Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

Lai, Zhao; Kane, Nolan C.; Kozik, Alexander; Hodgins, Kathryn A.; Dlugosch, Katrina M.; Barker, Michael S.; Matvienko, Marta; Yu, Qian; Turner, Kathryn G.; Pearl, Stephanie A.; Bell, Graeme Douglas Milton; Zou, Yi; Grassa, Chris; Guggisberg, Alessia; Adams, Keith L.; Anderson, James V.; Horvath, David P.; Kesseli, Rick; Burke, John M.; Michelmore, Richard W.; Rieseberg, Loren H.

doi:10.3732/ajb.1100313

Cited by 80 publications

(103 citation statements)

References 74 publications

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“…2000) blastn search against an un‐annotated, normalized, 33.2‐Mbp expressed sequence tag (EST) library assembly derived from a single North American A. artemisiifolia individual collected in Minnesota (Lai et al. 2012), using an E‐value threshold of 10 −10 and reporting at most five best hits. Transcript sequences that matched the entire length of restriction site‐associated tag sequences with greater than 95% identity were chosen for further analysis.…”

Section: Methodsmentioning

confidence: 99%

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The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

Martin

Olsen

Samaniego

et al. 2016

Ecology and Evolution

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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 the species' native range, we characterized diallelic SNP loci via a reduced‐representation genotyping‐by‐sequencing (GBS) approach. We corroborate phylogeographic domains previously discovered using traditional sequencing methods, while demonstrating increased power to resolve weak genetic structure in this highly admixed plant species. By identifying exome polymorphisms underlying genetic differentiation, we suggest that geographic differentiation of this important invasive species has occurred more often within pathways that regulate growth and response to defense and stress, which may be associated with survival in North America's diverse climatic regions.

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Section: Methodsmentioning

confidence: 99%

“…The transcriptome assembly published by Lai et al. (2012) consists of 62,946 sequences. A total of 38,307 of these could be annotated with GO terms in the absence of an annotated ragweed transcriptome, so further analysis of transcriptome assembly was limited to the annotated sequences.…”

Section: Methodsmentioning

confidence: 99%

The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

Martin

Olsen

Samaniego

et al. 2016

Ecology and Evolution

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“…For some plants, leaf tissue was collected in the field. For each individual, RNA was extracted from young leaf tissues using a modified TRIzol Reagent protocol (Invitrogen, Carlsbad, CA) protocol 40 . Samples were quantified using NanoDrop (Thermo Fisher Scientific, Waltham, MA) and their quality verified on agarose gels.…”

Section: Methodsmentioning

confidence: 99%

Genomic islands of divergence are not affected by geography of speciation in sunflowers

et al. 2013

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Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis. Here, we report on transcriptome scans among four recently diverged pairs of sunflower (Helianthus) species that vary in the geographical context of speciation. We find that genetic divergence is lower in sympatric and parapatric comparisons, consistent with a role for gene flow in eroding neutral differences. However, genomic islands of divergence are numerous and small in all comparisons, and contrary to expectations, island number and size are not significantly affected by levels of interspecific gene flow. Rather, island formation is strongly associated with reduced recombination rates. Overall, our results indicate that the functional architecture of genomes plays a larger role in shaping genomic divergence than does the geography of speciation.

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“…To date, transcriptomes using next-generation sequencing of a few weedy species have been produced to aid the discovery of genes that contribute to herbicide resistance and other weediness traits, with most progress occurring in Conyza and Amaranthus spp. and Lolium rigidum (Lee et al, 2009;Peng et al, 2010;Riggins et al, 2010;Lai et al, 2012;Gaines et al, 2014).…”

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confidence: 99%

De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms

et al. 2014

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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 3503 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 complete mitochondrial genome (approximately 450 kb in 120 scaffolds). The nuclear genome is composed of 44,592 protein-coding genes. Genome resequencing of seven additional horseweed biotypes was performed. These sequence data were assembled and used to analyze genome variation. Simple sequence repeat and single-nucleotide polymorphisms were surveyed. Genomic patterns were detected that associated with glyphosate-resistant or -susceptible biotypes. The draft genome will be useful to better understand weediness and the evolution of herbicide resistance and to devise new management strategies. The genome will also be useful as another reference genome in the Compositae. To our knowledge, this article represents the first published draft genome of an agricultural weed.

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Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

Cited by 80 publications

References 74 publications

The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L.)

Genomic islands of divergence are not affected by geography of speciation in sunflowers

De Novo Genome Assembly of the Economically Important Weed Horseweed Using Integrated Data from Multiple Sequencing Platforms

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