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Open AccessArticle

De Novo Assembly and Characterization of Bud, Leaf and Flowers Transcriptome from Juglans Regia L. for the Identification and Characterization of New EST-SSRs

1
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shanxi 710069, China
2
USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, IN 47907, USA
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Om P. Rajora and Timothy A. Martin
Forests 2016, 7(10), 247; https://doi.org/10.3390/f7100247
Received: 24 August 2016 / Revised: 13 October 2016 / Accepted: 18 October 2016 / Published: 21 October 2016
Persian walnut (Juglans regia L.), valued for both its nut and wood, is an ecologically important temperate tree species native to the mountainous regions of central Asia. Despite its importance, there are still few transcriptomic resources in public databases for J. regia, limiting gene discovery and breeding. Here, more than 49.9 million sequencing reads were generated using Illumina sequencing technology in the characterization of the transcriptome of four J. regia organs (bud, leaf, female flowers, and male flowers). De novo assembly yielded 117,229 unigenes with an N50 of 1955 bp. Based on sequence similarity searches against known proteins, a total of 20,413 (17.41%) genes were identified and annotated. A set of 27,584 unigenes with SSR (simple sequence repeats) motifs were identified as potential molecular markers, and a sample of 77 of these EST-SSRs (express sequence tags) were further evaluated to validate their amplification and assess their polymorphism. Next, we developed 39 polymorphic microsatellite markers to screen 88 Persian walnut individuals collected from 11 populations. These markers and transcriptomic resources will be useful for future studies of population genetic structure, evolutionary ecology, and breeding of Persian walnut and other Juglans species. View Full-Text
Keywords: microsatellites; transcriptome; next-generation sequencing; genetic diversity; English walnut microsatellites; transcriptome; next-generation sequencing; genetic diversity; English walnut
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MDPI and ACS Style

Dang, M.; Zhang, T.; Hu, Y.; Zhou, H.; Woeste, K.E.; Zhao, P. De Novo Assembly and Characterization of Bud, Leaf and Flowers Transcriptome from Juglans Regia L. for the Identification and Characterization of New EST-SSRs. Forests 2016, 7, 247. https://doi.org/10.3390/f7100247

AMA Style

Dang M, Zhang T, Hu Y, Zhou H, Woeste KE, Zhao P. De Novo Assembly and Characterization of Bud, Leaf and Flowers Transcriptome from Juglans Regia L. for the Identification and Characterization of New EST-SSRs. Forests. 2016; 7(10):247. https://doi.org/10.3390/f7100247

Chicago/Turabian Style

Dang, Meng; Zhang, Tian; Hu, Yiheng; Zhou, Huijuan; Woeste, Keith E.; Zhao, Peng. 2016. "De Novo Assembly and Characterization of Bud, Leaf and Flowers Transcriptome from Juglans Regia L. for the Identification and Characterization of New EST-SSRs" Forests 7, no. 10: 247. https://doi.org/10.3390/f7100247

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