- Hass ’ transcriptome during fruit development. - 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. - Conclusions: Candidate 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.. - Avocado (Persea americana Mill.) belongs to the Laura- ceae family, one of the oldest and largest flowering plant families that includes over 50 genera [1]. - Due to its nutritional properties, avocado is one of the major fruit crops worldwide and its commercial production is based. - De- pending on the race and variety, the development of the avocado fruit may vary, but generally is characterized by a biphasic behavior: the first phase is fruit maturation and occur while the fruit is attached to the tree, this stage is pre-climacteric (on-tree storage) and is associated to low ethylene levels and respiration rate. - Later, a second phase or climacteric peak begins after the detachment of the fruit and it is characterized by an increase in ethylene. - Full list of author information is available at the end of the article. - 2019 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.. - During development, one of the main characteristics of avocado is the large ac- cumulation of oil fraction that is used as harvest and qual- ity indexes, which can be up to 9–15% of oil in fresh weight, levels that are dependent on maturity stage and growing conditions in ‘Hass’ avocado [7–10]. - One of these platforms, RNA sequencing (RNA-seq), is useful to find functional elements of the genome and to understand different developmental stages and tissues.. - To further elucidate some of the molecular factors in- volved in the regulation of fruit development of the eco- nomically important ‘Hass’ avocado variety, we conducted a de novo assembly of the transcriptome from the devel- oping mesocarp at first harvest) and 390 (second harvest) days after fruit set (DAFS) using HiSeq 2500 (Illumina) platform. - Illumina sequencing and assembly of the avocado de novo transcriptome. - In order to obtain insights of the dynamics of the ‘Hass’ av- ocado transcriptome during fruit development, RNA librar- ies were constructed and sequenced at four developmental stages and 390 DAFS) using a HiSeq 2500 (Illumina) sequencer. - In order to estimate the variability of gene global expres- sion among fruit development stages and their biological replicates, the PCA explained up to 36.4% of the. - during fruit development. - To compare transcriptomic data among samples, normalization of the reads through tran- scripts per million (TPM) was performed. - Functional annotation and global GO terms of the de novo transcriptome. - a PCA of the genes global expression from four development stages and 390 days after fruit set or DAFS) and their three biological replicates (R1, R2 and R3). - For the molecular function cat- egory, ‘Binding’ and ‘Catalytic activity’ accounted for most of the annotated genes (Fig. - On the other hand, in order to identify candidate genes involved in the development of avocado fruit, we compared samples from and 390 DAFS considering three biological replicates using differential expression analysis. - 2 Annotation and relevant GO terms of the de novo transcriptome assembled. - The de novo assembly and functional annotation of the avocado transcriptome. - In this study we report the de novo assembly of the ‘Hass’. - In this work, from a short-read assembly we could obtain 62,203 contigs and 62,167 genes using Trinity (Table 1), while a previous study of the ‘Hass’. - (Additional file 9), which is stored as TAG and involves the synthesis of fatty-acids (FA) in the plastid. - As previ- ously reported in avocado, the oil content and transcript levels of acyl-carrier proteins increase representing about 24% of the total fatty-acid gene expression during matur- ation of the mesocarp [18].. - These results are associated to a full development of the seed together with an increase in susceptibility to biotic stress during ripening, since the unripe mesocarp of avocado is more tolerant to pathogen attack [6]. - For example, changes re- lated to susceptibility to pathogen infection were previously observed in tomato, were the presence of the vacuolar pro- tease SlVPE3 is necessary for resistance against the fungal pathogen Botrytis cinerea during ripening [32].. - This is concomitant with the lignification of the endocarp for seed protection and the increasing suscepti- bility to pathogen infection during development [32, 38].. - In our case, the in- crease in the expression of the putative chitinase 1 (CBV_PAM2452), together with the ethylene-responsive transcription factor RAP2–4-like (CBV_PAM3819) could indicate the increase of ethylene