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Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum

Overview of attention for article published in BMC Genomics, January 2018
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Title
Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum
Published in
BMC Genomics, January 2018
DOI 10.1186/s12864-017-4407-x
Pubmed ID
Authors

Johan Fogelqvist, Georgios Tzelepis, Sarosh Bejai, Jonas Ilbäck, Arne Schwelm, Christina Dixelius

Abstract

Brassica plant species are attacked by a number of pathogens; among them, the ones with a soil-borne lifestyle have become increasingly important. Verticillium stem stripe caused by Verticillium longisporum is one example. This fungal species is thought to be of a hybrid origin, having a genome composed of combinations of lineages denominated A and D. In this study we report the draft genomes of 2 V. longisporum field isolates sequenced using the Illumina technology. Genomic characterization and lineage composition, followed by selected gene analysis to facilitate the comprehension of its genomic features and potential effector categories were performed. The draft genomes of 2 Verticillium longisporum single spore isolates (VL1 and VL2) have an estimated ungapped size of about 70 Mb. The total number of protein encoding genes identified in VL1 was 20,793, whereas 21,072 gene models were predicted in VL2. The predicted genome size, gene contents, including the gene families coding for carbohydrate active enzymes were almost double the numbers found in V. dahliae and V. albo-atrum. Single nucleotide polymorphisms (SNPs) were frequently distributed in the two genomes but the distribution of heterozygosity and depth was not independent. Further analysis of potential parental lineages suggests that the V. longisporum genome is composed of two parts, A1 and D1, where A1 is more ancient than the parental lineage genome D1, the latter being more closer related to V. dahliae. Presence of the mating-type genes MAT1-1-1 and MAT1-2-1 in the V. longisporum genomes were confirmed. However, the MAT genes in V. dahliae, V. albo-atrum and V. longisporum have experienced extensive nucleotide changes at least partly explaining the present asexual nature of these fungal species. The established draft genome of V. longisporum is comparatively large compared to other studied ascomycete fungi. Consequently, high numbers of genes were predicted in the two V. longisporum genomes, among them many secreted proteins and carbohydrate active enzyme (CAZy) encoding genes. The genome is composed of two parts, where one lineage is more ancient than the part being more closely related to V. dahliae. Dissimilar mating-type sequences were identified indicating possible ancient hybridization events.

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The data shown below were compiled from readership statistics for 41 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 41 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 8 20%
Student > Ph. D. Student 7 17%
Student > Master 5 12%
Student > Bachelor 3 7%
Student > Doctoral Student 3 7%
Other 4 10%
Unknown 11 27%
Readers by discipline Count As %
Agricultural and Biological Sciences 17 41%
Biochemistry, Genetics and Molecular Biology 10 24%
Social Sciences 2 5%
Computer Science 1 2%
Neuroscience 1 2%
Other 0 0%
Unknown 10 24%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 January 2018.
All research outputs
#20,879,072
of 23,498,099 outputs
Outputs from BMC Genomics
#9,420
of 10,787 outputs
Outputs of similar age
#380,880
of 445,025 outputs
Outputs of similar age from BMC Genomics
#196
of 221 outputs
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