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Tree Genetics & Genomes

, 14:51 | Cite as

Resources for studies of iron walnut (Juglans sigillata) gene expression, genetic diversity, and evolution

  • Xiaojia Feng
  • Xiaoying Yuan
  • Yiwei Sun
  • Yiheng Hu
  • Saman Zulfiqar
  • Xianheng Ouyang
  • Meng Dang
  • Huijuan Zhou
  • Keith Woeste
  • Peng Zhao
Original Article
  • 111 Downloads
Part of the following topical collections:
  1. Gene Expression

Abstract

Iron walnut (Juglans sigillata Dode) is a temperate deciduous tree indigenous to China. It is distributed mainly in southwestern China, where it is valued for its wood and nuts. Transcriptomic and genomic data for the species are limited. Our goal was to assemble the whole chloroplast genome of J. sigillata, to use transcriptome information from RNA-Seq to understand the gene space in J. sigillata, and to develop polymorphic simple sequence repeats (SSRs, microsatellites) useful for understanding the species’ population genetics. The chloroplast genome consisted of a large single copy (LSC) of 89,872 bp, an inverted region (IR) of 52,072 bp, and a short single copy (SSC) of 18,406 bp. The chloroplast genome consisted of 137 annotated genes, with 71 unique coding regions and eight coding regions that were repeated in the inverted region. De novo assembly of the transcriptome yielded 83,112 unigenes with an average length of 686.9 bp. A search against the Gene Ontology (GO) database identified 19,718 unigenes. We evaluated transcriptome-derived microsatellite markers and chloroplast sequence polymorphisms in 48 J. sigillata individuals from three populations and 66 individuals from five other Chinese walnut (Juglans) species. We found 20 expressed sequence tag-SSRs and four loci in the chloroplast that were polymorphic in J. sigillata. The number of alleles per locus ranged from 3 to 10. The whole chloroplast genome and these 24 informative loci will be useful for studies of population genetics, diversity, and genetic structure, and they will undoubtedly benefit future breeding studies of this walnut species.

Keywords

Juglans sigillata Microsatellites Transcriptome Chloroplast Iron Walnut 

Notes

Acknowledgments

Mention of a trademark, proprietary product, or vendor does not constitute a guarantee or warranty of the product by the U.S. Department of Agriculture and does not imply its approval to the exclusion of other products or vendors that also may be suitable.

Funding information

This study was funded by the National Natural Science Foundation of China (41471038, 31200500), the Program for Excellent Young Academic Backbones funding by Northwest University (338050070), and the Northwest University Training Programs of Innovation and Entrepreneurship for Graduates (Nos. 2016002, 20171037, 2018298).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Figure S1. a) Geographic distribution of three natural populations of Juglans sigillata and cluster analysis based on 20 EST-SSR. The pie charts indicate the sample collection locations (ArcMap version 10. 0; ESRI, 2010). The colors reflect three different genetic clusters as determined using STRUCTURE (Pritchard et al. 2000) and show color-coded grouping at the most likely K =3 as determined using the deltaK method of Evanno et al. (2005). The white frame pie charts indicate the six different genetic clusters as determined using STRUCTURE (Pritchard et al. 2000) and show color-coded grouping at the most likely K =6 as determined using the deltaK method of Evanno et al. (2005). b) Principal coordinate analyses (PCA) of three populations resolved into three genotype groups based on 20 microsatellite loci. (PDF 35596 kb)
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Figure S2: Nucleotide sequence variation of 66 individuals of five Chinese walnut (Juglans) species at six polymorphic loci. psbM-trnD [16 single nucleotide polymorphism (SNP)], trnE-UUC (26 SNPs), ycf3-trnS(9 SNPs), trnF-ndhJ (40 SNPs), psbA-trnK (2 SNPs), and rpoC1 (36 SNPs). Haplotypes from H1 to H21 are shown to the left of individual names (Table S3). (PDF 4870 kb)
11295_2018_1263_MOESM14_ESM.pdf (150 kb)
Figure S3: Nucleotide sequence variation of J. sigillata based on four chloroplast loci. psbM-trnD [7 single nucleotide polymorphism (SNP)], trnE-UUC (one SNP), ycf3-trnS(one SNP), and rpoC1 (one SNP). (PDF 149 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Xiaojia Feng
    • 1
  • Xiaoying Yuan
    • 1
  • Yiwei Sun
    • 1
  • Yiheng Hu
    • 1
  • Saman Zulfiqar
    • 1
  • Xianheng Ouyang
    • 1
  • Meng Dang
    • 1
  • Huijuan Zhou
    • 1
  • Keith Woeste
    • 2
  • Peng Zhao
    • 1
  1. 1.Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life SciencesNorthwest UniversityXi’anChina
  2. 2.USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteUSA

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