Deep sequencing of the Mexican avocado transcriptome, an ancient angiosperm with a high content of fatty acids.
BACKGROUND
Avocado (Persea americana) is an economically important tropical fruit considered to be a good source of fatty acids. Despite its importance, the molecular and cellular characterization of biochemical and developmental processes in avocado is limited due to the lack of transcriptome and genomic information.


RESULTS
The transcriptomes of seeds, roots, stems, leaves, aerial buds and flowers were determined using different sequencing platforms. Additionally, the transcriptomes of three different stages of fruit ripening (pre-climacteric, climacteric and post-climacteric) were also analyzed. The analysis of the RNAseqatlas presented here reveals strong differences in gene expression patterns between different organs, especially between root and flower, but also reveals similarities among the gene expression patterns in other organs, such as stem, leaves and aerial buds (vegetative organs) or seed and fruit (storage organs). Important regulators, functional categories, and differentially expressed genes involved in avocado fruit ripening were identified. Additionally, to demonstrate the utility of the avocado gene expression atlas, we investigated the expression patterns of genes implicated in fatty acid metabolism and fruit ripening.


CONCLUSIONS
A description of transcriptomic changes occurring during fruit ripening was obtained in Mexican avocado, contributing to a dynamic view of the expression patterns of genes involved in fatty acid biosynthesis and the fruit ripening process.
Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.|Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico.
Enrique
E
Ibarra-Laclette
Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.|Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico.
Alfonso
A
Méndez-Bravo
Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.|Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., 91070, Xalapa, Veracruz, Mexico.|Investigador Cátedra CONACyT en el Instituto de Ecología A.C., Veracruz, Mexico.
Claudia Anahí
CA
Pérez-Torres
Department of Biological Sciences, University at Buffalo, Buffalo, NY, 14260, USA.
Victor A
VA
Albert
Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA.
Keithanne
K
Mockaitis
Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37614, USA.|Department of Biomedical Sciences, East Tennessee State University, Johnson City, TN, 37614, USA.
Aruna
A
Kilaru
Instituto de Investigaciones Químico-Biológicas (IIQB), Universidad Michoacana de San Nicolás de Hidalgo, 58030, Morelia, Michoacán, Mexico.
Rodolfo
R
López-Gómez
Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico.
Jacob Israel
JI
Cervantes-Luevano
Laboratorio Nacional de Genómica para la Biodiversidad-Langebio/Unidad de Genómica Avanzada UGA, Centro de Investigación y Estudios Avanzados del IPN, 36500, Irapuato, Guanajuato, Mexico. lherrera@langebio.cinvestav.mx.
Luis
L
Herrera-Estrella
D005227:Fatty Acids / Q000378:metabolism*; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling / Q000379:methods*; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D027421:Persea / Q000737:chemistry / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D012639:Seeds / Q000235:genetics / Q000254:growth & development; D017423:Sequence Analysis, RNA / Q000379:methods*
D005227:Fatty Acids; D010940:Plant Proteins