scholarly journals Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

2020 ◽  
Vol 10 (9) ◽  
pp. 2965-2974 ◽  
Author(s):  
Wade R Roberts ◽  
Kala M Downey ◽  
Elizabeth C Ruck ◽  
Jesse C Traller ◽  
Andrew J Alverson
Keyword(s):  
Reference Genome ◽  
Lipid Production ◽  
Fold Increase ◽  
High Quality ◽  
Short Read Sequencing ◽  
Large Size ◽  
Reference Genome Assembly ◽  
Cell Wall Morphogenesis ◽  
Cyclotella Cryptica

Abstract The diatom, Cyclotella cryptica, is a well-established model species for physiological studies and biotechnology applications of diatoms. To further facilitate its use as a model diatom, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms.

scholarly journals Improved Reference Genome for Cyclotella Cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)

2020 ◽  
Author(s):  
Wade R. Roberts ◽  
Kala M. Downey ◽  
Elizabeth C. Ruck ◽  
Jesse C. Traller ◽  
Andrew J. Alverson
Keyword(s):  
Reference Genome ◽  
Lipid Production ◽  
Fold Increase ◽  
High Quality ◽  
Short Read Sequencing ◽  
Large Size ◽  
Reference Genome Assembly ◽  
Cell Wall Morphogenesis ◽  
Cyclotella Cryptica

ABSTRACTThe diatom, Cyclotella cryptica, is a well-established experimental model for physiological studies and, more recently, biotechnology applications of diatoms. To further facilitate its use as a model diatom species, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms.Data available fromNCBI BioProjects PRJNA628076 and PRJNA589195

scholarly journals A Chromosome-Scale Genome Assembly Resource for Myriosclerotinia sulcatula Infecting Sedge Grass (Carex sp.)

2020 ◽  
Vol 33 (7) ◽  
pp. 880-883
Author(s):  
Stefan Kusch ◽  
Heba M. M. Ibrahim ◽  
Catherine Zanchetta ◽  
Celine Lopez-Roques ◽  
Cecile Donnadieu ◽  
...  
Keyword(s):  
Host Range ◽  
Sclerotinia Sclerotiorum ◽  
Genome Assembly ◽  
Plant Pathogens ◽  
Reference Genome ◽  
Close Relative ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Reference Genome Assembly

The fungus Myriosclerotinia sulcatula is a close relative of the notorious polyphagous plant pathogens Botrytis cinerea and Sclerotinia sclerotiorum but exhibits a host range restricted to plants from the Carex genus (Cyperaceae family). To date, there are no genomic resources available for fungi in the Myriosclerotinia genus. Here, we present a chromosome-scale reference genome assembly for M. sulcatula. The assembly contains 24 contigs with a total length of 43.53 Mbp, with scaffold N50 of 2,649.7 kbp and N90 of 1,133.1 kbp. BRAKER-predicted gene models were manually curated using WebApollo, resulting in 11,275 protein-coding genes that we functionally annotated. We provide a high-quality reference genome assembly and annotation for M. sulcatula as a resource for studying evolution and pathogenicity in fungi from the Sclerotiniaceae family.

scholarly journals Construction of a chromosome-scale long-read reference genome assembly for potato

GigaScience ◽  
2020 ◽  
Vol 9 (9) ◽  
Author(s):  
Gina M Pham ◽  
John P Hamilton ◽  
Joshua C Wood ◽  
Joseph T Burke ◽  
Hainan Zhao ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Reference Genome ◽  
Agronomic Traits ◽  
Solanum Tuberosum L ◽  
Fold Increase ◽  
High Quality ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

Abstract Background Worldwide, the cultivated potato, Solanum tuberosum L., is the No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1–3 516 R44, a doubled monoploid clone of S. tuberosum Group Phureja, was published in 2011 using a whole-genome shotgun sequencing approach with short-read sequence data. Current advanced sequencing technologies now permit generation of near-complete, high-quality chromosome-scale genome assemblies at minimal cost. Findings Here, we present an updated version of the DM1–3 516 R44 genome sequence (v6.1) using Oxford Nanopore Technologies long reads coupled with proximity-by-ligation scaffolding (Hi-C), yielding a chromosome-scale assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8%) of the estimated 844 Mb genome, of which 741.5 Mb is non-gapped with 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore Technologies full-length complementary DNA sequencing enabled annotation of 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had a significantly improved representation of conserved orthologs compared with the previous annotation. The new assembly has improved contiguity with a 595-fold increase in N50 contig size, 99% reduction in the number of contigs, a 44-fold increase in N50 scaffold size, and an LTR Assembly Index score of 13.56, placing it in the category of reference genome quality. The improved assembly also permitted annotation of the centromeres via alignment to sequencing reads derived from CENH3 nucleosomes. Conclusions Access to advanced sequencing technologies and improved software permitted generation of a high-quality, long-read, chromosome-scale assembly and improved annotation dataset for the reference genotype of potato that will facilitate research aimed at improving agronomic traits and understanding genome evolution.

scholarly journals Classification of grain amaranths using chromosome-level genome assembly of ramdana, A. hypochondriacus

2020 ◽  
Author(s):  
Saptarathi Deb ◽  
Suvratha J ◽  
Samathmika Ravi ◽  
Raksha Rao K ◽  
Saurabh Whadgar ◽  
...  
Keyword(s):  
Reference Genome ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Draft Genome ◽  
Local Environment ◽  
High Quality ◽  
Low Coverage ◽  
High Quality Genome ◽  
Chromosome Level

ABSTRACTIn the age of genomics-based crop improvement, a high-quality genome of a local landrace adapted to the local environmental conditions is critically important. Grain amaranths produce highly nutritional grains with a multitude of desirable properties including C4 photosynthesis highly sought-after in other crops. For improving the agronomic traits of grain amaranth and for the transfer of desirable traits to dicot crops, a reference genome of a local landrace is necessary. Towards this end, our lab had initiated sequencing the genome of Amaranthus (A.) hypochondriacus (A.hyp_K_white) and had reported a draft genome in 2014. We selected this landrace because it is well adapted for cultivation in India during the last century and is currently a candidate for TILLING-based crop improvement. More recently, a high-quality chromosome-level assembly of A. hypochondriacus (PI558499, Plainsman) was reported. Here, we report a chromosome-level assembly of A.hyp_K_white (AhKP) using low-coverage PacBio reads, contigs from the reported draft genome of A.hyp_K_white, raw HiC data and reference genome of Plainsman. The placement of A.hyp_K_white on the phylogenetic tree of grain amaranths of known accessions clearly suggests that A.hyp_K_white is genetically distal from Plainsman and is most closely related to the accession PI619259 from Nepal (Ramdana). Furthermore, the classification of another accession, Suvarna, adapted to the local environment and selected for yield and other desirable traits, is clearly A. cruentus. A classification based on hundreds of thousands of SNPs validated taxonomy-based classification for a majority of the accessions providing the opportunity for reclassification of a few.

scholarly journals Genomic hitchhiking with moisture adaptation patterns stem prickleless in rose

2020 ◽  
Author(s):  
Mi-Cai Zhong ◽  
Xiao-Dong Jiang ◽  
Guo-Qian Yang ◽  
Wei-Hua Cui ◽  
Zhi-Quan Suo ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Regulatory Network ◽  
Molecular Basis ◽  
Reference Genome ◽  
Related Gene ◽  
High Quality ◽  
Expression Variation ◽  
Reference Genome Assembly ◽  
Gene Regulatory ◽  
Molecular Bases

Abstract“Rose with prickles” is a symbol of adversity and sacrifice but the molecular bases patterning prickle remains poorly explored. Here we generated a high-quality reference genome assembly for prickleless Rosa wichuraiana ‘Basye’s Thornless’ (BT), and identified genetic elements relating to stem prickle patterning. BT genome harbors a significant high proportion of Copia-type LTR (62.74% of LTRs) and diverges remarkably from that of R. chinensis Old Blush’, a founder genotype for rose domestication. Three negatively selected and fixed QTL were identified underlying BT prickleless. Differentially expressed genes in QTL were enriched for water-use-related genes, suggesting that prickleless might hitchhike the adaptation to moisture environments. While the prickle-related gene-regulatory-network (GRN) was highly conserved, expression variation of key candidate genes associated well with prickle-patterning divergence in roses. Our efforts provide fundamental resources and insights for Rosaceae genome evolution and molecular basis of key traits, thus should benefit rose improvement.

scholarly journals Flux Method Growth of Large Size Group IV–V 2D GeP Single Crystals and Photoresponse Application

Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 235
Author(s):  
Shuqi Zhao ◽  
Tongtong Yu ◽  
Ziming Wang ◽  
Shilei Wang ◽  
Limei Wei ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Single Crystals ◽  
High Performance ◽  
Group Iv ◽  
X Ray Diffraction ◽  
High Quality ◽  
Practical Applications ◽  
Large Size ◽  
Growth Method ◽  
Polarized Raman

Two-dimensional (2D) materials driven by their unique electronic and optoelectronic properties have opened up possibilities for their various applications. The large and high-quality single crystals are essential to fabricate high-performance 2D devices for practical applications. Herein, IV-V 2D GeP single crystals with high-quality and large size of 20 × 15 × 5 mm3 were successfully grown by the Bi flux growth method. The crystalline quality of GeP was confirmed by high-resolution X-ray diffraction (HRXRD), Laue diffraction, electron probe microanalysis (EPMA) and Raman spectroscopy. Additionally, intrinsic anisotropic optical properties were investigated by angle-resolved polarized Raman spectroscopy (ARPRS) and transmission spectra in detail. Furthermore, we fabricated high-performance photodetectors based on GeP, presenting a relatively large photocurrent over 3 mA. More generally, our results will significantly contribute the GeP crystal to the wide optoelectronic applications.

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 Approach to the Classification of Apparent Asphyxial Infant Deaths

2017 ◽  
Vol 7 (2) ◽  
pp. 200-211 ◽  
Author(s):  
Evan W. Matshes ◽  
Emma O. Lew
Keyword(s):  
Risk Factors ◽  
Sudden Infant Death Syndrome ◽  
Infant Death ◽  
Sudden Infant Death ◽  
Sudden Infant ◽  
Death Certification ◽  
High Quality ◽  
Infant Deaths ◽  
Unexpected Infant Death

Recent evidence indicates that with thorough, high quality death investigations and autopsies, forensic pathologists have recognized that many unexpected infant deaths are, in fact, asphyxial in nature. With this recognition has come a commensurate decrease in, and in some cases, abolition of, the label “sudden infant death syndrome” (SIDS). Current controversies often pertain to how and why some infant deaths are determined to be asphyxial in nature and whether or not apparent asphyxial circumstances are risk factors for SIDS, or rather, harbingers of asphyxial deaths. In an effort to sidestep these controversies, some forensic pathologists elected to instead use the noncommittal label “sudden unexpected infant death” (SUID), leading to the unfortunate consequence of SUID – like SIDS – gaining notoriety as an actual disease that could be diagnosed, studied, and ultimately cured. Although it is not possible to provide death certification guidance for every conceivable type of unexpected infant death, we recognize and propose a simple classification system for overarching themes that cover the vast majority of cases where infants die suddenly and unexpectedly.

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