Chloroplast Sequence of Treegourd (Crescentia cujete, Bignoniaceae) to Study Phylogeography and Domestication

Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?

(2015) N. Scarcelli et al.   Molecular Ecology Resources

Complete Chloroplast Genome of Tanaecium tetragonolobum: The First Bignoniaceae Plastome

(2015) Alison Gonçalves Nazareno et al.   PLoS One

Cost-effective enrichment hybridization capture of chloroplast genomes at deep multiplexing levels for population genetics and phylogeography studies

(2014) Cédric Mariac et al.   Molecular Ecology Resources

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

Complete Chloroplast Genome Sequence of Holoparasite Cistanche deserticola (Orobanchaceae) Reveals Gene Loss and Horizontal Gene Transfer from Its Host Haloxylon ammodendron (Chenopodiaceae)

(2013) Xi Li et al.   PLoS One

Round and large: morphological and genetic consequences of artificial selection on the gourd tree Crescentia cujete by the Maya of the Yucatan Peninsula, Mexico

(2012) Xitlali Aguirre-Dugua et al.   ANNALS OF BOTANY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Diversity of the calabash tree (Crescentia cujete L.) in Colombia

(2009) Johanna Arango-Ulloa et al.   AGROFORESTRY SYSTEMS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots

(2008) Rui-Jiang Wang et al.   BMC EVOLUTIONARY BIOLOGY