scholarly journals A chromosome-scale genome assembly of European Hazel (Corylus avellana L.) reveals targets for crop improvement

2019 ◽  
Author(s):  
Stuart J. Lucas ◽  
Kadriye Kahraman ◽  
Bihter Avşar ◽  
Richard J.A. Buggs ◽  
Ipek Bilge
Keyword(s):  
Powdery Mildew ◽  
Crop Improvement ◽  
Gene Families ◽  
Corylus Avellana ◽  
Genetic Maps ◽  
Health Concern ◽  
Protein Coding ◽  
Long Reads ◽  
Sequencing Strategy ◽  
Corylus Avellana L

AbstractEuropean hazelnut (Corylus avellana L.) is a tree crop of economic importance worldwide, but especially to northern Turkey, where the majority of production takes place. Hazelnut production is currently challenged by environmental stresses such as a recent outbreak of severe powdery mildew disease; furthermore, allergy to hazelnuts is an increasing health concern in some regions.In order to provide a foundation for utilizing the available hazelnut genetic resources for crop improvement, we produced the first fully assembled genome sequence and annotation for a hazelnut species, from Corylus avellana cv. ‘Tombul’, one of the most important Turkish varieties. A hybrid sequencing strategy combining short reads, long reads and proximity ligation methods enabled us to resolve heterozygous regions and produce a high-quality 370 Mb assembly that agrees closely with cytogenetic studies and genetic maps of the 11 C. avellana chromosomes, and covers 97.8% of the estimated genome size. The genome includes 28,409 high-confidence protein-coding genes, over 20,000 of which were functionally annotated based on homology to known plant proteins. We focused particularly on gene families encoding hazelnut allergens, and the MLO proteins that are an important susceptibility factor for powdery mildew. The complete assembly enabled us to differentiate between members of these families and identify novel homologs that may be important in mildew disease and hazelnut allergy. These findings provide examples of how the genome can be used to guide research and develop effective strategies for crop improvement in C. avellana.

scholarly journals The genome of the American groundhog, Marmota monax

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1137
Author(s):  
Daniela Puiu ◽  
Aleksey Zimin ◽  
Alaina Shumate ◽  
Yuchen Ge ◽  
Jiabin Qiu ◽  
...  
Keyword(s):  
Protein Coding ◽  
Marmota Monax ◽  
Protein Coding Genes ◽  
The North ◽  
Long Reads ◽  
Oxford Nanopore ◽  
A Genome ◽  
Sequencing Strategy ◽  
Alpine Marmot ◽  
Combined Data

We sequenced the genome of the North American groundhog, Marmota monax, also known as the woodchuck. Our sequencing strategy included a combination of short, high-quality Illumina reads plus long reads generated by both Pacific Biosciences and Oxford Nanopore instruments. Assembly of the combined data produced a genome of 2.74 Gbp in total length, with an N50 contig size of 1,094,236 bp. To annotate the genome, we mapped the genes from another M. monax genome and from the closely related Alpine marmot, Marmota marmota, onto our assembly, resulting in 20,559 annotated protein-coding genes and 28,135 transcripts. The genome assembly and annotation are available in GenBank under BioProject PRJNA587092.

scholarly journals The First Draft Genome of the Plasterer Bee Colletes gigas (Hymenoptera: Colletidae: Colletes)

2020 ◽  
Vol 12 (6) ◽  
pp. 860-866 ◽  
Author(s):  
Qing-Song Zhou ◽  
Arong Luo ◽  
Feng Zhang ◽  
Ze-Qing Niu ◽  
Qing-Tao Wu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Draft Genome ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Single Copy ◽  
Gene Family Evolution ◽  
Nesting Biology ◽  
Protein Coding ◽  
Final Assembly ◽  
Long Reads

