Study of spontaneous mutations in the transmission of poplar chloroplast genomes from mother to offspring
| Autor: | Meng Xu, Minren Huang, Haoran Wang, Huixin Pan, Sheng Zhu, Guangping Wang |
|---|---|
| Rok vydání: | 2017 |
| Předmět: |
0106 biological sciences
0301 basic medicine Populus trichocarpa clone (Java method) lcsh:QH426-470 Genotype lcsh:Biotechnology Single-nucleotide polymorphism 01 natural sciences Genome Polymorphism Single Nucleotide 03 medical and health sciences Genome Size lcsh:TP248.13-248.65 Genetics Transmission Chloroplast genome Genome Chloroplast Contig biology fungi DNA Chloroplast food and beverages biology.organism_classification Chloroplast lcsh:Genetics 030104 developmental biology Populus Chloroplast DNA Multi-pass sequencing Full-sibling family Mutation 010606 plant biology & botany Biotechnology Research Article |
| Zdroj: | BMC Genomics BMC Genomics, Vol 19, Iss 1, Pp 1-15 (2018) |
| ISSN: | 1471-2164 |
| Popis: | 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 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. Electronic supplementary material The online version of this article (10.1186/s12864-018-4813-8) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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