A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the GenusCitrus

Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation

(2015) Javier Terol et al.   BMC GENOMICS

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication

(2014) G Albert Wu et al.   NATURE BIOTECHNOLOGY

High-Resolution Genomic Analysis of Human Mitochondrial RNA Sequence Variation

(2014) A. Hodgkinson et al.   SCIENCE

Phylogenetic Relationships of Citrus and Its Relatives Based on matK Gene Sequences

(2013) Tshering Penjor et al.   PLoS One

Insights from the Complete Chloroplast Genome into the Evolution of Sesamum indicum L

(2013) Haiyang Zhang et al.   PLoS One

Balanced Gene Losses, Duplications and Intensive Rearrangements Led to an Unusual Regularly Sized Genome in Arbutus unedo Chloroplasts

(2013) Fernando Martínez-Alberola et al.   PLoS One

Complete Chloroplast Genome of Sedum sarmentosum and Chloroplast Genome Evolution in Saxifragales

(2013) Wenpan Dong et al.   PLoS One

A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the ‘true citrus fruit trees’ group (Citrinae, Rutaceae) and the origin of cultivated species

(2012) Andres Garcia-Lor et al.   ANNALS OF BOTANY

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping

(2012) Patrick Ollitrault et al.   BMC GENOMICS

The draft genome of sweet orange (Citrus sinensis)

(2012) Qiang Xu et al.   NATURE GENETICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

Molecular Phylogeny of the “True Citrus Fruit Trees” Group (Aurantioideae, Rutaceae) as Inferred from Chloroplast DNA Sequence

(2011) Zhen-hua LU et al.   Agricultural Sciences in China

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies

(2011) Andrés García-Lor et al.   MOLECULAR GENETICS AND GENOMICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Changes in Rubisco Kinetics during the Evolution of C4 Photosynthesis in Flaveria (Asteraceae) Are Associated with Positive Selection on Genes Encoding the Enzyme

(2010) Maxim V. Kapralov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic relationships of Citrus and its relatives based on rbcL gene sequences

(2010) Tshering Penjor et al.   Tree Genetics & Genomes

New universal mitochondrial PCR markers reveal new information on maternal citrus phylogeny

(2010) Yann Froelicher et al.   Tree Genetics & Genomes

A molecular phylogeny of the orange subfamily(Rutaceae: Aurantioideae) using nine cpDNA sequences

(2009) Randall J. Bayer et al.   AMERICAN JOURNAL OF BOTANY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

Molecular evolution and positive Darwinian selection of the chloroplast maturase matK

(2009) Da Cheng Hao et al.   JOURNAL OF PLANT RESEARCH

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

The age and biogeography of Citrus and the orange subfamily (Rutaceae: Aurantioideae) in Australasia and New Caledonia

(2008) Bernard E. Pfeil et al.   AMERICAN JOURNAL OF BOTANY

Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene

(2008) Per Erixon et al.   PLoS One