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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. Utilizing WGS, complete genomic data from one or more variants can be aligned to known genomic sequences 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 applications of WGS for characterizing plant and animal variants. With the cutting-edge Illumina platform and our expert bioinformatics analysis, we provide researchers with high quality data in a highly cost-effective manner. Bioinformatics analysis includes but is 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 3800 re-sequencing projects, and our data has been published in many noteworthy journals.
  • Unsurpassed data quality: We guarantee a Q30 score ≥ 80%, exceeding Illumina’s official guarantee of ≥ 75%. See our data example.
  • Cost-effective service: With the largest sequencing capacity in the world including the HiSeq X and NovaSeq systems, we provide greater data output, quicker turnaround time, and the 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
  • Illumina Novaseq6000 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

  • Input DNA:
    • Genomic DNA: ≥ 1.0 μg
    • Genomic DNA (PCR-free): ≥ 1.5 μg
    • Mitochondrion/Chloroplast DNA: ≥ 800 ng
  • DNA concentration: ≥ 20 ng/μl
  • Total volume: ≥ 20 μl
  • Purity: No degradation, no RNA contamination

Turnaround Time

  • Within 23 working days from verification of sample quality (without data analysis)
  • Additional 7 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
Sample Raw Base (bp) Clean Base (bp) Effective Rate (%) Error Rate (%) Q 20 (%) Q 30 (%) GC Content (%)
1 58,254,060,000 55,718,217,300 95.65 0.03 96.91 92.86 36.71
2 48,999,575,100 48,813,596,700 99.62 0.03 95.50 90.56 36.77
3 62,424,593,400 59,089,362,000 94.66 0.03 96.22 91.64 37.47
4 47,131,144,200 46,938,246,300 99.59 0.03 95.25 90.13 37.50
5 47,767,277,700 47,665,563,900 99.79 0.03 96.47 91.89 37.55
6 46,121,013,900 46,029,951,300 99.80 0.03 96.68 92.34 37.91
7 43,359,441,600 43,264,053,900 99.78 0.03 96.56 92.02 38.09
8 42,028,694,700 41,925,456,600 99.75 0.03 96.25 91.51 38.34
9 47,653,513,800 41,560,274,400 99.80 0.03 96.79 92.54 38.42
10 42,083,946,900 41,940,697,500 99.66 0.03 96.59 92.12 39.67

Project Example

The following studies utilized Novogene's sequencing services. Signatures of adaptation in the weedy rice genome Nature Genetics 49(5): 811-814 (2017) In this study, the whole genome sequencing approach was adopted to examine the genetic mechanisms underlying the evolution and adaptation of weedy rice. A total of 183 weedy accessions (including 18 SH weeds and 20 BHA weeds sequenced from this study and 145 previously published sequences) were analyzed to assess the evolutionary relationship among accessions. Genomic analysis indicated that all three weedy strains used in this study were derived after rice domestication and after within-crop differentiation. Further genome-wide selection scanning together with the selective sweep analysis identified candidate genes involved in adaptation of weedy rice genomes. This study indicated that de-domestication played a significant role in weedy rice evolution and the weedy strains might have evolved both early and late in rice cultivation. This study serves as a great example of using large-scale whole genome sequencing data to explore the underlying mechanisms in population biology and adaptive evolution.
Figure. Neighbor-joining tree of the 183 wild, cultivated, and weedy rice accessions Genetic variation in PTPN1 contributes to metabolic adaptation to high-altitude hypoxia in Tibetan migratory locusts Nature Communication 26;9(1):4991. (2018) In this study, researchers utilized Novogene’s Illumina HiSeq platform to sequence 24 migratory locusts representing two geographically distinct migratory locust populations in China. Genetic analysis revealed the positively selected genes in Tibetan locusts are predominantly involved in carbon and energy metabolism. We observed a notable signal of natural selection in the gene PTPN1, which encodes PTP1B, an inhibitor of insulin signaling pathway. This study reveal a specific mechanism for metabolic adaptation to high-altitude hypoxia by insects and improve the understanding of the complex biological features of high-altitude adaptation in animals.
Animal Plant Reseq Fig 1
Figure. Selective sweep and expression analysis of hypoxia adaptation  

Examples of Publications Using Novogene’s Services

Journal Title
Nature Communication 26;9(1):4991. (2018) Genetic variation in PTPN1 contributes to metabolic adaptation to high-altitude hypoxia in Tibetan migratory locusts
Nature Communication 20;9(1):5404. (2018) Genome re-sequencing reveals the evolutionary history of peach fruit edibility.
Nature Genetics, 50(6):803-813. (2018) Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield.
Molecular plant, 5;11(3):473. (2018) Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato
Nature Genetics, 49:811-814 (2017) Signatures of adaptation in the weedy rice genome.
Molecular Biology and Evolution, 34(9):2214-2228 (2017) Population genomics reveals speciation and introgression between Brown Norway rats and their sibling species.
Cell Research, 27(7):954-957 (2017) The genetics of tiger pelage color variations.
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, 33:2576-2592 (2016) Whole-genome sequencing of native sheep provides insights into rapid adaptations to extreme environments.
Molecular Biology and Evolution, 33:2670-2681 (2016) Population genomics reveals low genetic diversity and adaptation to hypoxia in snub-nosed monkeys.
Nature Genetics, 46:1303-1310 (2014) Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.
Nature Genetics, 45:1431-1438 (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, 45:51-58 (2012) The draft genome of watermelon (Citrullus lanatus) and re-sequencing of 20 diverse accessions.