Abstract Despite intense interest in bees, no genomes are available for the bee family Colletidae. Colletes gigas, one of the largest species of the genus Colletes in the world, is an ideal candidate to fill this gap. Endemic to China, C. gigas has been the focus of studies on its nesting biology and pollination of the economically important oil tree Camellia oleifera, which is chemically defended. To enable deeper study of its biology, we sequenced the whole genome of C. gigas using single-molecule real-time sequencing on the Pacific Bioscience Sequel platform. In total, 40.58 G (150×) of long reads were generated and the final assembly of 326 scaffolds was 273.06 Mb with a N50 length of 8.11 Mb, which captured 94.4% complete Benchmarking Universal Single-Copy Orthologs. We predicted 11,016 protein-coding genes, of which 98.50% and 84.75% were supported by protein- and transcriptome-based evidence, respectively. In addition, we identified 26.27% of repeats and 870 noncoding RNAs. The bee phylogeny with this newly sequenced colletid genome is consistent with available results, supporting Colletidae as sister to Halictidae when Stenotritidae is not included. Gene family evolution analyses identified 9,069 gene families, of which 70 experienced significant expansions (33 families) or contractions (37 families), and it appears that olfactory receptors and carboxylesterase may be involved in specializing on and detoxifying Ca. oleifera pollen. Our high-quality draft genome for C. gigas lays the foundation for insights on the biology and behavior of this species, including its evolutionary history, nesting biology, and interactions with the plant Ca. oleifera.

scholarly journals A chromosome‐scale genome assembly of European hazel ( Corylus avellana  L.) reveals targets for crop improvement

2021 ◽  
Author(s):  
Stuart J. Lucas ◽  
Kadriye Kahraman ◽  
Bihter Avşar ◽  
Richard J.A. Buggs ◽  
Ipek Bilge
Keyword(s):  
Genome Assembly ◽  
Crop Improvement ◽  
Corylus Avellana ◽  
Corylus Avellana L

scholarly journals First report of Erysiphe corylacearum, agent of powdery mildew, on hazelnut (Corylus avellana) in Romania

Plant Disease ◽  
2021 ◽  
Author(s):  
Marco Rosati ◽  
Marian Bogoescu ◽  
Davide Spadaro
Keyword(s):  
Powdery Mildew ◽  
Crop Protection ◽  
Its Region ◽  
Corylus Avellana ◽  
Morphological Identification ◽  
Conidial Suspension ◽  
Rdna Sequences ◽  
White Mycelium ◽  
Corylus Avellana L ◽  
Erysiphe Corylacearum

