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

**Yu Ge <sup>1</sup> , Zhihao Cheng <sup>1</sup> , Xiongyuan Si <sup>2</sup> , Weihong Ma <sup>1</sup> , Lin Tan <sup>1</sup> , Xiaoping Zang <sup>1</sup> , Bin Wu <sup>1</sup> , Zining Xu <sup>1</sup> , Nan Wang <sup>1</sup> , Zhaoxi Zhou <sup>1</sup> , Xinge Lin <sup>1</sup> , Xiangshu Dong 3,\* and Rulin Zhan 1,\***


Received: 12 August 2019; Accepted: 21 August 2019; Published: 23 August 2019

**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, alphaand 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.

**Keywords:** avocado; carotenoid biosynthesis; mesocarp; seed; de novo assembly from short read sequencing; full-length transcript sequencing; differentially expressed genes; gene dosage
