Genome Size Diversity and Its Impact on the Evolution of Land Plants

Pellicer, Jaume; Hidalgo, Oriane; Dodsworth, Steven; Leitch, Ilia J.

doi:10.3390/genes9020088

Cited by 278 publications

(212 citation statements)

References 77 publications

(90 reference statements)

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“…[117]. Proliferation of repetitive elements especially transposons, is known to be a major mechanism driving expansion of eukaryote genomes [118,119] and therefore, could be the reason the C. tanaceti genome is larger than average for fungi in the phylum Ascomycota (36.91 Mb) [120]. Repeat-induced-point mutation (RIP) is a fungal-specific mechanism for limiting transposon proliferation below destructive levels [39].…”

Section: Discussion Genome and The Repeat Content Of Colletotrichum Tmentioning

confidence: 99%

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

Lelwala

Korhonen

Young

et al. 2019

Preprint

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23Colletotrichum tanaceti is an emerging foliar fungal pathogen of pyrethrum (Tanacetum 24 cinerariifolium), posing a threat to the global pyrethrum industry. Despite being reported 25 consistently from field surveys in Australia, the molecular basis of pathogenicity of C.26 tanaceti on pyrethrum is unknown. Herein, the genome of C. tanaceti (isolate BRIP57314) 27 was assembled de novo and annotated using transcriptomic evidence. The inferred 28 pathogenicity gene suite of C. tanaceti comprised a large array of genes encoding secreted 29 effectors, proteases, CAZymes and secondary metabolites. Comparative analysis of its 30 CAZyme pathogenicity profiles with those of closely related species suggested that C. 31tanaceti had additional hosts to pyrethrum. The genome of C. tanaceti had a high repeat 32 content and repetitive elements were located significantly closer to genes inferred to 33 influence pathogenicity than other genes. These repeats are likely to have accelerated 34 mutational and transposition rates in the genome, resulting in a rapid evolution of certain 35CAZyme families in this species. The C. tanaceti genome consisted of a gene-sparse, A-T 36 rich region facilitating a "two-speed" genome. Pathogenicity genes within this region were 37 likely to have a higher evolutionary rate than the 'core' genome. This "two-speed" genome 38 phenomenon in certain Colletotrichum spp. was hypothesized to have caused the clustering of 39 species based on the pathogenicity genes, to deviate from taxonomy. With the large repertoire 40 of pathogenicity factors that can potentially evolve rapidly in response to control measures, 41 C. tanaceti may pose a high-risk to global pyrethrum production. Knowledge of the 42 pathogenicity genes will facilitate future research in disease management of C. tanaceti and 43 other Colletotrichum spp.. 44 45 46 Evolution 65 tanaceti has been consistently reported in Australian field surveys of the crop [19] since 2013 66 [17] and causes leaf anthracnose, with black, water-soaked, sunken lesions [17]. Due to its 67 hemibiotrophic lifestyle, characteristic symptoms of C. tanaceti are not evident on leaves 68 until around 120 hours after infection [17, 20], when it switches from biotrophy to 69 necrotrophy. A significant reduction in green leaf area occurs usually 10 days after infection 70 [17]. This suggests a rapid disease cycle for C. tanaceti in pyrethrum and, given its 71 aggressiveness, the potential for serious crop damage. 4 72The molecular basis of pathogenicity of C. tanaceti, which includes the pathogenicity genes 73 and their evolution, has not been studied. Colletotrichum tanaceti has only been reported 74 from pyrethrum in Australia, but may have crossed over from another plant host species. 75However, cross-host pathogenicity has not yet been assessed and the pathogen's origin and 76 the potential host range are currently unknown. Therefore, the threat posed by C. tanaceti to 77 the local and global pyrethrum industry remains largely unknown. 78The genome sequence of an emer...

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Section: Discussion Genome and The Repeat Content Of Colletotrichum Tmentioning

confidence: 99%

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

Lelwala

Korhonen

Young

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…Genomic research continues to be advanced by technologies such as single molecule sequencing (e.g., Nanopore (Michael et al, 2018)). At the same time, plant genomes offer particular challenges, e.g., the spectrum of genome sizes in plants is wider than that of animals (Pellicer, Hidalgo, Dodsworth, & Leitch, 2018), and polyploidy and ancient genome duplications increase the complexity of many crop genomes (Michael & VanBuren, 2015).…”

Section: Nucleic Acidsmentioning

confidence: 99%

Directions for research and training in plant omics: Big Questions and Big Data

et al. 2019

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A key remit of the NSF ‐funded “Arabidopsis Research and Training for the 21 st Century” ( ART ‐21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research using Arabidopsis thaliana can play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al., Plant Physiology , 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the second ART ‐21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post‐doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.

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“…Quantification of phenotypic and genotypic changes in landrace requires an easily quantifiable character. Genome size (GS), being an indicator of evolutionary distance [1], is an important biodiversity trait [2] for molecular characterization of living organisms at a rapid pace. Many authors have proposed adaptive significance of GS variation [3][4][5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

Genome Size Unaffected by Variation in Morphological Traits, Temperature, and Precipitation in Turnip

et al. 2019

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Genome size (GS) was proposed as proxy for gross phenotypic and environmental changes in plants. GS organismal complexity is an enigma in evolutionary biology. While studies pertaining to intraspecific GS variation are abundant, literatures reporting the adaptive significance of GS are largelymissing. During food shortage, Brassica rapa var. rapa (turnip) is used as food and fodder for sustaining the livelihood of residents in the Qinghai Tibetan Plateau (QTP), which is also known as “the roof of the world”. Thus, climatic extremities make this region a natural environment to test adaptive significance of GS variation in turnip landraces. Therefore, from the QTP and its adjacent regions (the Hengduanshan and the Himalayas), we investigated adaptive evolution of GS in turnip landraces. Tuber diameter of turnip landraces was found to be significantly correlated with most of the environmental factors. GS was also shown not to be associated with morphological traits, temperature, and precipitation. Moreover, principal component analyses based on the whole dataset trisected the landraces into three distinct populations based on landrace usage—Hengduanshan, QTP, and the Himalayas. Nonetheless, our cumulative dataset showed evidence of adaptation of turnip landrace to different environments throughnonassociated genomic and phenomic plasticity.

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Genome Size Diversity and Its Impact on the Evolution of Land Plants

Cited by 278 publications

References 77 publications

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

Comparative genome analysis indicates rapid evolution of pathogenicity genes inColletotrichum tanaceti

Directions for research and training in plant omics: Big Questions and Big Data

Genome Size Unaffected by Variation in Morphological Traits, Temperature, and Precipitation in Turnip

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