biosynthesis, which regu- lates the ripening of climacteric fruit such as avocado [44].. - For subcluster 11, genes that constantly decrease their expression are mainly part of the cell wall structure and lipid metabolism. - Transcripts that were strongly expressed either at the start of the developmental process (150 DAFS) or at the end of the process (390 DAFS) were searched. - In this work, the transcript changes of the mesocarp of. - ment in the search for potential biomarkers for this process. - In addition, candidate genes related to lipid metabolism, ethylene signaling pathway, auxin signaling pathway, cell signaling, and components of the cell wall were identified due to their differential expression during the developing fruit, providing a foundation to further characterize these genes in the search for molecular applications. - ‘Hass’ is the most important variety in the world repre-. - senting 95% of the cultivated area, characterized by te accumulation of high levels of oil content and a quint- essentially fairly thick skin that turns near black when fully ripe. - RNA was extracted using RNeasy mini kit (QIAGEN, Germantown, MD, USA) from a homogenous sample of the fruit mesocarp following the manufacturer ’ s instruc- tion. - After assembly, we used the CD-HIT software (http://weizhongli-lab.org/cd-hit/) to remove du- plicated contigs and CORSET software (https://github.- com/Oshlack/Corset/) to filter out contigs with less than 36 reads.. - Quality check and annotation of the novo transcriptome Quality assessment was performed with two approaches:. - (i) a biological approach that used two ultra-conserved protein gene finder software: Core Eukaryotic Gene Mapping Approach (CEGMA) and Benchmarking Univer- sal Single-Copy Orthologs (BUSCO) and (ii) an informatic approach, DETONATE and TransRate to assess the archi- tecture and quality of the contigs. - (DOCX 14 kb) Additional file 2: Functional annotation of the whole de novo transcriptome of Persea Americana cv. - Additional file 8: List of the primers used for validated gene expression levels by qRT-PCR. - BGD contributed to the design and implementation of the research, he performed funding acquisition and reviewed and edited manuscript. - doi.org/https://doi.org . - Persea americana (avocado): bringing ancient flowers to fruit in the genomics era. - https://doi.org/10.1002/bies.20721.. - https://doi.org/10.1002/jsfa . - Chemical changes during growth and storage of the avocado fruit. - https://doi.org/10.1016/j.sajb . - https://doi.org/10.3389/fpls.2012.. - https://doi.org/10.1371/journail.pone.0050226.. - https://doi.org/10.1016/j.jbiotec . - https://doi.org/10.1038/. - https://doi.org/10.. - Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acid. - https://doi.org/10.1186/s y.. - https://doi.org/10.1186/. - https://doi.org/10.1371/journal.pone.0130885.. - https://doi.org . - Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit:. - https://doi.org/10.1038/hortres.2014.11.. - https://doi.org/10.1038/hortres.2016.14.. - https://doi.org/10.1371/journal.pone.0179491.. - doi.org/10.17660/ActaHortic . - https://doi.org/10.1007/. - doi.org . - Changes in oxidative processes and components of the antioxidant system during tomato ripening. - https://doi.org/10.1186/s . - https://doi.org/10.1021/jf901839h.. - Sugar metabolism and fruit development in the tomato. - https://doi.org/10.2503/hortj.OKD-IR01.. - Metabolic and molecular changes of the phenylpropanoid pathway in tomato (Solanum lycopersicum) lines carrying different Solanum pennellii wild chromosomal regions. - Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence. - https://doi.org/10.1199/tab.. - https://doi.org/10.1111/ppl.. - https://doi.org/10.1007/s . - https://doi.org/10.1371/journal.pone.0169440.. - https://doi.org/10.1038/ncomms13245.. - https://doi.org/10.1093/jxb/ert283.. - https://doi.org/10.3389/fpls . - https://doi.org/10.1016/j.bbalip . - dynamics during fruit development. - Receptor serine/threonine protein kinases in signaling: analysis of the erecta receptor-like kinase of Arabidopsis thaliana. - https://doi.org/10.1046/j.. - https://doi.org/10.1016/j.. - https://doi.org/10.1111/nph.12685.. - https://doi.org/10.1104/pp.82.2.448.. - https://doi.org/10.1104/pp . - Lipid droplet-associated proteins (LDAPs) are involved in the. - https://doi.org/10.4161/psb.27141.. - https://doi.org/10.1104/pp.16.00322.. - https://doi.org/10.1038/nprot.2013.084.. - https://doi.org/10.1101/gr . - https://doi.org/10.1038/nmeth.1923.. - https://doi.org/10.1093/nar/gkx382.. - https://doi.org/. - 10.1371/journal.pone.0021800.
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