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Transposons played a major role in the diversification between the closely related almond ( Prunus dulcis ) and peach ( P. persica ) genomes: Results from the almond genome sequence
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Using geneid to Identify Genes
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Using MUMmer to Identify Similar Regions in Large Sequence Sets
inferredcites →https://doi.org/10.1002/0471250953.bi1108s33openalex-snapshot
Next Generation Sequence Assembly with AMOS
inferredcites →https://doi.org/10.1002/j.1460-2075.1990.tb07536.xopenalex-snapshot
Origin and evolution of retroelements based upon their reverse transcriptase sequences.
inferredcites →https://doi.org/10.1002/tax.602021openalex-snapshot
Endocarps of Prunus (Rosaceae: Prunoideae) from the early Eocene of Wutu, Shandong Province, China
inferredcites →https://doi.org/10.1007/978-1-59745-251-9_3openalex-snapshot
Multiple Alignment of DNA Sequences with MAFFT
inferredcites →https://doi.org/10.1007/bf00123275openalex-snapshot
The genus Amygdalus L. (Rosaceae): Species relationships, distribution and evolution under domestication
inferredcites →https://doi.org/10.1007/bf00222918openalex-snapshot
Phylogenetic relationships of cultivated Prunus species from an analysis of chloroplast DNA variation
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Construction of a saturated linkage map for Prunus using an almond×peach F2 progeny
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Genome-wide InDel marker system for application in rice breeding and mapping studies
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Wild almonds gone wild: revisiting Darwin’s statement on the origin of peaches
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Combining conservative and variable markers to infer the evolutionary history of Prunus subgen. Amygdalus s.l. under domestication
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An InDel-based linkage map of hot pepper (Capsicum annuum)
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Barremian-Aptian angiospermid pollen records from southern England
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Epipalaeolithic (19,000 BP) cereal and fruit diet at Ohalo II, Sea of Galilee, Israel
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Basic Local Alignment Search Tool
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EMBOSS: The European Molecular Biology Open Software Suite
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Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes
inferredcites →https://doi.org/10.1038/1695openalex-snapshot
The paleontology of intergene retrotransposons of maize
inferredcites →https://doi.org/10.1038/hortres.2015.16openalex-snapshot
High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond × peach progenies
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A transposon-induced epigenetic change leads to sex determination in melon
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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
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A transposable element in a NAC gene is associated with drought tolerance in maize seedlings
inferredcites →https://doi.org/10.1038/ng.2586openalex-snapshot
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution
inferredcites →https://doi.org/10.1038/nmeth.1701openalex-snapshot
SignalP 4.0: discriminating signal peptides from transmembrane regions
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Genome re-sequencing reveals the evolutionary history of peach fruit edibility
inferredcites →https://doi.org/10.1038/s41592-018-0001-7openalex-snapshot
Accurate detection of complex structural variations using single-molecule sequencing
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Peaches Preceded Humans: Fossil Evidence from SW China
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Comparative mapping and marker-assisted selection in Rosaceae fruit crops
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
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The Variation of Animals and Plants Under Domestication. Charles Darwin
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Fagaceous Flowers, Fruits, and Cupules from the Campanian (Late Cretaceous) of Central Georgia, USA
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New Genus of Fossil Fagaceae from the Santonian (Late Cretaceous) of Central Georgia, U. S. A.
