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

Yiheng Hu¹  Meng Dang¹  Huijuan Zhou¹  Tian Zhang¹  Peng Zhao¹  Keith E. Woeste² 

[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;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;

关键词: microsatellites;    transcriptome;    next-generation sequencing;    genetic diversity;    English walnut;   

DOI  :  10.3390/f7100247

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown