Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 52
Author(s):  
Ashley G. Yow ◽  
Hamed Bostan ◽  
Raúl Castanera ◽  
Valentino Ruggieri ◽  
Molla F. Mengist ◽  
...  
Keyword(s):  
Gene Prediction ◽  
Haplotype Diversity ◽  
Fold Increase ◽  
Ananas Comosus ◽  
High Quality ◽  
Tropical Fruit ◽  
Related Sequence ◽  
New Genes ◽  
High Level ◽  
High Quality Genome

Pineapple (Ananas comosus (L.) Merr.) is the second most important tropical fruit crop globally, and ‘MD2’ is the most important cultivated variety. A high-quality genome is important for molecular-based breeding, but available pineapple genomes still have some quality limitations. Here, PacBio and Hi-C data were used to develop a new high-quality MD2 assembly and gene prediction. Compared to the previous MD2 assembly, major improvements included a 26.6-fold increase in contig N50 length, phased chromosomes, and >6000 new genes. The new MD2 assembly also included 161.6 Mb additional sequences and >3000 extra genes compared to the F153 genome. Over 48% of the predicted genes harbored potential deleterious mutations, indicating that the high level of heterozygosity in this species contributes to maintaining functional alleles. The genome was used to characterize the FAR1-RELATED SEQUENCE (FRS) genes that were expanded in pineapple and rice. Transposed and dispersed duplications contributed to expanding the numbers of these genes in the pineapple lineage. Several AcFRS genes were differentially expressed among tissue-types and stages of flower development, suggesting that their expansion contributed to evolving specialized functions in reproductive tissues. The new MD2 assembly will serve as a new reference for genetic and genomic studies in pineapple.

scholarly journals Chromosome-scale assembly of the yellow mealworm genome

2021 ◽  
Vol 1 ◽  
pp. 94
Author(s):  
Evangelia Eleftheriou ◽  
Jean-Marc Aury ◽  
Benoît Vacherie ◽  
Benjamin Istace ◽  
Caroline Belser ◽  
...  
Keyword(s):  
Gene Prediction ◽  
Scale Production ◽  
Rna Seq ◽  
High Quality ◽  
Yellow Mealworm ◽  
Promising Alternative ◽  
Alternative Protein ◽  
Oxford Nanopore ◽  
Mealworm Beetle ◽  
High Quality Genome

Background: The yellow mealworm beetle, Tenebrio molitor, is a promising alternative protein source for animal and human nutrition and its farming involves relatively low environmental costs. For these reasons, its industrial scale production started this century. However, to optimize and breed sustainable new T. molitor lines, the access to its genome remains essential. Methods: By combining Oxford Nanopore and Illumina Hi-C data, we constructed a high-quality chromosome-scale assembly of T. molitor. Then, we combined RNA-seq data and available coleoptera proteomes for gene prediction with GMOVE. Results: We produced a high-quality genome with a N50 = 21.9Mb with a completeness of 99.5% and predicted 21,435 genes with a median size of 1,780 bp. Gene orthology between T. molitor and Tribolium castaneaum showed a highly conserved synteny between the two coleoptera. Conclusions: The present genome will greatly help fundamental and applied research such as genetic breeding and will contribute to the sustainable production of the yellow mealworm.

scholarly journals Whole-genome assembly of Corylus avellana cv‘Tonda Gentile delle Langhe’ using linked-reads (10X Genomics)

2021 ◽  
Author(s):  
Vera Pavese ◽  
Emile Cavalet Giorsa ◽  
Lorenzo Barchi ◽  
Alberto Acquadro ◽  
Daniela Torello Marinoni ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Prediction ◽  
Corylus Avellana ◽  
Individual Plant ◽  
High Quality ◽  
Premium Price ◽  
High Quality Sequence ◽  
Sporophytic Incompatibility ◽  
Corylus Avellana L ◽  
High Level

Abstract The European hazelnut (Corylus avellana L.; 2n=2x=22) is a worldwide economically important tree nut that is cross-pollinated due to sporophytic incompatibility. Therefore, any individual plant is highly heterozygous. Cultivars are clonally propagated using mound layering, rooted suckers and micropropagation. In recent years, the interest in this crop has increased, due to a growing demand related to the recognized health benefits of nut consumption. C. avellana cv ‘Tonda Gentile delle Langhe’ (‘TGdL’) is well-known for its high kernel quality, and the premium price paid for this cultivar is an economic benefit for producers in northern Italy. Assembly of a high-quality genome is a difficult task in many plant species because of the high level of heterozygosity. We assembled a chromosome-level genome sequence of ′TGdL′ with a two-step approach. First, 10X Genomics Chromium Technology was used to create a high-quality sequence, which was then assembled into scaffolds with cv ′Tombul′ genome as the reference. Eleven pseudomolecules were obtained, corresponding to 11 chromosomes. A total of 11,046 scaffolds remained unplaced, representing 11% of the genome (46,504,161 bp). Gene prediction, performed with Maker-P software, identified 27,791 genes (AED ≤ 0.4 and 92% of BUSCO completeness), whose function was analysed with BlastP and InterProScan software. To characterise ‘TGdL’ specific genetic mechanisms, Orthofinder was used to detect orthologs between hazelnut and closely related species. The ‘TGdL’ genome sequence is expected to be a powerful tool to understand hazelnut genetics and allow detection of markers/genes for important traits to be used in targeted breeding programs.

scholarly journals High quality genome assembly of the amitochondriate eukaryote Monocercomonoides exilis

2021 ◽  
Vol 7 (12) ◽  
Author(s):  
Sebastian Cristian Treitli ◽  
Priscila Peña-Diaz ◽  
Paweł Hałakuc ◽  
Anna Karnkowska ◽  
Vladimír Hampl
Keyword(s):  
Genome Assembly ◽  
Complete Genome ◽  
Untranslated Region ◽  
Gene Prediction ◽  
Draft Genome ◽  
High Quality ◽  
Kozak Sequence ◽  
Oxford Nanopore ◽  
High Quality Genome ◽  
Polyadenylation Signals

Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.

High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan

2021 ◽  
Author(s):  
Hui Zhang ◽  
Yuexing Wang ◽  
Ce Deng ◽  
Sheng Zhao ◽  
Peng Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Quality ◽  
Rice Hybrid ◽  
High Quality Genome

scholarly journals 2D-3D integration of hexagonal boron nitride and a high-κ dielectric for ultrafast graphene-based electro-absorption modulators

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hitesh Agarwal ◽  
Bernat Terrés ◽  
Lorenzo Orsini ◽  
Alberto Montanaro ◽  
Vito Sorianello ◽  
...  
Keyword(s):  
Boron Nitride ◽  
Hafnium Oxide ◽  
High Speed ◽  
Hexagonal Boron Nitride ◽  
Temperature Stability ◽  
Cost Effective ◽  
Fold Increase ◽  
Building Blocks ◽  
High Quality ◽  
New Device

AbstractElectro-absorption (EA) waveguide-coupled modulators are essential building blocks for on-chip optical communications. Compared to state-of-the-art silicon (Si) devices, graphene-based EA modulators promise smaller footprints, larger temperature stability, cost-effective integration and high speeds. However, combining high speed and large modulation efficiencies in a single graphene-based device has remained elusive so far. In this work, we overcome this fundamental trade-off by demonstrating the 2D-3D dielectric integration in a high-quality encapsulated graphene device. We integrated hafnium oxide (HfO2) and two-dimensional hexagonal boron nitride (hBN) within the insulating section of a double-layer (DL) graphene EA modulator. This combination of materials allows for a high-quality modulator device with high performances: a ~39 GHz bandwidth (BW) with a three-fold increase in modulation efficiency compared to previously reported high-speed modulators. This 2D-3D dielectric integration paves the way to a plethora of electronic and opto-electronic devices with enhanced performance and stability, while expanding the freedom for new device designs.

scholarly journals An Experimental Study on the Sources of Strontium in Mineral Water and General Rules of Its Dissolution—A Case Study of Chengde, Hebei

Water ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 699
Author(s):  
Ruifeng Wang ◽  
Xiong Wu ◽  
Yanliang Zhai ◽  
Yuxuan Su ◽  
Chenhui Liu
Keyword(s):  
Experimental Study ◽  
Mineral Water ◽  
Surrounding Rock ◽  
Mechanism Of Formation ◽  
High Quality ◽  
General Rules ◽  
Leaching Experiment ◽  
High Level ◽  
Impact Experiments

Chengde City boasts a wealth of high-quality mineral water resources characterized by a high level of strontium (Sr), a low level of sodium, and low alkalinity. In order to study the mechanism of formation of Sr-bearing mineral water in Chengde and to scientifically guide future mineral water exploration, taking three typical mineral water exploration areas in Chengde as examples, this paper studies the sources of Sr in mineral water and the general rules of its dissolution via a laboratory static leaching experiment and impact experiments, and it provides an analysis of the characteristics of typical rock samples. The research results indicate that the content of Sr in surrounding rock and the characteristics of minerals existing in surrounding rock jointly control the dissolution of Sr in water; that CO2 can promote the formation of mineral water containing Sr; and that temperature increases may boost the dissolution of Sr from carbonate minerals but also inhibit the dissolution of Sr from silicate minerals.

scholarly journals High-Quality Genome Resource of the Pathogen of Diaporthe (Phomopsis) phragmitis Causing Kiwifruit Soft Rot

2020 ◽  
Author(s):  
Pu Liu ◽  
Wang Xiaojie ◽  
Dong Hongjie ◽  
Jianbin Lan ◽  
Kuan Liang ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Management Strategies ◽  
Soft Rot ◽  
Fruit Rot ◽  
Economic Plant ◽  
High Quality ◽  
Total Size ◽  
Genome Wide ◽  
Solid Foundation ◽  
High Quality Genome

Diaporthe spp. are critical plant pathogens that cause wood cankers, wilt, dieback, and fruit rot in a wide variety of economic plant hosts and are regarded as one of the most acute threats faced by kiwifruit industry worldwide. Diaporthe phragmitis strain NJD1 is a highly pathogenic isolate of soft rot of kiwifruit. Here, we present a high-quality genome-wide sequence of D. phragmitis NJD1 that was assembled into 28 contigs containing a total size of 58.33 Mb and N50 length of 3.55 Mb. These results lay a solid foundation for understanding host–pathogen interaction and improving disease management strategies.

scholarly journals Role of embB in natural and acquired resistance to ethambutol in mycobacteria.

1997 ◽  
Vol 41 (10) ◽  
pp. 2270-2273 ◽  
Author(s):  
F Alcaide ◽  
G E Pfyffer ◽  
A Telenti
Keyword(s):  
Nontuberculous Mycobacteria ◽  
Practical Implication ◽  
Acquired Resistance ◽  
Fold Increase ◽  
Drug Susceptibility ◽  
Natural Resistance ◽  
Intrinsic Resistance ◽  
Resistant Strains ◽  
High Level

The mycobacterial embCAB operon encodes arabinosyl transferases, putative targets of the antimycobacterial agent ethambutol (EMB). Mutations in embB lead to resistance to EMB in Mycobacterium tuberculosis. The basis for natural, intrinsic resistance to EMB in nontuberculous mycobacteria (NTM) is not known; neither is the practical implication of resistance to EMB in the absence of embB mutations in M. tuberculosis well understood. The conserved embB resistance-determining region (ERDR) of a collection of 13 strains of NTM and 12 EMB-resistant strains of M. tuberculosis was investigated. Genotypes were correlated with drug susceptibility phenotypes. High-level natural resistance to EMB (MIC, . or =64 microg/ml) was associated with a variant amino acid motif in the ERDR of M. abscessus, M. chelonae, and M. leprae. Transfer of the M. abscessus emb allele to M. smegmatis resulted in a 500-fold increase in the MICs. In M. tuberculosis, embB mutations were associated with MICs of > or =20 microg/ml while resistance not associated with an ERDR mutation generally resulted in MICs of < or =10 microg/ml. These data further support the notion that the emb region determines intrinsic and acquired resistance to EMB and might help in the reassessment of the current recommendations for the screening and treatment of infections with EMB-resistant M. tuberculosis and NTM.

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