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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 3800 re-sequencing projects, and our data has been published in many 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: With the largest sequencing capacity in the world including 30 HiSeqX and 25 NovaSeq systems, 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
  • Purity: No degradation, no DNA 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 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


Population genomics reveals low genetic diversity and adaptation to hypoxia in snub-nosed monkeys
Molecular Biology and Evolution 33 (10): 2670-2681 (2016)

In this study, researchers utilized Novogene’s Illumina HiSeq platform to sequence the whole genomes of 38 snub-nosed monkeys from four species, with subsequent population genomic analyses. Several hypoxia-related genes that were under selection were identified in the black snub-nosed monkey. This study involving the resequencing and reconstruction of multiple snub-nosed monkey genomes provides the first genomic information on the phylogenetic relationships, genetic diversity, and climate adaptation of these monkeys and on the shaping of the demography and evolution of this genus.

Animal Plant Reseq Fig 1

Figure. Geographic distribution, phylogenetics, and population structure of snub-nosed monkeys

Examples of Publications Using Novogene’s Services

JournalTitle
Nature Genetics, 45:51-58 (2012)The draft genome of watermelon (Citrullus lanatus) and re-sequencing of 20 diverse accessions.
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, 46:1303-1310 (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, 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, 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.
  Whole Genome Sequencing on HiSeq X (Human/ Animal/ Plant)
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