inferredcites →https://doi.org/10.1093/bioinformatics/17.9.847openalex-snapshot
InterProScan – an integration platform for the signature-recognition methods in InterPro
inferredcites →https://doi.org/10.1093/bioinformatics/bti310openalex-snapshot
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
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DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
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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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Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btq609openalex-snapshot
Assigning duplication events to relative temporal scales in genome-wide studies
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A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
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Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
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CD-HIT: accelerated for clustering the next-generation sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt476openalex-snapshot
The MaSuRCA genome assembler
inferredcites →https://doi.org/10.1093/bioinformatics/btt509openalex-snapshot
Infernal 1.1: 100-fold faster RNA homology searches
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btw271openalex-snapshot
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction
inferredcites →https://doi.org/10.1093/bioinformatics/btw369openalex-snapshot
Assemblytics: a web analytics tool for the detection of variants from an assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btw663openalex-snapshot
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btx153openalex-snapshot
GenomeScope: fast reference-free genome profiling from short reads
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The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding
inferredcites →https://doi.org/10.1093/gbe/evy073openalex-snapshot
Plant Lineage-Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted-Repeat Transposable Elements (MITEs)
inferredcites →https://doi.org/10.1093/genetics/8.4.390openalex-snapshot
THE FACTOR FOR BITTERNESS IN THE SWEET ALMOND
inferredcites →https://doi.org/10.1093/jhered/93.1.77openalex-snapshot
MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs
inferredcites →https://doi.org/10.1093/molbev/msj024openalex-snapshot
Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds
inferredcites →https://doi.org/10.1093/molbev/msw242openalex-snapshot
Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication
inferredcites →https://doi.org/10.1093/nar/25.5.955openalex-snapshot
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkl091openalex-snapshot
M-Coffee: combining multiple sequence alignment methods with T-Coffee
inferredcites →https://doi.org/10.1093/nar/gkl200openalex-snapshot
AUGUSTUS: ab initio prediction of alternative transcripts
inferredcites →https://doi.org/10.1093/nar/gkm260openalex-snapshot
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments
inferredcites →https://doi.org/10.1093/nar/gkm321openalex-snapshot
KAAS: an automatic genome annotation and pathway reconstruction server
inferredcites →https://doi.org/10.1093/nar/gkq1109openalex-snapshot
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
inferredcites →https://doi.org/10.1093/nar/gkq1189openalex-snapshot
CDD: a Conserved Domain Database for the functional annotation of proteins
inferredcites →https://doi.org/10.1093/nar/gkq769openalex-snapshot
Allotopic expression of mitochondrial-encoded genes in mammals: achieved goal, undemonstrated mechanism or impossible task?
inferredcites →https://doi.org/10.1093/nar/gkq862openalex-snapshot
MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences
inferredcites →https://doi.org/10.1093/nar/gkr948openalex-snapshot
InterPro in 2011: new developments in the family and domain prediction database
inferredcites →https://doi.org/10.1093/nar/gkr988openalex-snapshot
KEGG for integration and interpretation of large-scale molecular data sets
inferredcites →https://doi.org/10.1093/nar/gks1183openalex-snapshot
PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants
inferredcites →https://doi.org/10.1093/nar/gkt1000openalex-snapshot
P-MITE: a database for plant miniature inverted-repeat transposable elements
inferredcites →https://doi.org/10.1093/nar/gkt1177openalex-snapshot
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
inferredcites →https://doi.org/10.1093/nar/gku1063openalex-snapshot
Rfam 12.0: updates to the RNA families database
inferredcites →https://doi.org/10.1093/nar/gku557openalex-snapshot
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm
inferredcites →https://doi.org/10.1093/nar/gkv1344openalex-snapshot
The Pfam protein families database: towards a more sustainable future
inferredcites →https://doi.org/10.1093/nar/gkw294openalex-snapshot
Redundans: an assembly pipeline for highly heterozygous genomes
inferredcites →https://doi.org/10.1093/sysbio/syq010openalex-snapshot
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
inferredcites →https://doi.org/10.1093/sysbio/syt022openalex-snapshot
PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment
inferredcites →https://doi.org/10.1093/treephys/tpt050openalex-snapshot
The evolution and function of vessel and pit characters with respect to cavitation resistance across 10 Prunus species
inferredcites →https://doi.org/10.1098/rspb.2001.1782openalex-snapshot
Evolution of the angiosperms: calibrating the family tree
inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot
ABySS: A parallel assembler for short read sequence data
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1101/gr.5396706openalex-snapshot
SyMAP: A system for discovering and viewing syntenic regions of FPC maps
inferredcites →https://doi.org/10.1104/pp.110.155119openalex-snapshot
Lignin Biosynthesis and Structure
inferredcites →https://doi.org/10.1104/pp.110.167577openalex-snapshot
Distribution of SUN, OVATE, LC , and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity
inferredcites →https://doi.org/10.1104/pp.18.00922openalex-snapshot
Elucidation of the Amygdalin Pathway Reveals the Metabolic Basis of Bitter and Sweet Almonds (Prunus dulcis)
inferredcites →https://doi.org/10.1111/j.1439-0523.2006.01178.xopenalex-snapshot
Overcoming hybridization barriers in potato
inferredcites →https://doi.org/10.1111/j.1439-0523.2007.01329.xopenalex-snapshot
Mapping major genes and quantitative trait loci controlling agronomic traits in almond
inferredcites →https://doi.org/10.1111/nph.14461openalex-snapshot
Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics
inferredcites →https://doi.org/10.1111/tpj.12283openalex-snapshot
Three distinct mutational mechanisms acting on a single gene underpin the origin of yellow flesh in peach
inferredcites →https://doi.org/10.1111/tpj.14070openalex-snapshot
Insertion of a transposon‐like sequence in the 5′‐flanking region of the YUCCA gene causes the stony hard phenotype
inferredcites →https://doi.org/10.1186/1471-2105-11-24openalex-snapshot
ETE: a python Environment for Tree Exploration
inferredcites →https://doi.org/10.1186/1471-2105-11-431openalex-snapshot
Hidden Markov model speed heuristic and iterative HMM search procedure
inferredcites →https://doi.org/10.1186/1471-2105-15-211openalex-snapshot
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
inferredcites →https://doi.org/10.1186/1471-2105-6-298openalex-snapshot
Kalign – an accurate and fast multiple sequence alignment algorithm
inferredcites →https://doi.org/10.1186/1471-2105-6-31openalex-snapshot
Automated generation of heuristics for biological sequence comparison
inferredcites →https://doi.org/10.1186/1471-2105-6-9openalex-snapshot
GATA: a graphic alignment tool for comparative sequence analysis
inferredcites →https://doi.org/10.1186/1471-2105-8-64openalex-snapshot
Minimus: a fast, lightweight genome assembler
inferredcites →https://doi.org/10.1186/1471-2105-9-18openalex-snapshot
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
inferredcites →https://doi.org/10.1186/gb-2008-9-1-r7openalex-snapshot
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
inferredcites →https://doi.org/10.1186/gb-2008-9-10-235openalex-snapshot
Large-scale assignment of orthology: back to phylogenetics?
inferredcites →https://doi.org/10.1186/s12864-017-3606-9openalex-snapshot
The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity
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A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea
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ALLMAPS: robust scaffold ordering based on multiple maps
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Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
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Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus , a threespine stickleback parasite
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Genome sequence of the olive tree, Olea europaea
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Combined Evidence Annotation of Transposable Elements in Genome Sequences
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Considering Transposable Element Diversification in De Novo Annotation Approaches
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A Unique Mutation in a MYB Gene Cosegregates with the Nectarine Phenotype in Peach
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PASTEC: An Automatic Transposable Element Classification Tool
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InDel markers: An extended marker resource for molecular breeding in chickpea
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Integrated value-chain and risk assessment of Pig-Related Zoonoses in Ghana
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Evolutionary Genomics of Peach and Almond Domestication
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21st Century Approach to Improving Burbank’s ‘Stoneless’ Plum
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Extraction of High-Molecular-Weight Genomic DNA for Long-Read Sequencing of Single Molecules
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Guns, Germs, and Steel: The Fates of Human Societies.
inferredcites →https://doi.org/10.2307/4117045openalex-snapshot
The Anther: Form, Function and Phylogeny
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Addressing the “hardest puzzle in American pomology:” Phylogeny of Prunus sect. Prunocerasus (Rosaceae) based on seven noncoding chloroplast DNA regions
inferredcites →https://doi.org/10.5962/bhl.title.40638openalex-snapshot
The California fruits and how to grow them;
inferredcites →https://doi.org/10.5962/bhl.title.54462openalex-snapshot
The California fruits and how to grow them;
inferredcites →https://doi.org/10.5962/bhl.title.84435openalex-snapshot
The variation of animals and plants under domestication /
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-3-030-30302-0_10openalex-snapshot
Discovery of Quantitative Trait Loci for Nut and Quality Traits in Almond
inferred← citeshttps://doi.org/10.1007/978-3-030-30302-0_2openalex-snapshot
Origin and Domestication of Wild Bitter Almond. Recent Advancements on Almond Bitterness
inferred← citeshttps://doi.org/10.1007/978-3-030-30302-0_8openalex-snapshot
Transcriptional Changes Associated to Flower Bud Dormancy and Flowering in Almond: DNA Sequence Motifs, mRNA Expression, Epigenetic Modifications and Phytohormone Signaling
inferred← citeshttps://doi.org/10.1007/978-3-319-97946-5_8openalex-snapshot
Genomic-Based Breeding for Climate-Smart Peach Varieties
inferred← citeshttps://doi.org/10.1038/s41598-020-67264-3openalex-snapshot
Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Six Almond Species (Prunus spp. L.)
inferred← citeshttps://doi.org/10.1093/g3journal/jkac065openalex-snapshot
Whole-genome sequence and methylome profiling of the almond [ Prunus dulcis (Mill.) D.A. Webb] cultivar ‘Nonpareil’
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