List of works - Aureliano Bombarely

A Snapshot of the Emerging Tomato Genome Sequence

A convoluted tale of hybridization between two Petunia species from a transitional zone in South America

scientific article published in 2022

A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research

scientific article

A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency

scientific article

Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development

scientific article published on 25 November 2020

An Endophyte Constructs Fungicide-Containing Extracellular Barriers for Its Host Plant.

scientific article

Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

scientific article

Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm.

scientific article published on 15 November 2017

Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation

scientific article published on 01 October 2019

Central role of FaGAMYB in the transition of the strawberry receptacle from development to ripening

scientific article

Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

Collagen duplicate genes of bone and cartilage participate during regeneration of zebrafish fin skeleton

scientific article published on 6 August 2015

Combining transcriptome analysis and GWAS for identification and validation of marker genes in the Physalis peruviana-Fusarium oxysporum pathosystem

scientific article published on 22 March 2021

Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

scientific article published on 26 February 2015

Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean

scientific article

De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis

scientific article published on 24 November 2015

De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus.

scientific article published on 7 November 2017

De-novo assembly of zucchini genome reveals a whole genome duplication associated with the origin of theCucurbitagenus

article published in 2017

Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

scientific article

DeepTE: a computational method for de novo classification of transposons with convolutional neural network

scientific article published on 16 May 2020

Demethylation of oligogalacturonides by FaPE1 in the fruits of the wild strawberry Fragaria vesca triggers metabolic and transcriptional changes associated with defence and development of the fruit

article

Designing a transcriptome next-generation sequencing project for a nonmodel plant species

scientific article

Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell.

scientific article published on 3 August 2017

Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity

scientific article published on 16 October 2019

ERAMOSA controls lateral branching in snapdragon

scientific article published in February 2017

Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice

scientific article published in 2022

Expression-level support for gene dosage sensitivity in three Glycine subgenus Glycine polyploids and their diploid progenitors.

scientific article published on 15 July 2016

From manual curation to visualization of gene families and networks across Solanaceae plant species

scientific article published on 15 May 2013

Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa).

scientific article published on 23 October 2017

Generation and analysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies

scientific article

Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit

scientific article

Genetic insights into the modification of the pre-fertilization mechanisms during plant domestication

scientific article published on 01 June 2019

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass

scientific article published on 30 July 2019

Genome sequence of mungbean and insights into evolution within Vigna species

scientific article published on 11 November 2014

Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.).

scientific article published on 27 December 2019

Genomic analysis of the native European Solanum species, S. dulcamara.

scientific article

Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya (<scp>Annona cherimola</scp>)

scientific article published in 2023

Genomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencing

scientific article published on 04 March 2019

HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation

scientific article published in 2023

How genomics can help biodiversity conservation

How many species are there? Lineage diversification and hidden speciation in Solanaceae from highland grasslands in southern South America

scientific article published in 2024

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

scientific article

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida.

scientific article published on 27 May 2016

Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex

scientific article

Modifying Anthocyanins Biosynthesis in Tomato Hairy Roots: A Test Bed for Plant Resistance to Ionizing Radiation and Antioxidant Properties in Space

scientific article published on 24 February 2022

Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

scientific article published on 23 August 2017

Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species

scientific article published on 25 March 2022

Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data

scientific article

Partially Resistant Avocado Rootstock Dusa® Shows Prolonged Upregulation of Nucleotide Binding-Leucine Rich Repeat Genes in Response to Phytophthora cinnamomi Infection

scientific article published on 11 March 2022

Population genomics indicates micro‐refuges and riverine barriers for a southern South American grassland nightshade

scientific article published in 2021

Roses for Darwin

scientific article published on 01 July 2018

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases.

scientific article

Species boundaries in the Astragalus cusickii complex delimited using molecular phylogenetic techniques

scientific article published on 8 June 2017

The Genome Database for Rosaceae (GDR): year 10 update

scientific article

The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian Cricket

article

The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons

article

The SUD1 gene encodes a putative E3 ubiquitin ligase and is a positive regulator of 3-hydroxy-3-methylglutaryl coenzyme a reductase activity in Arabidopsis

scientific article

The Sol Genomics Network (SGN)--from genotype to phenotype to breeding

scientific article

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

scientific article

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

scientific article published on 25 November 2012

The era of reference genomes in conservation genomics

scientific article published in March 2022

The wild side of a major crop: soybean's perennial cousins from Down Under

scientific article

TobEA: an atlas of tobacco gene expression from seed to senescence

scientific article

Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes

scientific article published on 14 June 2019

Transcriptome Landscape Variation in the Genus Thymus

scientific article published on 16 August 2019

Transcriptomic Analysis of L. Roots during the Early Infection Process.

scientific article published on March 2017

Transcriptomic analysis of Petunia hybrida in response to salt stress using high throughput RNA sequencing.

scientific article

Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity.

scientific article

Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.).

scientific article published on 27 March 2020

Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

scientific article published on 08 October 2019

XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED.

scientific article published on 25 July 2017

siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass.

scientific article published on 24 July 2018

List of works by Aureliano Bombarely

A Snapshot of the Emerging Tomato Genome Sequence

A convoluted tale of hybridization between two Petunia species from a transitional zone in South America

A draft genome sequence of Nicotiana benthamiana to enhance molecular plant-microbe biology research

A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency

Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development

An Endophyte Constructs Fungicide-Containing Extracellular Barriers for Its Host Plant.

Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins

Assessment of Genetic Diversity and Population Structure in Iranian Cannabis Germplasm.

Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation

Central role of FaGAMYB in the transition of the strawberry receptacle from development to ripening

Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

Collagen duplicate genes of bone and cartilage participate during regeneration of zebrafish fin skeleton

Combining transcriptome analysis and GWAS for identification and validation of marker genes in the <i>Physalis peruviana</i>-<i>Fusarium oxysporum</i> pathosystem

Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives

Complete plastome sequences from Glycine syndetika and six additional perennial wild relatives of soybean

De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis

De novo assembly of the zucchini genome reveals a whole-genome duplication associated with the origin of the Cucurbita genus.

De-novo assembly of zucchini genome reveals a whole genome duplication associated with the origin of theCucurbitagenus

Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

DeepTE: a computational method for de novo classification of transposons with convolutional neural network

Demethylation of oligogalacturonides by FaPE1 in the fruits of the wild strawberry Fragaria vesca triggers metabolic and transcriptional changes associated with defence and development of the fruit

Designing a transcriptome next-generation sequencing project for a nonmodel plant species

Dissecting Tissue-Specific Transcriptomic Responses from Leaf and Roots under Salt Stress in Petunia hybrida Mitchell.

Draft Assembly of Phytophthora capsici from Long-Read Sequencing Uncovers Complexity

ERAMOSA controls lateral branching in snapdragon

Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice

Expression-level support for gene dosage sensitivity in three Glycine subgenus Glycine polyploids and their diploid progenitors.

From manual curation to visualization of gene families and networks across Solanaceae plant species

Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa).

Generation and analysis of ESTs from strawberry (Fragaria xananassa) fruits and evaluation of their utility in genetic and molecular studies

Genetic and genome-wide transcriptomic analyses identify co-regulation of oxidative response and hormone transcript abundance with vitamin C content in tomato fruit

Genetic insights into the modification of the pre-fertilization mechanisms during plant domestication

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass

Genome sequence of mungbean and insights into evolution within Vigna species

Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.).

Genomic analysis of the native European Solanum species, S. dulcamara.

Genomics in neglected and underutilized fruit crops: A chromosome‐scale genome sequence of cherimoya (<scp><i>Annona cherimola</i></scp>)

Genomics-based diversity analysis of Vanilla species using a Vanilla planifolia draft genome and Genotyping-By-Sequencing

HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation

How genomics can help biodiversity conservation

How many species are there? Lineage diversification and hidden speciation in Solanaceae from highland grasslands in southern South America

Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida.

Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex

Modifying Anthocyanins Biosynthesis in Tomato Hairy Roots: A Test Bed for Plant Resistance to Ionizing Radiation and Antioxidant Properties in Space

Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Neutral and outlier single nucleotide polymorphisms disentangle the evolutionary history of a coastal Solanaceae species

Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data

Partially Resistant Avocado Rootstock Dusa<sup>®</sup> Shows Prolonged Upregulation of <i>Nucleotide Binding-Leucine Rich Repeat</i> Genes in Response to <i>Phytophthora cinnamomi</i> Infection

Population genomics indicates micro‐refuges and riverine barriers for a southern South American grassland nightshade

Roses for Darwin

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases.

Species boundaries in the Astragalus cusickii complex delimited using molecular phylogenetic techniques

The Genome Database for Rosaceae (GDR): year 10 update

The Genomic Architecture of a Rapid Island Radiation: Recombination Rate Variation, Chromosome Structure, and Genome Assembly of the Hawaiian Cricket

The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons

The SUD1 gene encodes a putative E3 ubiquitin ligase and is a positive regulator of 3-hydroxy-3-methylglutaryl coenzyme a reductase activity in Arabidopsis

The Sol Genomics Network (SGN)--from genotype to phenotype to breeding

The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

The era of reference genomes in conservation genomics

The wild side of a major crop: soybean's perennial cousins from Down Under

TobEA: an atlas of tobacco gene expression from seed to senescence

Tools and Strategies for Long-Read Sequencing and De Novo Assembly of Plant Genomes

Transcriptome Landscape Variation in the Genus Thymus

Transcriptomic Analysis of L. Roots during the Early Infection Process.

Transcriptomic analysis of Petunia hybrida in response to salt stress using high throughput RNA sequencing.

Transcriptomics-based screen for genes induced by flagellin and repressed by pathogen effectors identifies a cell wall-associated kinase involved in plant immunity.

Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.).

Whole-Genome Resequencing of Seven Eggplant (Solanum melongena) and One Wild Relative (S. incanum) Accessions Provides New Insights and Breeding Tools for Eggplant Enhancement

XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA-RELATED.

siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass.