De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development 06 Biological Sciences 0604 Genetics

Cristian Vergara-Pulgar, Karin Rothkegel, Mauricio González-Agüero, Romina Pedreschi, Reinaldo Campos-Vargas, Bruno G. Defilippi, Claudio Meneses

Resultado de la investigación: Article

5 Citas (Scopus)

Resumen

Background: 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 (x=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.

Idioma originalEnglish
Número de artículo108
PublicaciónBMC Genomics
Volumen20
N.º1
DOI
EstadoPublished - 6 feb 2019

Huella dactilar

Persea
Biological Science Disciplines
Transcriptome
Fruit
Genes
Lauraceae
Biomarkers
Angiosperms
Benchmarking
Indoleacetic Acids
Chromosome Mapping
Eukaryota
Diploidy
Lipid Metabolism
Cell Wall

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Citar esto

Vergara-Pulgar, Cristian ; Rothkegel, Karin ; González-Agüero, Mauricio ; Pedreschi, Romina ; Campos-Vargas, Reinaldo ; Defilippi, Bruno G. ; Meneses, Claudio. / De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development 06 Biological Sciences 0604 Genetics. En: BMC Genomics. 2019 ; Vol. 20, N.º 1.
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title = "De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development 06 Biological Sciences 0604 Genetics",
abstract = "Background: 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 (x=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.",
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De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development 06 Biological Sciences 0604 Genetics. / Vergara-Pulgar, Cristian; Rothkegel, Karin; González-Agüero, Mauricio; Pedreschi, Romina; Campos-Vargas, Reinaldo; Defilippi, Bruno G.; Meneses, Claudio.

En: BMC Genomics, Vol. 20, N.º 1, 108, 06.02.2019.

Resultado de la investigación: Article

TY - JOUR

T1 - De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development 06 Biological Sciences 0604 Genetics

AU - Vergara-Pulgar, Cristian

AU - Rothkegel, Karin

AU - González-Agüero, Mauricio

AU - Pedreschi, Romina

AU - Campos-Vargas, Reinaldo

AU - Defilippi, Bruno G.

AU - Meneses, Claudio

PY - 2019/2/6

Y1 - 2019/2/6

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AB - Background: 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 (x=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.

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KW - Biomarkers

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KW - RNA-Seq

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