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Animal & Plant Whole Genome Resequencing

Service Overview
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Animal and Plant Genome SequencingWith advancements in next-generation sequencing technology, whole genome resequencing (WGS) has become the most rapid and effective method to unravel, at the genomic level, the underlying mechanisms of species origin, development, growth, and evolution. Using WGS, the complete genome data from one or more variants can be aligned to known genomic sequence(s) for the species. Applications of WGS include detection of genetic differences between variants, transposon fingerprinting for assessing germplasm diversity and lineages, and mapping loci associated with specific traits, such as disease resistance.

Novogene is highly experienced in the applications of WGS for characterizing plant and animal variants. With cutting-edge Illumina HiSeq X™ Ten platform and our expert bioinformatics analysis, we provide researchers with high quality data in a highly cost-effective manner. Bioinformatics analysis includes but not limited to detecting SNPs, InDels, structure variations, and copy number variations with high accuracy and verification rates.

The Novogene Advantage

  • Extensive experience: We have completed over 600 animal and plant genome re-sequencing projects, and our data has been published in top-tier journals.
  • Unsurpassed data quality: We guarantee a Q30 score ≥ 80%, exceeding Illumina’s official guarantee of ≥ 75%. See our data example.
  • Cost-effective service: By employing state-of-the-art HiSeq X Ten platform that has enabled the $1000 human genome, we provide higher data output, faster turnaround time, and lowest prices possible for plant and animal genome sequencing projects of any size.
  • High verification rate: We promise that the verification rate of SNPs is higher than 95%.

Project Workflow

Animal & Plant Genome Resequencing Workflow

Sequencing Strategy

  • 350 bp insert DNA library
  • HiSeq X Ten platform, paired-end 150 bp

Data Quality Guarantee

  • Novogene guarantees its data output. The quality of our data, as measured by the percentage of bases with a sequencing quality score above Q30 (PE150, ≥ 80%), exceeds Illumina’s official guideline (PE150, ≥ 75%).

Sample Requirements

  • DNA amount: ≥ 1.4 μg (for two libraries preparation, quantified by Qubit 2.0)
  • Total volume: ≥ 20 μl
  • OD260/280 = 1.8 - 2.0 without degradation or RNA contamination

Turnaround Time

  • Within 15 working days from verification of sample quality (without data analysis)
  • Additional 10 working days for data analysis

Analysis Pipeline

Animal and Plant Genome Resequencing Analysis Pipeline

Table. Representative data quality results of plant whole genome sequencing on HiSeq X Ten from Novogene
SampleRaw Base (bp) Clean Base (bp)Effective Rate (%)Error Rate (%)Q 20 (%)Q 30 (%)GC Content (%)
158,254,060,00055,718,217,30095.650.0396.9192.8636.71
248,999,575,10048,813,596,70099.620.0395.5090.5636.77
362,424,593,40059,089,362,00094.660.0396.2291.6437.47
447,131,144,20046,938,246,30099.590.0395.2590.1337.50
547,767,277,70047,665,563,90099.790.0396.4791.8937.55
646,121,013,90046,029,951,30099.800.0396.6892.3437.91
743,359,441,60043,264,053,90099.780.0396.5692.0238.09
842,028,694,70041,925,456,60099.750.0396.2591.5138.34
947,653,513,80041,560,274,40099.800.0396.7992.5438.42
1042,083,946,90041,940,697,50099.660.0396.5992.1239.67

Project Example

The following study utilized Novogene's sequencing services.

The Genetic Basis of White Tigers
Current Biology, 23:1031–1035 (2013)

In this study on tiger variants, researchers examined the genetic basis for white fur, an autosomal recessive trait that is often selected in tiger breeding programs. Using WGS, restriction-site-associated DNA sequencing (RAD-seq), and a genome-wide association study (GWAS), the genomes of 16 captive tigers were analyzed. The white fur trait was mapped to a missense mutation in a transporter protein gene potentially associated with melanogenesis, furthering our understanding of the natural diversity in tiger populations and the factors that contribute to mammalian pigmentation.

Genetic Mapping of Tigers

Figure. Genetic Mapping of the White Tiger Mutation Based on RAD-Seq and Whole Genome Sequencing

Examples of Publications Using Novogene’s Services

JournalTitle
Nature Genetics, 45:51 (2012)The draft genome of watermelon (Citrullus lanatus) and re-sequencing of 20 diverse accessions.
Nature Genetics, 45:1431 (2013)Genomic analysis identifies distinct patterns of selection in domesticated pigs and Tibetan wild boars.
Current Biology, 23:1031–1035 (2013)The genetic basis of white tigers.
Nature Genetics, 46:1310 (2014)Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.
Molecular Biology and Evolution, 33:1337-1348 (2016)Genomic analyses reveal demographic history and temperate adaptation of the newly discovered honey bee subspecies apis mellifera sinisxinyuan n. ssp.
Molecular Biology and Evolution (2016)Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments.
Molecular Biology and Evolution (2016)Population genomics reveals low genetic diversity and adaptation to hypoxia in snub-nosed monkeys.
  Whole Genome Sequencing on HiSeq X (Human/ Animal/ Plant)
  Whole Exome Sequencing
  mRNA-Seq
  LncRNA Sequencing
  Small RNA Sequencing
  Whole Genome Bisulfite Sequencing
  ChIP-Seq
  Animal & Plant Re-Sequencing
  Genotyping by Sequencing
  de novo Sequencing
  Pan-genome Sequencing
  Metagenomic Sequencing
  Single-cell DNA Sequencing
  Single-cell RNA Sequencing
  16S/18S/ITS Amplicon
  Others- please specify
  Human
  Others