Tree Genetics & Genomes

, 11:82

Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency in Populus tremula × alba 717-1B4

  • Liang-Jiao Xue
  • Magdy S. Alabady
  • Mohammad Mohebbi
  • Chung-Jui Tsai
Short Communication

DOI: 10.1007/s11295-015-0907-5

Cite this article as:
Xue, LJ., Alabady, M.S., Mohebbi, M. et al. Tree Genetics & Genomes (2015) 11: 82. doi:10.1007/s11295-015-0907-5
Part of the following topical collections:
  1. Genome Biology

Abstract

Populus species are widely distributed across the Northern Hemisphere. The genetic diversity makes the genus an ideal study system for traits of ecological or agronomic significance. However, sequence variation between the genome-sequenced Populus trichocarpa Nisqually-1 and many other Populus species and hybrids poses significant challenges for research that employs sequence-sensitive approaches, such as next-generation sequencing and site-specific genome editing. Using the routinely transformed genotype Populus tremula × alba 717-1B4 as a test case, we utilized established variant-calling pipelines with affordable re-sequencing (~20×) and publicly available transcriptome data to generate a variant-substituted custom genome (sPta717). The sPta717 genome harbors over 10 million SNPs or small indels relative to the P. trichocarpa v3 reference genome. When applied to RNA-Seq analysis, the fraction of uniquely mapped reads increased by 13–28 % relative to that obtained with the P. trichocarpa reference genome, depending on read length and sequence type. The enhanced mapping rates enabled detection of several hundred more expressed genes and improved the differential expression analysis. Similar improvements were observed for DNA-Seq and ChIP-Seq data mapping. The sPta717 genome is also instrumental in guide RNA (gRNA) design for CRISPR-mediated genome editing. We showed that a majority of gRNAs designed from the P. trichocarpa reference genome contain mismatches with the corresponding target sequences of sPta717, likely rendering those gRNAs ineffective in transgenic 717. A website is provided for querying the sPta717 genome by gene model or homology search. The same approach should be applicable to other outcrossing species with a closely related reference genome.

Keywords

Re-sequencing SNP Substituted genome RNA-Seq CRISPR 

Supplementary material

11295_2015_907_MOESM1_ESM.docx (28 kb)
Supplemental 1Table S1. Tissue sources of total RNA used for cDNA-primed genome amplification. Table S2. List of NGS datasets used in this study. Table S3. Identification of 717 genomic variants. Table S4. Number of expressed genes detected using the two different genomes. Table S5. Mapping rates of DNA-Seq and ChIP-Seq reads. Table S6. Re-annotation of Affymetrix probe-sets using the sPta717 genome (DOCX 28.3 kb)
11295_2015_907_MOESM2_ESM.pdf (2.8 mb)
Supplemental 2Figure S1. Comparisons of bark and xylem RNA-Seq data analysis using the variant-substituted P. tremula x abla 717 (sPta717) genome or the P. trichocarpa (Ptr_v3) reference genome. (a-b) Transcript abundance in bark (a) and xylem (b). Genes with significantly different FPKM values are highlighted in red (higher in sPta717) or blue (higher in Ptr_v3). (c-d) Transcriptional response of bark (c) and xylem (d) to drought. Genes are color-coded if they were found to exhibit significant differences by either genome (black), by sPta717 only (red), by Ptr_v3 (blue) or neither (gray). Significant difference threshold was Q ≤0.05 and fold change ≥2. (PDF 2.75 mb)

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.School of Forestry and Natural ResourcesUniversity of GeorgiaAthensUSA
  2. 2.Department of GeneticsUniversity of GeorgiaAthensUSA
  3. 3.Institute of BioinformaticsUniversity of GeorgiaAthensUSA
  4. 4.Department of Plant BiologyUniversity of GeorgiaAthensUSA
  5. 5.Department of Computer ScienceUniversity of GeorgiaAthensUSA

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