科研之友
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摘要
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 8500x 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 beta' 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.
- 出版日期2018-5-29
- 单位南京林业大学
