Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome
BMC GENOMICS
Authors: Putintseva, Yuliya A.; Bondar, Eugeniya I.; Simonov, Evgeniy P.; Sharov, Vadim V.; Oreshkova, Natalya V.; Kuzmin, Dmitry A.; Konstantinov, Yuri M.; Shmakov, Vladimir N.; Belkov, Vadim I.; Sadovsky, Michael G.; Keech, Olivier; Krutovsky, Konstantin V.
Abstract
Background: Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from similar to 222 Kbp inBrassica napusto 11.3 Mbp inSilene conica. To date, in comparison with the number of plant species, only a few plant mitogenomes have been sequenced and released, particularly for conifers (the Pinaceae family). Conifers cover an ancient group of land plants that includes about 600 species, and which are of great ecological and economical value. Among them, Siberian larch (Larix sibiricaLedeb.) represents one of the keystone species in Siberian boreal forests. Yet, despite its importance for evolutionary and population studies, the mitogenome of Siberian larch has not yet been assembled and studied. Results: Two sources of DNA sequences were used to search for mitochondrial DNA (mtDNA) sequences: mtDNA enriched samples and nucleotide reads generated in the de novo whole genome sequencing project, respectively. The assembly of the Siberian larch mitogenome contained nine contigs, with the shortest and the largest contigs being 24,767 bp and 4,008,762 bp, respectively. The total size of the genome was estimated at 11.7 Mbp. In total, 40 protein-coding, 34 tRNA, and 3 rRNA genes and numerous repetitive elements (REs) were annotated in this mitogenome. In total, 864 C-to-U RNA editing sites were found for 38 out of 40 protein-coding genes. The immense size of this genome, currently the largest reported, can be partly explained by variable numbers of mobile genetic elements, and introns, but unlikely by plasmid-related sequences. We found few plasmid-like insertions representing only 0.11% of the entire Siberian larch mitogenome. Conclusions: Our study showed that the size of the Siberian larch mitogenome is much larger than in other so far studied Gymnosperms, and in the same range as for the annual flowering plantSilene conica(11.3 Mbp). Similar to other species, the Siberian larch mitogenome contains relatively few genes, and despite its huge size, the repeated and low complexity regions cover only 14.46% of the mitogenome sequence.
Resequencing of 297 melon accessions reveals the genomic history of improvement and loci related to fruit traits in melon
PLANT BIOTECHNOLOGY JOURNAL
Authors: Liu, Shi; Gao, Peng; Zhu, Qianglong; Zhu, Zicheng; Liu, Hongyu; Wang, Xuezheng; Weng, Yiqun; Gao, Meiling; Luan, Feishi
Abstract
Domestication and improvement are two important stages in crop evolution. Melon (Cucumis meloL.) is an important vegetable crop with wide phenotypic diversity in many horticultural traits, especially fruit size, flesh thickness and aroma, which are likely the results of long-term extensive selection during its evolution. However, selective signals in domestication and improvement stages for these remarkable variations remain unclear. We resequenced 297 wild, landrace and improved melon accessions and obtained 2 045 412 high-quality SNPs. Population structure and genetic diversity analyses revealed independent and two-step selections in two subspecies of melon: ssp.meloand ssp.agrestisduring melon breeding. We detected 233 (similar to 18.35 Mbp) and 159 (similar to 17.71 Mbp) novel potential selective signals during the improvement stage in ssp.agrestisand spp.melo, respectively. Twoalcohol acyltransferasegenes (CmAATs) unique to the melon genome compared with other cucurbit crops may have undergone stronger selection in ssp.agrestisfor the characteristic aroma as compared with other cucurbits. Genome-wide association analysis identified eight fruit size and seven flesh thickness signals overlapping with selective sweeps. Compared with thin-skinned ssp.agrestis, thick-skinned ssp.melohas undergone a stronger selection for thicker flesh. In most melon accessions,CmCLV3has pleiotropic effects on carpel number and fruit shape. Findings from this study provide novel insights into melon crop evolution, and new tools to advance melon breeding.