De novo assembly of Persea americana cv. ‘Hass’ transcriptome during fruit development

Abstract

BackgroundAvocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The flowering and fruit set are particularly prolonged processes, lasting between one to three months, generating important differences in physiological ages of the fruit within the same tree. So far there is no detailed genomic information regarding this species, being the cultivar ‘Hass’ especially important for avocado growers worldwide. With the aim to explore the fruit avocado transcriptome and to identify candidate biomarkers to monitore fruit development, we carried out an RNA-Seq approach during 4 stages of ‘Hass’ fruit development: 150 days after fruit set (DAFS), 240 DAFS, 300 DAFS (harvest) and 390 DAFS (late-harvest).ResultsThe ‘Hass’ de novo transcriptome contains 62,203 contigs (x̅=988 bp, N50 = 1050 bp). We found approximately an 85 and 99% of complete ultra-conserved genes in eukaryote and plantae database using BUSCO (Benchmarking Universal Single-Copy Orthologs) and CEGMA (Core Eukaryotic Gene Mapping Approach), respectively. Annotation was performed with BLASTx, resulting in a 58% of annotated contigs (90% of differentially expressed genes were annotated). Differentially expressed genes analysis (DEG; with False Discovery Rate ≤ 0.01) found 8672 genes considering all developmental stages. From this analysis, genes were clustered according to their expression pattern and 1209 genes show correlation with the four developmental stages.ConclusionsCandidate genes are proposed as possible biomarkers for monitoring the development of the ‘Hass’ avocado fruit associated with lipid metabolism, ethylene signaling pathway, auxin signaling pathway, and components of the cell wall.Electronic supplementary materialThe online version of this article (10.1186/s12864-019-5486-7) contains supplementary material, which is available to authorized users.

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

“…In this study, 93.82% (71,627 of 76,345) of the nonredundant transcripts were annotated based on similarities with sequences in public databases. Thus, a greater proportion of transcripts were annotated in this study than in previous investigations involving NGS data for various avocado races (49.00%) [18] and for avocado mesocarp samples (57.50%) [55]. We determined that the mean length of the avocado nonredundant transcripts was2330 bp, implying that our sequences were long enough to represent full-length transcripts.…”

“…Transcriptome sequencing is a useful technique for obtaining a large number of transcripts for organisms lacking a reference sequence, at least partly because it is inexpensive and can be completed rapidly [51][52][53]. To date, several short-read next-generation sequencing (NGS) transcriptome databases have been developed for avocado mesocarp samples [54,55] and avocado mixed tissue samples [18,56]. However, both the number and length of the transcript sequences derived from these short-read NGS studies have hamperedtheirapplication ingenetics and molecular biology research [41].…”

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

“…De novo assembly of avocado cv. "Hass" transcriptome during mesocarp development was conducted and identified tissue-specific regulation and biosynthesis of TAG, respectively [7,8]. Moreover, the transcriptomes of aerial buds, leaves, flowers, stems, seeds, and roots from an unknown Mexican accession were determined using different sequencing platforms, and it revealed strong differences in gene expression patterns between different organs [6].…”

“…Many commercial avocado accessions are thus often natural or artificial hybrids [5]. 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.…”

Primary Metabolism in Avocado Fruit

“…It has been previously reported that at early stages of fruit set in avocado, about 44% of the flesh weight is due to sugars which continue to increase during rapid fruit growth but then decline during oil accumulation (Liu et al, 1999b). One fourth of total oil content accumulation in avocado has been reported to occur during early stages of development and Vergara-Pulgar et al (2019) have recently reported enrichment of transcripts related to lipid localization, fatty acid synthase activity and acyl carrier activity involved in fatty acid biosynthesis when comparing mesocarp of 150 DAFS (days after fruit set) with 240 DAFS, respectively. Acetyl-CoA carboxylase the regulatory enzyme that controls the rate of fatty acid synthesis and catalyzes the first reaction to generate malonyl-CoA was also detected in avocado and oil palm (Dussert et al, 2013; Kilaru et al, 2015).…”