Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas

The Pacific oyster (Crassostrea gigas) is a extensively distributed marine bivalve of nice ecological and financial significance. In this examine, we offer a high-quality chromosome-level genome assembled utilizing Pacific Bioscience lengthy reads and Hi-C-based and linkage-map-based scaffolding applied sciences and a high-resolution variation map constructed utilizing large-scale resequencing evaluation. The 586.8-Mb genome consists of 10 pseudo-chromosome sequences starting from 38.6 to 78.9 Mb, containing 301 contigs with an N50 measurement of 3.1 Mb. A complete of 30,078 protein-coding genes have been predicted, of which 22,757 (75.7%) have been high-reliability annotations supported by a homologous match to a curated protein in the SWISS-PROT database or transcript expression.

Although a medium stage of repeat elements (57.2%) was detected, the genomic content material of the segmental duplications reached 26.2%, which is the highest amongst the reported genomes. By entire genome resequencing evaluation of 495 Pacific oysters, a complete variation map was constructed, comprised of 4.78 million single nucleotide polymorphisms, 0.60 million brief insertions and deletions, and 49,333 copy quantity variation areas.

The structural variations can result in a mean inter-individual genomic divergence of 0.21, indicating their essential position in shaping the Pacific oyster genome range. The great amount of mosaic distributed repeat components, small variations, and copy quantity variations point out that the Pacific oyster is a diploid organism with a particularly excessive genomic complexity at the intra- and inter-individual stage. The genome and variation maps can enhance our understanding of oyster genome range and enrich the sources for oyster molecular evolution, comparative genomics, and genetic analysis.

sRNAanno-a database repository of uniformly annotated small RNAs in crops

Small RNAs (sRNAs) are important regulatory molecules, and there are three main sRNA lessons in crops: microRNAs (miRNAs), phased small interfering RNAs (phased siRNAs or phasiRNAs), and heterochromatic siRNAs (hc-siRNAs). Excluding miRNAs, the different two lessons usually are not effectively annotated or accessible in public databases for most sequenced plant genomes. We carried out a complete sRNA annotation of 143 plant species which have absolutely sequenced genomes and next-generation sequencing sRNA information publicly accessible.

The outcomes can be found through a web based repository known as sRNAanno ( www.plantsRNAs.org ). Compared with different public plant sRNA databases, we obtained was rather more miRNA annotations, that are extra full and dependable as a result of of the constant and extremely stringent standards utilized in our miRNA annotations. sRNAanno additionally gives free entry to genomic info for >22,721 PHAS loci and >22 million hc-siRNA loci annotated from these 143 plant species. Both miRNA and PHAS loci might be simply browsed to view their predominant options, and a assortment of archetypal trans-acting siRNA 3 (TAS3) genes have been annotated individually for fast entry.

To facilitate the ease of sRNA annotation, sRNAanno gives free service for sRNA annotations to the neighborhood. In abstract, the sRNAanno database is a nice useful resource to facilitate genomic and genetic analysis on plant small RNAs.  Cultivated strawberry (Fragaria × ananassa) is a vital fruit crop species whose fruits are loved by many worldwide. An octoploid of hybrid origin, the advanced genome of this species was just lately sequenced, serving as a key reference genome for cultivated strawberry and associated species of the Rosaceae household.

The present annotation of the F. ananassa genome primarily depends on ab initio predictions and, to a lesser extent, transcriptome information. Here, we current the construction and useful reannotation of the F. ananassa genome primarily based on one PacBio full-length RNA library and ninety-two Illumina RNA-Seq libraries. This improved annotation of the F. ananassa genome, v1.0.a2, includes a complete of 108,447 gene fashions, with 97.85% full BUSCOs. The fashions of 19,174 genes have been modified, 360 new genes have been recognized, and 11,044 genes have been discovered to have alternatively spliced isoforms.

