family derived from a cross between I69 and I45, and will improve the application of chloroplast genomic information in modern  Populus  breeding programs.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4813-8) contains supplementary material, which is available to authorized users.

Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring