Illumina sequencing of the chloroplast genome of common ragweed ( Ambrosia artemisiifolia L.)

Nagy, Erzsébet; Hegedűs, Géza; Taller, János; Kutasy, Barbara; Virág, Eszter

doi:10.1016/j.dib.2017.10.009

Cited by 10 publications

(11 citation statements)

References 11 publications

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“…Furthermore, investigation of plastid genome structures could trigger further breakthroughs in applied sciences. For example herbicides like PSI and PSII inhibitors have their target genes in the chloroplast genome thus understanding the chloroplast genome may indirectly support the exploration of herbicide resistance and development of novel control methods [ 89 ]; while plastid engineering can also be useful to develop resistance to various abiotic and biotic stress factors based on discovered resistance traits. Here we report the complete chloroplast genome sequence of Solanum dulcamara as a genomic tool for potential plastid genome comparative studies.…”

Section: Discussionmentioning

confidence: 99%

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

2018

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Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp). It consists of 112 unique genes from which 81 are protein-coding, 27 tRNA and four rRNA genes. All bittersweet plastid genes including non-functional ones and even intergenic spacer regions are transcribed in primary plastid transcripts covering 95.22% of the genome. These are later substantially edited in a post-transcriptional phase to activate gene functions. By comparing the bittersweet plastid genome with all available Solanaceae sequences we found that gene content and synteny are highly conserved across the family. During genome comparison we have identified several annotation errors, which we have corrected in a manual curation process then we have identified the major plastid genome structural changes in Solanaceae. Interpreted in a phylogenetic context they seem to provide additional support for larger clades. The plastid genome sequence of bittersweet could help to benchmark Solanaceae plastid genome annotations and could be used as a reference for further studies. Such reliable annotations are important for gene diversity calculations, synteny map constructions and assigning partitions for phylogenetic analysis with de novo sequenced plastomes of Solanaceae.

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Section: Discussionmentioning

confidence: 99%

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

2018

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“…Several methods have been used to sequence chloroplast genomes in plants, including primer walking [11][12][13][14] and high-throughput sequencing (HTS) [15]. HTS, both with isolated chloroplast DNA [16][17][18] and total cellular DNA [19][20][21], has been employed to generate physical maps of the chloroplast genome. However, the junctions of LSC/IRa, IRa/SSC, SSC/IRb and IRb/LSC need to be resolved using additional experimentation [22].…”

Section: Introductionmentioning

confidence: 99%

Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae

et al. 2020

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Background: Chloroplast genome information is critical to understanding forms of photosynthesis in the plant kingdom. During the evolutionary process, plants have developed different photosynthetic strategies that are accompanied by complementary biochemical and anatomical features. Members of family Chenopodiaceae have species with C 3 photosynthesis, and variations of C 4 photosynthesis in which photorespiration is reduced by concentrating CO 2 around Rubisco through dual coordinated functioning of dimorphic chloroplasts. Among dicots, the family has the largest number of C 4 species, and greatest structural and biochemical diversity in forms of C 4 including the canonical dual-cell Kranz anatomy, and the recently identified single cell C 4 with the presence of dimorphic chloroplasts separated by a vacuole. This is the first comparative analysis of chloroplast genomes in species representative of photosynthetic types in the family. Results: Methodology with high throughput sequencing complemented with Sanger sequencing of selected loci provided high quality and complete chloroplast genomes of seven species in the family and one species in the closely related Amaranthaceae family, representing C 3 , Kranz type C 4 and single cell C 4 (SSC 4) photosynthesis six of the eight chloroplast genomes are new, while two are improved versions of previously published genomes. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality and repeat region sequences. Comparison of the chloroplast genomes with previously sequenced plastid genomes revealed similar genome organization, gene order and content with a few revisions. High-quality complete chloroplast genome sequences resulted in correcting the orientation the LSC region of the published Bienertia sinuspersici chloroplast genome, identification of stop codons in the rpl23 gene in B. sinuspersici and B. cycloptera, and identifying an instance of IR expansion in the Haloxylon ammodendron inverted repeat sequence. The rare observation of a mitochondria-to-chloroplast inter-organellar gene transfer event was identified in family Chenopodiaceae. Conclusions: This study reports complete chloroplast genomes from seven Chenopodiaceae and one Amaranthaceae species. The depth of coverage obtained using high-throughput sequencing complemented with targeted resequencing of certain loci enabled superior resolution of the border junctions, directionality, and repeat region

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“…The CP genome map is a circular DNA molecule that includes a SSC region, a LSC region, and two inverted-repeat (IRa and IRb) regions ( Sato et al, 1999 ). Several CP genomes from Asteraceae have previously been reported, including CP genomes from Aster ( Choi and Park, 2015 ), Ambrosia ( Nagy et al, 2017 ), Carthanus ( Lu et al, 2015 ), and Taraxacum ( Salih et al, 2017 ). However, only one CP genome from Ligularia , for L. fischeri , has previously been published ( Lee et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Identification of Ligularia Herbs Using the Complete Chloroplast Genome as a Super-Barcode

et al. 2018

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More than 30 Ligularia Cass. (Asteraceae) species have long been used in folk medicine in China. Morphological features and common DNA regions are both not ideal to identify Ligularia species. As some Ligularia species contain pyrrolizidine alkaloids, which are hazardous to human and animal health and are involved in metabolic toxification in the liver, it is important to find a better way to distinguish these species. Here, we report complete chloroplast (CP) genomes of six Ligularia species, L. intermedia, L. jaluensis, L. mongolica, L. hodgsonii, L. veitchiana, and L. fischeri, obtained through high-throughput Illumina sequencing technology. These CP genomes showed typical circular tetramerous structure and their sizes range from 151,118 to 151,253 bp. The GC content of each CP genome is 37.5%. Every CP genome contains 134 genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and two pseudogenes (ycf1 and rps19). From the mVISTA, there were no potential coding or non-coding regions to distinguish these six Ligularia species, but the maximum likelihood tree of the six Ligularia species and other related species showed that the whole CP genome can be used as a super-barcode to identify these six Ligularia species. This study provides invaluable data for species identification, allowing for future studies on phylogenetic evolution and safe medical applications of Ligularia.

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Illumina sequencing of the chloroplast genome of common ragweed ( Ambrosia artemisiifolia L.)

Cited by 10 publications

References 11 publications

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

Methods of analysis of chloroplast genomes of C3, Kranz type C4 and Single Cell C4 photosynthetic members of Chenopodiaceae

Identification of Ligularia Herbs Using the Complete Chloroplast Genome as a Super-Barcode

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