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9 results for “plastid genome sequences”
Variation of and associations with the depth and evenness of sequencing coverage in a sample of archived plastid genomes
<p>Depth and evenness of sequencing coverage are considered potential indicators of genome assembly quality. In plastid genomics, where new data generation has outpaced the development of suitable assembly quality indicators, these coverage metrics could offer insights into the quality of plastomes of different sizes, structures, or taxonomic origins. However, the typical variation of sequencing depth and evenness among archived plastid genomes, their variability between plastome partitions, and any association with methodological factors have yet to be evaluated. This study explores the variation of sequencing depth and evenness across a sample of publicly accessible plastid genomes and their potential associations with plastome structure, assembly accuracy, and the methodological provenance of the genome data using statistical tests. Our results indicate significant differences in sequencing depth across the four structural partitions as well as between the coding and non-coding sections of the genomes, a significant correlation between sequencing evenness and the number of ambiguous nucleotides, and a significant difference in sequencing evenness between several DNA sequencing platforms. These findings highlight that many publicly accessible plastid genomes are based on sequence data with highly variable sequencing depth and evenness and that this variation is influenced, at least partially, by genome structure and methodological factors.</p>
Data from: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure
PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. METHODS: We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata L'Hér. (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. RESULTS: Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ~22% of the plastome nucleotide content. Among the largest repeats (>2 kb) we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. CONCLUSION: We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome, and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats.
Osmanthus plastid genome sequence for: Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae)
<p><span>Species of <em>Osmanthus</em> are economically important ornamental trees, yet information regarding their plastid genomes (plastomes) has rarely been reported, thus hindering taxonomic and evolutionary studies of this small but enigmatic genus. Here, we performed comparative genomics and evolutionary analyses on plastomes of 16 of the 28 currently accepted species, with 11 plastomes newly sequenced. Phylogenetic studies identified four main lineages within the genus that are here designated: 'Caucasian <em>Osmanthus</em>' (corresponding to <em>O</em>. <em>decorus</em>), '<em>Siphosmanthus</em>' (corresponding to <em>O</em>. sect. <em>Siphosmanthus</em>), '<em>O</em>. <em>serrulatus</em> + <em>O</em>. <em>yunnanensis</em>', and 'Core <em>Osmanthus</em>' (corresponding to <em>O</em>. sect. <em>Osmanthus</em> + <em>O</em>. sect. <em>Linocieroides</em>). Molecular clock analysis suggested that <em>Osmanthus</em> split from its sister clade c. 15.83 Ma. The estimated crown ages of the lineages were the following: genus <em>Osmanthus</em> at 12.66 Ma; '<em>Siphosmanthus</em>' clade at 5.85 Ma; '<em>O. serrulatus </em>+<em> O. yunnanensis</em>' at 4.89 Ma; 'Core <em>Osmanthus</em>' clade at 6.2 Ma. Ancestral state reconstructions and trait mapping showed that ancestors of <em>Osmanthus</em> were spring-flowering and originated at lower elevations. Phylogenetic principal component analysis clearly distinguished spring-flowering species from autumn-flowering species, suggesting that flowering time differentiation is related to the difference in ecological niches. Nucleotide substitution rates of 80 common genes showed a slow evolutionary pace and low nucleotide variations, all genes being subjected to purifying selection.</span></p>
Osmanthus plastid genome sequence for: Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae)
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Data from: Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome
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Data from: Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure
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Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
To date, publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae. Here we report 13 new plastid genomes of legumes spanning all three subfamilies. The genomes representing Caesalpinioideae and Mimosoideae are highly conserved in gene content and gene order, similar to the ancestral angiosperm genome organization. Genomes within the Papilionoideae, however, have reduced sizes due to deletions in nine intergenic spacers primarily in the large single copy region. Our study also indicates that rps16 has been independently lost at least five times in legumes, with additional gene and intron losses scattered among the papilionoids. Additionally, genera from two distinct lineages within the papilionoids, Lupinus and Robinia, have a parallel inversion of 36 kb and 39 kb, respectively. This parallel inversion is novel as it appears to be caused by a 29 bp repeat within two trnS genes. This repeat is present in all available legume plastid genomes indicating that there is the potential for this inversion to be present in more species. This case of a homoplasious inversion is also evidence that some inversion events may not be reliable phylogenetic markers.
Sequencing of historical plastid genomes reveal exceptional genetic diversity in rye before the start of systematic breeding
<p>The files found in this repository are sequencing files of historical rye samples used for generating the analyses presented in the Komluski et al. manuscript. The metadata.csv contains sampling sites and taxon information for the respective sequence file.</p>
Data from: Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids
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