 Construction of a chromosome-level genome and variation map for the Pacific oyster Crassostrea gigas

Algorithmic Annotation of Functional Roles for Components of 3,044 Human Molecular Pathways

Current strategies of high-throughput molecular and genomic analyses enabled to reconstruct hundreds of human molecular pathways. Knowledge of molecular pathways construction and structure taken together with the gene expression information may also help interrogating the pathway activation ranges (PALs) utilizing completely different bioinformatic algorithms. In flip, the pathway activation profiles can characterize molecular processes, that are differentially regulated and give numeric traits of the extent of their activation or inhibition. However, completely different pathway nodes might have completely different features towards total pathway regulation, and calculation of PAL requires data of molecular operate of each node in the pathway in phrases of its activator or inhibitory position.

Genomic DNA Kit

20-abx098076
  • EUR 439.00
  • EUR 244.00
  • 200 rxns
  • 50 rxns

Human Genomic DNA

BIO-35025 500µl @ 200ng/µl Ask for price

Human Genomic DNA

X11000 0.2 ml Ask for price
Description: reagents widely cited

Genomic DNA from Human Adult Normal Tissue: Uterus, from a single donor

D1234274 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Human Tumor Tissue: Uterus Tumor, from a single donor

D1235274 50 ug
EUR 446
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Human Adult Normal Tissue: Uterus: Cervix, from a single donor

D1234275 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA Isolation Kit

55R-1362 50 assays
EUR 385
Description: Genomic DNA Isolation Kit for use in the research laboratory

Genomic DNA - Rat Male

D1434999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Rat Female

D1434999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Dog Male

D1734999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Dog Female

D1734999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Rabbit Male

D1834999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Rabbit Female

D1834999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Porcine Male

D1934999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Porcine Female

D1934999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Bovine Male

D1B34999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Bovine Female

D1B34999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Chicken Male

D1C34999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Chicken Female

D1C34999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Hamster Male

D1H34999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Hamster Female

D1H34999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Horse Male

D1O34999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Horse Female

D1O34999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Human Male

D1234999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Human Female

D1234999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA Extraction Kit

K5016005 1 kit
EUR 329

Genomic DNA Isolation Kit

K281-50
EUR 272

Soil Genomic DNA Kit

K1411-250
EUR 561

Soil Genomic DNA Kit

K1411-50
EUR 316

Insect Genomic DNA Kit

K1412-250
EUR 561

Insect Genomic DNA Kit

K1412-50
EUR 316

Mollusc Genomic DNA Kit

K1413-250
EUR 561

Mollusc Genomic DNA Kit

K1413-50
EUR 316

Yeast Genomic DNA Kit

K1414-250
EUR 561

Yeast Genomic DNA Kit

K1414-50
EUR 316

Fungal Genomic DNA Kit

K1415-250
EUR 561

Fungal Genomic DNA Kit

K1415-50
EUR 316

Plant Genomic DNA Kit

20-abx098077
  • EUR 411.00
  • EUR 230.00
  • 200 rxns
  • 50 rxns

Bacteria Genomic DNA Kit

20-abx098080
  • EUR 105.00
  • EUR 244.00
  • 2 rxns
  • 50 rxns

Micro Genomic DNA Kit

20-abx098242
  • EUR 105.00
  • EUR 328.00
  • 2 rxns
  • 50 rxns

Blood Genomic DNA Kit

abx098868-50rxns 50 rxns
EUR 272

Plant Genomic DNA Kit

abx294004-50preps 50 preps
EUR 398

Animal Genomic DNA Kit

abx294005-100preps 100 preps
EUR 523

Animal Genomic DNA Kit

abx294005-50preps 50 preps
EUR 398

Human Brain Genomic DNA

X11001 10 µg Ask for price
Description: kits suitable for this type of research

Genomic DNA Isolation Kit

K2118-50 50 assays
EUR 321

AccuRT Genomic DNA Removal Kit

G488 200 Reactions
EUR 82

Genomic DNA - Cynomolgus Monkey Male

D1534999-Cy-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Cynomolgus Monkey Female

