<i>easyfm</i>: An easy software suite for file manipulation of Next Generation Sequencing data on desktops

Jung, Hyungtaek; Jeon, Byong‐Hun; Ortiz‐Barrientos, Daniel

doi:10.1101/2021.09.29.462291

Cited by 1 publication

(1 citation statement)

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“…25 While interpreting chromatograms is a common skill among weed scientists, doing so for a dataset much larger than the one examined here seems impractical because it is not automated. Although numerous NGS analysis tools exist, 43 including graphical user interface (GUI)-based tools, 44 there are only a few examples of similar tools for Sanger trace analyses that are only partially GUI-based. 45 We interpreted the data with the following assumptions: (a) haplotypes differing by several SNPs (> 10%) originated from independent selection events; and (b) the presence of the same mutant haplotype within different populations indicates gene flow and non-independent selection of the same mutation in identical WT ALS haplotypes.…”

Section: Origin and Spread Of 574-leu Haplotypesmentioning

confidence: 99%

Genetic basis and origin of resistance to acetolactate synthase inhibitors in Amaranthus palmeri from Spain and Italy

Manicardi

Scarabel

Llenes

et al. 2023

Pest Management Science

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BACKGROUNDAmaranthus palmeri is an aggressive annual weed native to the United States, which has become invasive in some European countries. Populations resistant to acetolactate synthase (ALS) inhibitors have been recorded in Spain and Italy, but the evolutionary origin of the resistance traits remains unknown. Bioassays were conducted to identify cross‐resistance to ALS inhibitors and a haplotype‐based genetic approach was used to elucidate the origin and distribution of resistance in both countries.RESULTSAmaranthus palmeri populations were resistant to thifensulfuron‐methyl and imazamox, and the 574‐Leu mutant ALS allele was found to be the main cause of resistance among them. In two Spanish populations, 376‐Glu and 197‐Thr mutant ALS alleles were also found. The haplotype analyses revealed the presence of two and four distinct 574‐Leu mutant haplotypes in the Italian and Spanish populations, respectively. None was common to both countries, but some mutant haplotypes were shared between geographically close populations or between populations more than 100 km apart. Wide genetic diversity was found in two very close Spanish populations.CONCLUSIONALS‐resistant A. palmeri populations were introduced to Italy and Spain from outside Europe. Populations from both countries have different evolutionary histories and originate from independent introduction events. ALS resistance then spread over short and long distances by seed dispersal. The higher number and genetic diversity among mutant haplotypes from the Spanish populations indicated recurrent invasions. The implementation of control tactics to limit seed dispersal and the establishment of A. palmeri is recommended in both countries. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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Section: Origin and Spread Of 574-leu Haplotypesmentioning

confidence: 99%