Romania has an area dedicated to hazelnut (Corylus avellana L.), covering 890 hectares as of 2019. During October 2020, powdery mildew symptoms were observed on the upper side of leaves of hazelnut ‘Tonda di Giffoni’ in two commercial orchards in Dudeștii Vechi, Romania (Fig. 1). The disease was present on 70% of the trees in planting, with at least 5 leaves per tree having powdery mildew. Micromorphological examination revealed amphigenous, hyaline, branched, septate mycelial patches of 2.3 to 3.6 μm in diameter. Conidiophores measured 24-60 × 5-6 (average: 45 × 6) μm and consisted of erect, cylindrical to flexuous foot cells, followed by 1-2 shorter cells. Ellipsoid, ovoid to doliform conidia were produced singly and they measured 19-35 × 16-24 (average: 28 × 19) μm. Chasmothecia were spherical, 75 to 107 (average: 88) μm in diameter. Nine to thirteen straight, sometimes flexuous, appendages measured 54 to 92 (average: 66) μm in length and they had five times dichotomous branched apices with curved tips (Fig. 2). Each chasmothecium contained three to five ellipsoid, ovoid to subglobose asci measuring 41-58 × 29-55 μm (average 52 × 43) μm. The asci contained four to eight ascospores measuring 13-24 × 11-15 (average 18 × 14) μm. Morphological identification was confirmed by sequencing the ITS-region of rDNA using two isolates from leaves, stored as frozen mycelium at -20°C. PCR was performed with Erysiphales-specific primer pair PMITS1/PMITS2 (Cunnington et al. 2003). The obtained sequences were deposited in GenBank (Accession n° MW423075, MW423076). Blast analysis of both sequences had 100% identity to ITS rDNA sequences of Erysiphe corylacearum from Azerbaijan (Abasova et al. 2018; Accession n° LC270863), Turkey (Sezer et al. 2017; KY082910), Switzerland (Beenken et al. 2020; MN82272), Iran (Arzanlou et al. 2018; MH047243), Italy (Mezzalama et al. 2020; MW045425) and 99% identity from Georgia (Meparishvili et al. 2019; MK157199). The sequences had a lower percent identity (83%) to Phyllactinia guttata (Accession n° AB080558) (Fig. 3). Pathogenicity was verified on one-year-old plants of C. avellana ‘Tonda di Giffoni’, which were artificially inoculated with a conidial suspension from infected leaves (n = 25). Inoculated plants were incubated at 20 to 28°C with 70 to 80% relative humidity. White mycelium appeared on the upper surface of the leaves at 8 to 10 days after inoculation. No symptoms were found on control plants sprayed with sterile water. The fungus present on inoculated leaves was morphologically identical to the original isolates from diseased trees from the field. E. corylacearum is native to East Asia and was previously reported in Japan on wild species of Corylus (Takamatsu et al. 2015; Accession n° LC009928). The pathogen most likely spread into Europe from east to west of Europe (Heluta et al. 2019), through the Caucasus, starting from Turkey, Azerbaijan, Georgia, and Iran. P. guttata was considered the only causal agent of powdery mildew on hazelnut in most countries, including Romania (Brown 1995). Compared to P. guttata, which generally develops a mycelium on the underside of leaves, E. corylacearum grows with a white mycelium on the upper side of the leaves. Recently, E. corylacearum on C. avellana was reported also in Ukraine (Heluta et al. 2019), from which it could have moved to Romania. Crop protection strategies for hazelnut should be revised according to the new pathogen occurrence.

scholarly journals Long-reads assembly of the Brassica napus reference genome, Darmor-bzh

2020 ◽  
Author(s):  
Mathieu Rousseau-Gueutin ◽  
Caroline Belser ◽  
Corinne Da Silva ◽  
Gautier Richard ◽  
Benjamin Istace ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Reference Genome ◽  
Crop Improvement ◽  
Genetic Maps ◽  
Sequencing Data ◽  
Long Reads ◽  
Gene Catalogue ◽  
Genome Assemblies ◽  
Agronomically Important Traits ◽  
Selection Of

AbstractBackgroundThe combination of long-reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allow to access the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like telomeres and centromeres. The Brassica genus is not exempt and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the Brassica genus.FindingsHere, we report the new long-reads assembly of Darmor-bzh genome (Brassica napus) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a Brassica genome to date (contigs N50 > 10Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.ConclusionUsing these cutting edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable for the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

scholarly journals Long-read assembly of the Brassica napus reference genome Darmor-bzh

GigaScience ◽  
2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Mathieu Rousseau-Gueutin ◽  
Caroline Belser ◽  
Corinne Da Silva ◽  
Gautier Richard ◽  
Benjamin Istace ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Reference Genome ◽  
Crop Improvement ◽  
Genetic Maps ◽  
Sequencing Data ◽  
Long Reads ◽  
Gene Catalogue ◽  
Long Read ◽  
Genome Assemblies ◽  
Selection Of

Abstract Background The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus. Findings Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. Conclusion Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

Ecological plasticity of nut crops of the collections of the federal scientific center for agroecology RAS

2019 ◽  
pp. 105-115
Author(s):  
А.Ш. Хужахметова
Keyword(s):  
Corylus Avellana ◽  
Taxonomic Composition ◽  
Morphological Features ◽  
Scientific Center ◽  
Significance Level ◽  
Ecological Plasticity ◽  
Protective Forest ◽  
Corylus Avellana L ◽  
Academy Of Sciences ◽  
Trees And Shrubs

