Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence (Q90141892)

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scientific article published on 22 October 2019

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English	Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence	scientific article published on 22 October 2019

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11 April 2020

Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence (English)

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11 April 2020

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11 April 2020

Konstantinos G Alexiou

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Raúl Castanera

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Jordi Garcia-Mas

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Josep M. Casacuberta

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11 April 2020

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Fabio Barteri

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Amit Dhingra

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Henri Duval

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Ángel Fernández I Martí

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Leonor Frias

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Beatriz Galán

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José L García

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Werner Howad

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Jèssica Gómez-Garrido

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Marta Gut

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Jordi Morata

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Pere Puigdomènech

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Paolo Ribeca

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María J Rubio Cabetas

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Anna Vlasova

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Michelle Wirthensohn

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Toni Gabaldón

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11 April 2020

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22 October 2019

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11 April 2020

The Plant Journal

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11 April 2020

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11 April 2020

455-472

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11 April 2020

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tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

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The paleontology of intergene retrotransposons of maize

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EMBOSS: the European Molecular Biology Open Software Suite

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InterProScan--an integration platform for the signature-recognition methods in InterPro

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Evolution of the angiosperms: calibrating the family tree

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MapChart: software for the graphical presentation of linkage maps and QTLs

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Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes

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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

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Mauve: multiple alignment of conserved genomic sequence with rearrangements

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GMAP: a genomic mapping and alignment program for mRNA and EST sequences

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Combined evidence annotation of transposable elements in genome sequences

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Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

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Kalign--an accurate and fast multiple sequence alignment algorithm

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M-Coffee: combining multiple sequence alignment methods with T-Coffee

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AUGUSTUS: ab initio prediction of alternative transcripts

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SyMAP: A system for discovering and viewing syntenic regions of FPC maps

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Minimus: a fast, lightweight genome assembler

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FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments

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KAAS: an automatic genome annotation and pathway reconstruction server

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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

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LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

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Using MUMmer to identify similar regions in large sequence sets

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DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

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ABySS: a parallel assembler for short read sequence data

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Fast and accurate short read alignment with Burrows-Wheeler transform

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

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Circos: an information aesthetic for comparative genomics

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Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

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ETE: a python Environment for Tree Exploration

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BEDTools: a flexible suite of utilities for comparing genomic features

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MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

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CDD: a Conserved Domain Database for the functional annotation of proteins

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1 reference

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STAR: ultrafast universal RNA-seq aligner

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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12 December 2020

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1 reference

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12 December 2020

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High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond × peach progenies

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12 December 2020

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Redundans: an assembly pipeline for highly heterozygous genomes

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CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

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12 December 2020

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1 reference

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12 December 2020

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1 reference

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12 December 2020

based on heuristic

inferred from PubMed ID database lookup

PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

GenomeScope: Fast reference-free genome profiling from short reads.

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Plant lineage-specific amplification of transcription factor binding motifs by Miniature Inverted-repeat Transposable Elements (MITEs).

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Accurate detection of complex structural variations using single-molecule sequencing

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea.

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Attention sports fans! The far-reaching contributions of bud sport mutants to horticulture and plant biology

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Insertion of a transposon-like sequence in the 5'-flanking region of the YUCCA gene causes the stony hard phenotype

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Elucidation of the Amygdalin Pathway Reveals the Metabolic Basis of Bitter and Sweet Almonds (Prunus dulcis)

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Using geneid to Identify Genes

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Genome re-sequencing reveals the evolutionary history of peach fruit edibility

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

genetics and applications after de novo genome sequencing: achievements and prospects

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Mutation of a bHLH transcription factor allowed almond domestication

1 reference

https://pubmed.ncbi.nlm.nih.gov/31529539

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1111/TPJ.14538

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31529539%20AND%20SRC:MED&resulttype=core&format=json

11 April 2020

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31529539%20AND%20SRC:MED&resulttype=core&format=json

11 April 2020

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31529539%20AND%20SRC:MED&resulttype=core&format=json

11 April 2020

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