Transcriptome Profiling Provides Insight into the Genes in Carotenoid Biosynthesis during the Mesocarp and Seed Developmental Stages of Avocado (Persea americana).

Yu Ge,Xiangshu Dong,Nan Wang,Xiongyuan Si,Xinge Lin,Bin Wu,Rulin Zhan,Zhaoxi Zhou,Xiaoping Zang,Zining Xu,Zhihao Cheng,Lin Tan,Weihong Ma

doi:10.3390/ijms20174117

Abstract

Avocado (Persea americana Mill.) is an economically important crop because of its high nutritional value. However, the absence of a sequenced avocado reference genome has hindered investigations of secondary metabolism. For next-generation high-throughput transcriptome sequencing, we obtained 365,615,152 and 348,623,402 clean reads as well as 109.13 and 104.10 Gb of sequencing data for avocado mesocarp and seed, respectively, during five developmental stages. High-quality reads were assembled into 100,837 unigenes with an average length of 847.40 bp (N50 = 1725 bp). Additionally, 16,903 differentially expressed genes (DEGs) were detected, 17 of which were related to carotenoid biosynthesis. The expression levels of most of these 17 DEGs were higher in the mesocarp than in the seed during five developmental stages. In this study, the avocado mesocarp and seed transcriptome were also sequenced using single-molecule long-read sequencing to acquired 25.79 and 17.67 Gb clean data, respectively. We identified 233,014 and 238,219 consensus isoforms in avocado mesocarp and seed, respectively. Furthermore, 104 and 59 isoforms were found to correspond to the putative 11 carotenoid biosynthetic-related genes in the avocado mesocarp and seed, respectively. The isoform numbers of 10 out of the putative 11 genes involved in the carotenoid biosynthetic pathway were higher in the mesocarp than those in the seed. Besides, alpha- and beta-carotene contents in the avocado mesocarp and seed during five developmental stages were also measured, and they were higher in the mesocarp than in the seed, which validated the results of transcriptome profiling. Gene expression changes and the associated variations in gene dosage could influence carotenoid biosynthesis. These results will help to further elucidate carotenoid biosynthesis in avocado.

Highlights

Avocado (Persea americana Mill.) is a member of the family Lauraceae of the order Laurales, and widely grown in countries and regions with a tropical-to-cool climate [1,2,3]
The RNA extracted from 15 mesocarp and seed samples were analyzed by RNA sequencing (RNA-seq), with three replicates per avocado fruit developmental stage
The metabolite profiling via high-performance liquid chromatography (HPLC) in the avocado mesocarp and seed during five developmental stages in this study validated the results of our Next-generation high-throughput sequencing technology (NGST) and single-molecule real-time (SMRT) transcriptome profiling

Summary

Introduction

Avocado (Persea americana Mill.) is a member of the family Lauraceae of the order Laurales, and widely grown in countries and regions with a tropical-to-cool climate [1,2,3]. Avocado is among the most economically important subtropical/tropical fruit crops worldwide, with considerable increases in yield reported in several countries, including Mexico, the USA, Indonesia, Chile, Spain, Israel, Colombia, South Africa, and Australia [4]. Certain avocado constituents, such as carotenoids, lipids, sugars, proteins, minerals, vitamins, and other nutrients and active ingredients, provide nutritional and health benefits [5,6,7]. The plant carotenoid metabolic pathway has been well elucidated This pathway consists of a series of chemical reactions, including condensations, dehydrogenations, cyclizations, hydroxylations, and epoxidations [12]

Methods

Results

Conclusion