Abstract
BackgroundChloroplasts 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.ResultsHere, 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).ConclusionsThis 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 Populus breeding programs.
Highlights
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
The feasibility of the reference-assisted strategy was assessed on the basis of several aspects, including the degree of chloroplast sequence similarity between the target and reference species, the de novo assembly of short-read data simulated from the reference chloroplast genome, and the proportion of the chloroplast reads in all of the reads generated from whole-cell sequencing
Sequence similarities of Populus chloroplast DNAs (cpDNAs) The highly conserved features of the chloroplast genomes are well-known. It was unclear whether the reference-assisted method was suitable for constructing the Populus chloroplast genome from whole-genome sequencing reads, owing to the unknown levels of sequence similarity among cpDNAs from species in the genus Populus L
Summary
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. The genetic improvement of traits associated with growth is a major facet of Populus breeding [1]. Populus deltoides as the maternal parent and Populus × euramericana as the paternal parent is usually superior to those of its reciprocal cross [7]. Determining the genetic mechanism underlying the differences between reciprocal crosses is beneficial for parental selection as an important part of Populus breeding programs. The comparison of high-quality chloroplast genomes has the potential to provide chloroplast genome-associated information for the genetic improvement of Populus through the use of hybrid breeding technology
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