Ontology highlight
ABSTRACT:
PROVIDER: PRJNA616180 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11445722_1.fastq.gz | Fastqsanger.gz | |||
| SRR11445722_2.fastq.gz | Fastqsanger.gz | |||
| SRR11445723_1.fastq.gz | Fastqsanger.gz | |||
| SRR11445723_2.fastq.gz | Fastqsanger.gz | |||
| SRR11445724_1.fastq.gz | Fastqsanger.gz |
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Project description:Salvia is an important genus from the Lamiaceae with approximately 1000 species distributed globally. Several Salvia species are commercially important because of their medicinal and culinary properties. We report the construction of the first fingerprinting array for Salvia species enriched with polymorphic and divergent DNA sequences and demonstrate the potential of this array for fingerprinting several economically important members of this genus. In order to generate the Salvia Subtracted Diversity Array (SDA), a Suppression Subtractive Hybridization (SSH) was performed between a pool of ten Salvia species and a pool of non-angiosperm and angiosperms (excluding the Lamiaceae) to selectively isolate Salvia-specific sequences. A total of 285 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. DNA fingerprints were obtained for fifteen Salvia genotypes including three that were not part of the original subtraction pool. Hierarchical cluster analysis indicated that the Salvia-specific SDA was capable of differentiating closely related species of S. officinalis and S. miltiorrhiza and was also able to reveal genetic relationships consistent with geographical origins. Species-specific features were also found for S. elegans, S. officinalis, S. sclarea, S. przewalskii and S. runcinata.
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Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.
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