Показана актуальность изучения экологической пластичности древесных растений в связи с необходимостью подбора адаптированного видового состава деревьев и кустарников для защитных лесных насаждений в условиях климатических изменений. Установлено, что экологическая пластичность и пределы толерантности растений связаны со свойством организмов адаптироваться к тому или иному диапазону факторов среды. В статье представлен таксономический состав орехоплодных культур коллекций ФНЦ агроэкологии РАН. Это шесть видов рода Juglans: J. regia, J. mandshurica, J. cinerea, J. rupestris, J. ailanthifolia, J. nigra и три вида рода Corylus: С. avellana L., С. аmericana W., сорта С. pontica C. Koch Президент, Футкурами, Черкесский2. Приведены сведения о положительном опыте культивирования Corylus avellana L. в плантационных насаждениях (1,6 га, посадка рядовая, схема размещения 55 м) в условиях южных черноземов. Цель исследований изучить экологическую пластичность орехоплодных кустарников коллекций ФНЦ агроэкологии РАН. На примере родового комплекса Corylus получены материалы по экологической пластичности орехоплодных кустарников в условиях каштановых (кадастр. 34:36:0000:14:0178), светлокаштановых почв (34:34:000000:122 34:34:060061:10). Установлены уровни изменчивости морфологических признаков ассимиляционного аппарата и плодов С. avellana L., сортов С. pontica C. Koch., которые согласуются с зимо и засухоустойчивостью. Кластерный анализ позволил выявить корреляцию признаков при 5 уровне значимости. Для целей защитного лесоразведения и озеленения засушливых районов рекомендованы Corylus avellana и Черкесский2 с выраженной вариабельностью морфологических признаков, которая указывает на их широкую экологическую валентность и адаптационные возможности в рассматриваемых условиях. The urgency of studying the ecological plasticity of woody plants in connection with the need to select an adapted species composition of trees and shrubs for protective forest plantations in the context of climate change is shown. It is established that the ecological plasticity and tolerance range of plants is associated with the ability of organisms to adapt to a particular range of environmental factors. The article presents the taxonomic composition of nut crops in the collections of FSC Agroecology RAS. Six species of Juglans: J. regia, J. mandshurica, J. cinerea, J. rupestris, J. ailanthifolia, J. nigra and three species of the genus Corylus: С. avellana L., С. аmericana W., varieties of C. pontica C. Koch the President, Futkurami, Circassian2. Data on positive experience of cultivation of Corylus avellana L. in plantation plantings (1,6 hectares, landing ordinary, the scheme of placement of 55 m) in the conditions of southern chernozems are given. The purpose of the research is to study the ecological plasticity of nutbearing shrubs of the collections of the Federal scientific center for Agroecology Russian Academy of Sciences. For example, a generic complex Corylus submissions received on the environmental plasticity of nut bushes in the conditions of brown (the cadaster nubmer 34:36:0000:14:0178), light chestnut soils (34:34:000000:122 34:34:060061:10). The levels of variability of morphological features of the assimilation apparatus and fruits of Corylus avellana L., С. pontica C. Koch varieties were established., which are consistent with winter and drought resistance. Cluster analysis revealed the correlation of features at 5 significance level. Corylus avellana and Circassian2 with a pronounced variability of morphological features, which indicates their broad ecological valence and adaptation capabilities in the conditions under consideration, are recommended for the purposes of protective afforestation and greening of dry areas.

Nondormant mutants in a temperate tree species, Corylus avellana L.

1985 ◽  
Vol 70 (6) ◽  
pp. 687-692 ◽  
Author(s):  
M. M. Thompson ◽  
D. C. Smith ◽  
J. E. Burgess
Keyword(s):  
Tree Species ◽  
Corylus Avellana ◽  
Corylus Avellana L
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