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

Feng, Xiaojia, Yuan, Xiaoying, Sun, Yiwei, Hu, Yiheng, Zulfiqar, Saman, Ouyang, Xianheng, Dang, Meng, Zhou, Huijuan, Woeste, Keith, Zhao, Peng
Tree genetics & genomes 2018 v.14 no.4 pp. 51
Juglans sigillata, alleles, breeding, chloroplast genome, chloroplasts, evolution, gene expression, gene ontology, genetic markers, genetic variation, genomics, loci, microsatellite repeats, population genetics, sequence analysis, transcriptome, transcriptomics, trees, unigenes, walnuts, China
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.