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

Yu Ge,Rulin Zhan,Bin Wu,Minghong Zou,Haihong Chen,Zining Xu,Teng Zhang,Tao Wang,Funing Ma,Lin Tan

doi:10.3390/f10050411

Abstract

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.

Highlights

Avocado belongs to the family Lauraceae of the order Laurales, which includes some of the oldest flowering plants in the fossil record and which was already widespread in the Early Cretaceous [1].According to Chanderbali [2], Laurales belong to a key clade, the magnoliids, containing most basal angiosperms in the widely accepted angiosperm phylogeny
The apical buds were from the developing buds emerging from shoot apical meristem, the flowers were from whole inflorescences with flowers at two stages of development, the leaves were from the two development stages of unexpanded and expanded leaves, the stems were from segments from young and old branches, and the root samples were from in vitro propagated seedlings [36]
A total of 29–45 million clean reads and 4.30–6.68 Gb of sequence data were generated from six cDNA libraries (Table S1)

Summary

Introduction

Avocado belongs to the family Lauraceae of the order Laurales, which includes some of the oldest flowering plants in the fossil record and which was already widespread in the Early Cretaceous [1].According to Chanderbali [2], Laurales (avocado and relatives) belong to a key clade, the magnoliids, containing most basal angiosperms in the widely accepted angiosperm phylogeny. The two “subtropical” (Guatemalan and Mexican) ecotypes, a species native to Mesoamerica, are widely grown in warm to cool subtropical and Mediterranean climates in different countries and regions, while the “tropical” lowland (West Indian) ecotype is cultivated in tropical countries and warm subtropical regions [4]. These three ecotypes are distinguished and identified according to their genetic and morphological differences [1]. The only available transcriptome data, to our knowledge, is that of the Hass cultivar, classified as a Guatemalan × Mexican hybrid, and an unknown Mexican accession [6,7,8], which extremely restricts genetic and breeding studies

Methods

Results

Discussion

Conclusion