D1534999-Cy-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Rhesus Monkey Male

D1534999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Rhesus Monkey Female

D1534999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Guinea Pig Male

D1G34999-G01 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA - Guinea Pig Female

D1G34999-G02 100 ug
EUR 188
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Bacterial Genomic DNA Isolation Kit

K309-100
EUR 376

Plant Genomic DNA extraction buffer

20-abx098075
  • EUR 286.00
  • EUR 105.00
  • 100 ml
  • 1.2 ml

Marine Animal Genomic DNA Kit

20-abx098079
  • EUR 105.00
  • EUR 244.00
  • 2 rxns
  • 50 rxns

FFPE Tissue Genomic DNA Kit

abx098866-50rxns 50 rxns
EUR 272

Genomic DNA Extraction and Purification

EP10012 100 Tests
EUR 505

Genomic DNA Extraction KitAnimal Tissue

FYG102-100P 100 Preps Ask for price

Genomic DNA Extraction KitAnimal Tissue

FYG102-300P 300 Preps Ask for price

Genomic DNA Extraction KitAnimal Tissue

FYG102-50P 50 Preps Ask for price

Genomic DNA Extraction Maxi KitPlant

FYG104-10P 10 Preps Ask for price

Genomic DNA Extraction Maxi KitPlant

FYG104-25P 25 Preps Ask for price

Zenoquick Genomic DNA Purification Kit

Z2003-200 200 preps
EUR 631

Zenoprep Genomic DNA Purification Kit

Z2004-400 400 preps
EUR 550

ISOLATE II Genomic DNA Kit

BIO-52065 10 preps Ask for price

ISOLATE II Genomic DNA Kit

BIO-52066 50 preps Ask for price

ISOLATE II Genomic DNA Kit

BIO-52067 250 preps Ask for price

Genomic DNA from Mouse Normal Tissue: Brain

D1334035 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Mouse Normal Tissue: Heart

D1334122 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Mouse Normal Tissue: Kidney

D1334142 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Mouse Normal Tissue: Liver

D1334149 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Mouse Normal Tissue: Lung

D1334152 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Mouse Normal Tissue: Spleen

D1334246 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Mouse Normal Tissue: Stomach

D1334248 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Mouse Tail Genomic DNA Extraction Kit(250)

M9100-250 250 prep
EUR 536

100 BP DNA LADDER, 500UL PER KIT

M-DNA-100BP 1/pk
EUR 73
Description: Bioscience Mol Bio; DNA Ladder

1 KB DNA LADDER, 500UL PER KIT

M-DNA-1KB 1/pk
EUR 70
Description: Bioscience Mol Bio; DNA Ladder

Genomic DNA from Mouse Normal Tissue: Skeletal Muscle

D1334171 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Mouse Normal Tissue: Small Intestine

D1334226 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Mammalian Cell Genomic DNA Isolation Kit

K967-100
EUR 381

Plant Tissue Genomic DNA Isolation Kit

K316-100
EUR 376

Rapid Fungal Genomic DNA Isolation Kit

FT71415 50Preps
EUR 76.64

Rapid Animal Genomic DNA Extraction Kit

AT4780 10Preps
EUR 69.03

Rapid Animal Genomic DNA Extraction Kit

AT4781 50Preps
EUR 126.13

Rapid Animal Genomic DNA Extraction Kit

AT4782 250preps
EUR 354.5

Rapid Bacteria Genomic DNA Isolation Kit

BS8225 50Preps
EUR 76.64

Rapid Yeast Genomic DNA Extraction Kit

BS8227 50Preps
EUR 76.64

Rapid Blood Genomic DNA Extraction Kit

BT4782 50Preps
EUR 76.64

Genomic DNA Kit (No RNase A)

20-abx098862
  • EUR 398.00
  • EUR 230.00
  • 200 rxns
  • 50 rxns

Genomic DNA Extraction Mini KitPlant Tissue

FYG103-100P 100 Preps Ask for price

Easy3-Plant Genomic DNA Isolation Kit

FYG503-100P 100 Preps Ask for price

Easy3-Plant Genomic DNA Isolation Kit

FYG503-500P 500 Preps Ask for price

Fully CpG Methylated Human Genomic DNA

X10000 10 µg/100 µl Ask for price
Description: The best epigenetics products

LumiPure genomic DNA from AnySample Kit, 50

21573 50 preps
EUR 108

Genomic DNA from Rat Normal Tissue: Brain

D1434035 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Rat Normal Tissue: Heart

D1434122 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Rat Normal Tissue: Kidney

D1434142 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Rat Normal Tissue: Liver

D1434149 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Rat Normal Tissue: Lung

D1434152 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Rat Normal Tissue: Stomach

D1434248 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Rat Normal Tissue: Testis

D1434260 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Rat Normal Tissue: Thymus

D1434264 100 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Plant Normal Tissue: Arabidopsis

D1634310 10 ug
EUR 493
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Plant Normal Tissue: Arabidopsis

D1634310-5 5 ug
EUR 282
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Plant Normal Tissue: Corn

D1634330 10 ug
EUR 222
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Plant Normal Tissue: Orange

D1634340 10 ug
EUR 222
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Plant Normal Tissue: Potato

D1634350 10 ug
EUR 222
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Plant Normal Tissue: Rice

D1634360 10 ug
EUR 222
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

Genomic DNA from Plant Normal Tissue: Wheat

D1634390 10 ug
EUR 222
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

FFPE Genomic DNA - Human Tumor Tissue: Breast

D2235086 2 ug
EUR 821
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

FFPE Genomic DNA - Human Tumor Tissue: Colon

D2235090 2 ug
EUR 821
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

FFPE Genomic DNA - Human Tumor Tissue: Lung

D2235152 2 ug
EUR 821
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

FFPE Genomic DNA - Human Tumor Tissue: Pancreas

D2235188 2 ug
EUR 821
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

FFPE Genomic DNA - Human Tumor Tissue: Stomach

D2235248 2 ug
EUR 821
Description: Can be used for various studies in the realm of gene expression, both normal and pathological. It is an excellent control and suitable for educational purposes.

96 Well Breast Tumor Genomic DNA Plate

D8235086-1 1 plate
EUR 316

96 Well Colon Tumor Genomic DNA Plate

D8235090-1 1 plate
EUR 316

96 Well Lung Tumor Genomic DNA Plate

D8235152-1 1 plate
EUR 316

96 Well Stomach Tumor Genomic DNA Plate

D8235248-1 1 plate
EUR 316

Blood genomic DNA extraction and purification kit

K1443-100
EUR 479

Blood Genomic DNA Extraction Mini Kit (100prep)

FABGK-100 100 preps
EUR 165

Blood Genomic DNA Extraction Mini Kit (300prep)

FABGK-300 300 preps
EUR 266

FavorPrep Genomic DNA Clean-Up Kit (50prep)

FAGDC-001 50 preps
EUR 129

FavorPrep Genomic DNA Clean-Up Kit (200prep)

FAGDC-001-1 200 preps
EUR 204

Plant Genomic DNA Extraction Mini Kit (50prep)

FAPGK-001 50 preps
EUR 158

Thus, high-throughput annotation of useful roles of pathway nodes is required for the complete evaluation of the pathway activation profiles. We proposed an algorithm that identifies useful roles of the pathway elements and utilized it to annotate 3,044 human molecular pathways extracted from the Biocarta, Reactome, KEGG, Qiagen Pathway Central, NCI, and HumanCYC databases and together with 9,022 gene merchandise. The ensuing knowledgebase might be utilized for the direct calculation of the PALs and establishing massive scale profiles of the signaling, metabolic, and DNA restore pathway regulation utilizing excessive throughput gene expression information. We additionally present a bioinformatic instrument for PAL information calculations utilizing the present pathway knowledgebase.