Ontology type: schema:ScholarlyArticle Open Access: True
2019-12
AUTHORSCristian Vergara-Pulgar, Karin Rothkegel, Mauricio González-Agüero, Romina Pedreschi, Reinaldo Campos-Vargas, Bruno G. Defilippi, Claudio Meneses
ABSTRACTBACKGROUND: Avocado (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). RESULTS: The '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. 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. More... »
PAGES108
http://scigraph.springernature.com/pub.10.1186/s12864-019-5486-7
DOIhttp://dx.doi.org/10.1186/s12864-019-5486-7
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PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/30727956
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"description": "BACKGROUND: Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~\u2009920 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\u2009days after fruit set (DAFS), 240 DAFS, 300 DAFS (harvest) and 390 DAFS (late-harvest).\nRESULTS: The 'Hass' de novo transcriptome contains 62,203 contigs (x\u0305=988\u2009bp, N50\u2009=\u20091050\u2009bp). 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\u2009\u2264\u20090.01) 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.\nCONCLUSIONS: 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.",
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"name": "De novo assembly of Persea americana cv. \u2018Hass\u2019 transcriptome during fruit development",
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