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- Title
Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring.
- Authors
Zhu, Sheng; Xu, Meng; Wang, Haoran; Pan, Huixin; Wang, Guangping; Huang, Minren
- Abstract
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 <italic>Populus</italic>. 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 <italic>Populus trichocarpa</italic> 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 <italic>rpoC1</italic> 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 F1 full-sibling family derived from a cross between I69 and I45, and will improve the application of chloroplast genomic information in modern <italic>Populus</italic> breeding programs.
- Subjects
GENOMES; PLANT genomes; NUCLEOTIDE sequencing; CHLOROPLAST DNA; PLANT genetics
- Publication
BMC Genomics, 2018, Vol 19, Issue 1, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/s12864-018-4813-8