Sequencing the Plastid Genome of Giant Ragweed (Ambrosia trifida, Asteraceae) From a Herbarium Specimen (original) (raw)
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Ambrosia (Asteraceae) is a taxonomically difficult genus of weedy, wind-pollinated plants with an apparent center of diversity in the Sonoran Desert of North America. Determining Ambrosia's evolutionary relationships has been the subject of much interest, with numerous studies using morphological characters, cytology, comparative phytochemistry, and chloroplast restriction site variation to produce conflicting accounts the relationships between Ambrosia species, as well as the classification of their close relatives in Franseria and Hymenoclea. To resolve undetermined intra-generic relationships within Ambrosia, we used DNA extracted from tissues obtained from seed banks and herbarium collections to generate multi-locus genetic data representing nearly all putative species, including four from South America. We performed Bayesian and Maximum-Likelihood phylogenetic analyses of six chloroplast-genome and two nuclear-genome markers, enabling us to infer monophyly for the genus, re...
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Horseweed (Conyza canadensis), a member of the Compositae (Asteraceae) family, was the first broadleaf weed to evolve resistance to glyphosate. Horseweed, one of the most problematic weeds in the world, is a true diploid (2n = 2x = 18), with the smallest genome of any known agricultural weed (335 Mb). Thus, it is an appropriate candidate to help us understand the genetic and genomic bases of weediness. We undertook a draft de novo genome assembly of horseweed by combining data from multiple sequencing platforms (454 GS-FLX, Illumina HiSeq 2000, and PacBio RS) using various libraries with different insertion sizes (approximately 350 bp, 600 bp, 3 kb, and 10 kb) of a Tennessee-accessed, glyphosate-resistant horseweed biotype. From 116.3 Gb (approximately 350× coverage) of data, the genome was assembled into 13,966 scaffolds with 50% of the assembly = 33,561 bp. The assembly covered 92.3% of the genome, including the complete chloroplast genome (approximately 153 kb) and a nearly compl...
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Background: The spread of herbicide-resistance Ambrosia artemisiifolia threatens not only the production of agricultural crops, but also the composition of weed communities. The reduction of their spread would positively affect the biodiversity and beneficial weed communities in the arable habitats. Detection of resistant populations would help to reduce herbicide exposure which may contribute to the development of sustainable agroecosystems. Methods: This study focuses on the application of target-site resistance (TSR) diagnostic of A. artemisiifolia caused by different herbicides. We used targeted amplicon sequencing (TAS) on Illumina Miseq platform to detect amino acid changes in herbicide target enzymes of resistant and wild-type plants. Results: 16 mutation points of four enzymes targeted by four herbicide groups, such as Photosystem II (PSII), Acetohydroxyacid synthase (AHAS), 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) and protoporphyrinogen IX oxidase (PPO) inhibitor...
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Expressed Sequence Tags from a variety of plant species have been useful for comparative genomics. The evolution of the Chloridoideae subfamily, previously lacking sequence data, was clarified by analysis of Bermudagrass (Cynodon dactylon) ESTs generated from a normalized cDNA library. Using EST collections, we generated unigene sets and analyzed them to further elucidate the evolutionary history of grass subfamilies. A total of eight grasses (C. dactylon, Sorghum bicolor, Saccharum officinarum, Zea mays, Oryza sativa, Hordeum vulgare, Festuca arundinacea, and Triticum aestivum) in four subfamilies and five tribes were analyzed using two different approaches—synonymous substitution rates (Ks) and phylogenetic trees. Ks distributions of paralogous genes suggested several duplication events in C. dactylon, S. bicolor, H. vulgare, and T. aestivum. Phylogenetic analysis with the unigene sets indicated that the analyzed grasses diverged from a common ancestor after a shared ancient polyploidization (ca. 50.0 ~ 67.8 million years ago). Ks distributions of orthologous genes suggested that the Chloridoideae and Panicoideae subfamilies diverged about 34.6 ~ 38.5 million years ago. With the evidence described in this study, we found traces of genomic changes in some grass subfamilies after the divergence of the PACC and BEP clades as well as divergence of Chloridoideae subfamily.
Molecular ecology resources, 2016
Population genetic studies of non-model organisms frequently employ reduced representation library (RRL) methodologies, many of which rely on protocols in which genomic DNA is digested by one or more restriction enzymes. However, because high molecular weight DNA is recommended for these protocols, samples with degraded DNA are generally unsuitable for RRL methods. Given that ancient and historic specimens can provide key temporal perspectives to evolutionary questions, we explored how custom-designed RNA probes could enrich for RRL loci (Restriction Enzyme-Associated Loci baits, or REALbaits). Starting with Genotyping-by-Sequencing (GBS) data generated on modern common ragweed (Ambrosia artemisiifolia L.) specimens, we designed 20,000 RNA probes to target well-characterized genomic loci in herbarium voucher specimens dating from 1835-1913. Compared to shotgun sequencing, we observed enrichment of the targeted loci at 19-151-fold. Using our GBS capture pipeline on a dataset of 38 he...
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Common ragweed (Ambrosia artemisiifolia L.) is an invasive, wind-pollinated plant nearly ubiquitous in disturbed sites in its eastern North American native range and present across growing portions of Europe, Africa, Asia, and Australia. Phenotypic divergence between European and native-range populations has been described as rapid evolution. However, a recent study demonstrated major human-mediated shifts in ragweed genetic structure before introduction to Europe and suggested that native-range genetic structure and local adaptation might fully explain accelerated growth and other invasive characteristics of introduced populations. Genomic differentiation that potentially influenced this structure has not yet been investigated, and it remains unclear whether substantial admixture during historical disturbance of the native range contributed to the development of invasiveness in introduced European ragweed populations. To investigate fine-scale population genetic structure across th...