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Open AccessArticle

Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

1
Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou 570102, China
2
Institute of Vegetables, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
3
Tianjin Derit Seed Industry Co. Ltd., Tianjin 300384, China
4
College of Agriculture, Guangxi Vocational and Technical College, Nanning 530226, China
5
South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
*
Author to whom correspondence should be addressed.
Forests 2019, 10(5), 411; https://doi.org/10.3390/f10050411
Received: 11 April 2019 / Revised: 7 May 2019 / Accepted: 8 May 2019 / Published: 12 May 2019
(This article belongs to the Section Forest Ecophysiology and Biology)
Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies. View Full-Text
Keywords: Persea americana; ecological races; next-generation sequencing; microsatellites; genetic diversity Persea americana; ecological races; next-generation sequencing; microsatellites; genetic diversity
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Ge, Y.; Tan, L.; Wu, B.; Wang, T.; Zhang, T.; Chen, H.; Zou, M.; Ma, F.; Xu, Z.; Zhan, R. Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers. Forests 2019, 10, 411.

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