Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms

Ruhlman, Tracey A.; Lee, Seung Bum; Jansen, Robert K.; Hostetler, Jessica B.; Tallon, Luke J.; Town, Christopher D.; Daniell, Henry

doi:10.1186/1471-2164-7-222

Cited by 89 publications

(54 citation statements)

References 101 publications

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“…These five assemblies were then aligned with Kalign [23], generating a consensus sequence of 155,834 nt (Table 1). Alignment of the de novo assembly with the published carrot plastid genome [24] showed full-length coverage, with 99% identity relative to the published sequence including 49 nt of difference in cumulative sequence SNPs, and 433 nt of cumulative indels, with a maximum indel length of 20 nt.…”

Section: Resultsmentioning

confidence: 99%

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

et al. 2012

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BackgroundSequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA.ResultsSequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome.ConclusionsThis study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.

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Section: Resultsmentioning

confidence: 99%

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

et al. 2012

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“…Short dispersed repeats are considered to be one of the major factors promoting cp genome rearrangements because they are common in highly rearranged algal and angiosperm genomes, and many rearrangement endpoints are associated with such repeats [8], 67–70. The role of short dispersed repeats in unrearranged cp genomes is still unclear [71], [72]. All of these repeats, together with the aforementioned SSRs, are informative sources for developing markers for population studies [36].…”

Section: Discussionmentioning

confidence: 99%

“…Significant progress in chloroplast transformation has been made in the model species tobacco as well as in a few major crops [78], [79]. Although the trnI / trnA and accD / rbcL intergenic spacer regions have been widely used as gene introduction sites for vector construction [79], the transformation efficiency is impaired when the sequences for homologous recombination are divergent among distantly related species [71]. The availability of the complete cp genome sequence of Salvia miltiorrhiza is helpful to identify the optimal intergenic spacers for transgene integration and to develop site-specific cp transformation vectors.…”

Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

et al. 2013

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Salvia miltiorrhiza is an important medicinal plant with great economic and medicinal value. The complete chloroplast (cp) genome sequence of Salvia miltiorrhiza, the first sequenced member of the Lamiaceae family, is reported here. The genome is 151,328 bp in length and exhibits a typical quadripartite structure of the large (LSC, 82,695 bp) and small (SSC, 17,555 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,539 bp). It contains 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs. The genome structure, gene order, GC content and codon usage are similar to the typical angiosperm cp genomes. Four forward, three inverted and seven tandem repeats were detected in the Salvia miltiorrhiza cp genome. Simple sequence repeat (SSR) analysis among the 30 asterid cp genomes revealed that most SSRs are AT-rich, which contribute to the overall AT richness of these cp genomes. Additionally, fewer SSRs are distributed in the protein-coding sequences compared to the non-coding regions, indicating an uneven distribution of SSRs within the cp genomes. Entire cp genome comparison of Salvia miltiorrhiza and three other Lamiales cp genomes showed a high degree of sequence similarity and a relatively high divergence of intergenic spacers. Sequence divergence analysis discovered the ten most divergent and ten most conserved genes as well as their length variation, which will be helpful for phylogenetic studies in asterids. Our analysis also supports that both regional and functional constraints affect gene sequence evolution. Further, phylogenetic analysis demonstrated a sister relationship between Salvia miltiorrhiza and Sesamum indicum. The complete cp genome sequence of Salvia miltiorrhiza reported in this paper will facilitate population, phylogenetic and cp genetic engineering studies of this medicinal plant.

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“…As outgroup sequences for phylogenetic analysis, cp genome 56 (NC_008325.1) and nrITS sequence (AY552527.1) of Daucus carota (carrot) belonging to the Apiaceae family were used.…”

Section: Methodsmentioning

confidence: 99%

Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species

Kim

Nguyen

Dong

et al. 2017

Sci Rep

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We produced complete sequences and conducted comparative analysis of the maternally inherited chloroplast (cp) genomes and bi-parentally inherited 45S nuclear ribosomal RNA genes (nrDNA) from ten Araliaceae species to elucidate the genetic diversity and evolution in that family. The cp genomes ranged from 155,993 bp to 156,730 bp with 97.1–99.6% similarity. Complete 45S nrDNA units were about 11 kb including a 5.8-kb 45S cistron. Among 79 cp protein-coding genes, 74 showed nucleotide variations among ten species, of which infA, rpl22, rps19 and ndhE genes showed the highest Ks values and atpF, atpE, ycf2 and rps15 genes showed the highest Ka/Ks values. Four genes, petN, psaJ, psbF, and psbN, related to photosynthesis and one gene, rpl23, related to the ribosomal large subunit remain conserved in all 10 Araliaceae species. Phylogenetic analysis revealed that the ten species could be resolved into two monophyletic lineages, the Panax-Aralia and the Eleutherococcus-Dendropanax groups, which diverged approximately 8.81–10.59 million years ago (MYA). The Panax genus divided into two groups, with diploid species including P. notoginseng, P. vietnamensis, and P. japonicus surviving in Southern Asia and a tetraploid group including P. ginseng and P. quinquefolius Northern Asia and North America 2.89–3.20 MYA.

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Complete plastid genome sequence of Daucus carota: Implications for biotechnology and phylogeny of angiosperms

Cited by 89 publications

References 101 publications

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

The Complete Chloroplast Genome Sequence of the Medicinal Plant Salvia miltiorrhiza

Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species

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