Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes

The whole chloroplast genome of wild rice (Oryza australiensis)

(2014) Zhiqiang Wu et al.   Mitochondrial DNA

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe

(2014) Christopher P. Middleton et al.   PLoS One

Accurate indel prediction using paired-end short reads

(2013) Dominik Grimm et al.   BMC GENOMICS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chloroplast genome analysis of Australian eucalypts – Eucalyptus, Corymbia, Angophora, Allosyncarpia and Stockwellia (Myrtaceae)

(2013) Michael J. Bayly et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Multilocus estimation of divergence times and ancestral effective population sizes ofOryzaspecies and implications for the rapid diversification of the genus

(2013) Xin-Hui Zou et al.   NEW PHYTOLOGIST

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

(2012) P. Roxanne Steele et al.   AMERICAN JOURNAL OF BOTANY

Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees

(2012) M. P. Mahmud et al.   BIOINFORMATICS

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

Current challenges in de novo plant genome sequencing and assembly

(2012) Michael C Schatz et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Stable chloroplast transformation of immature scutella and inflorescences in wheat (Triticum aestivum L.)

(2011) C. Cui et al.   ACTA BIOCHIMICA ET BIOPHYSICA SINICA

The phylogeny of the BEP clade in grasses revisited: Evidence from the whole-genome sequences of chloroplasts

(2011) Zhi-Qiang Wu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The chloroplast transformation toolbox: selectable markers and marker removal

(2011) Anil Day et al.   PLANT BIOTECHNOLOGY JOURNAL

The evolution of the plastid chromosome in land plants: gene content, gene order, gene function

(2011) Susann Wicke et al.   PLANT MOLECULAR BIOLOGY

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

(2011) Wenyu Zhang et al.   PLoS One

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

(2011) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice

(2011) Daniel L. E. Waters et al.   Ecology and Evolution

Microindel detection in short-read sequence data

(2010) Peter Krawitz et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Nuclear and plastid genetic engineering of plants: Comparison of opportunities and challenges

(2010) Benjamin Meyers et al.   BIOTECHNOLOGY ADVANCES

Genome assembly quality: Assessment and improvement using the neutral indel model

(2010) S. Meader et al.   GENOME RESEARCH

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Chloroplast genome sequences from total DNA for plant identification

(2010) Catherine J. Nock et al.   PLANT BIOTECHNOLOGY JOURNAL

Chloroplast transformation of rapeseed (Brassica napus) by particle bombardment of cotyledons

(2010) Lin Cheng et al.   PLANT CELL REPORTS

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) P. Librado et al.   BIOINFORMATICS

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

(2009) Matthew Parks et al.   BMC BIOLOGY

A molecular phylogeny and a revised classification of tribe Lepisoreae (Polypodiaceae) based on an analysis of four plastid DNA regions

(2009) LI WANG et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogeny of the paleotropical fern genus Lepisorus (Polypodiaceae, Polypodiopsida) inferred from four chloroplast DNA regions

(2009) Li Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research

(2009) Bao-Rong Lu et al.   Progress in Natural Science-Materials International

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

Insertion-deletion polymorphisms (indels) as genetic markers in natural populations

(2008) Ülo Väli et al.   BMC GENETICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Botanical identities

(2008) Heidi Ledford   NATURE

Analysis of 142 genes resolves the rapid diversification of the rice genus

(2008) Xin-Hui Zou et al.   GENOME BIOLOGY

Genome assembly forensics: finding the elusive mis-assembly

(2008) Adam M Phillippy et al.   GENOME BIOLOGY