Comparative analysis of chloroplast genomes of cultivars and wild species of sweetpotato (Ipomoea batatas [L.] Lam)

Comparative chloroplast genomics of the genus Taxodium

(2020) Hao Duan et al.   BMC GENOMICS

IbBBX24 Promotes the Jasmonic Acid Pathway and Enhances Fusarium Wilt Resistance in Sweet Potato

(2020) Huan Zhang et al.   PLANT CELL

Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato

(2020) Lei Zhang et al.   Horticulture Research

Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes

(2020) Xu Zhang et al.   BMC PLANT BIOLOGY

A Defense Pathway Linking Plasma Membrane and Chloroplasts and Co-opted by Pathogens

(2020) Laura Medina-Puche et al.   CELL

Synthetic conversion of leaf chloroplasts into carotenoid-rich plastids reveals mechanistic basis of natural chromoplast development

(2020) Briardo Llorente et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A systematic comparison of eight new plastome sequences from Ipomoea L

(2019) Jianying Sun et al.   PeerJ

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development

(2019) Ming Li et al.   BMC PLANT BIOLOGY

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

(2019) Stephan Greiner et al.   NUCLEIC ACIDS RESEARCH

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Current status in whole genome sequencing and analysis of Ipomoea spp.

(2019) Sachiko Isobe et al.   PLANT CELL REPORTS

Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species

(2019) Mahmoud Magdy et al.   Horticulture Research

OUP accepted manuscript

(2018)   BIOINFORMATICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Genetic Diversity and Population Structure of the USDA Sweetpotato (Ipomoea batatas) Germplasm Collections Using GBSpoly

(2018) Phillip A. Wadl et al.   Frontiers in Plant Science

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

(2018) Shan Wu et al.   Nature Communications

Ycf1/Tic214 Is Not Essential for the Accumulation of Plastid Proteins

(2017) Bettina Bölter et al.   Molecular Plant

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing

(2017) Wenjin Su et al.   PLoS One

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

(2016) Atsushi Hoshino et al.   Nature Communications

Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don

(2015) H. Hirakawa et al.   DNA RESEARCH

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

(2015) Jose Carbonell-Caballero et al.   MOLECULAR BIOLOGY AND EVOLUTION

YCF1: A Green TIC: Response to the de Vries et al. Commentary: Figure 1.

(2015) Masato Nakai   PLANT CELL

YCF1: A Green TIC?

(2015) Jan de Vries et al.   PLANT CELL

Molecular diversity and genetic structure of 380 sweetpotato accessions as revealed by SSR markers

(2015) Xin-sun YANG et al.   Journal of Integrative Agriculture

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

AFLP Fingerprinting and Genetic Diversity of Main Sweetpotato Varieties in China

(2012) De-gao LIU et al.   Journal of Integrative Agriculture

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetic diversity in Brazilian sweet potato (Ipomoea batatas (L.) Lam., Solanales, Convolvulaceae) landraces assessed with microsatellite markers

(2008) Elizabeth Ann Veasey et al.   GENETICS AND MOLECULAR BIOLOGY