CPGView: A package for visualizing detailed chloroplast genome structures

S Liu, Y Ni, J Li, X Zhang, H Yang… - Molecular ecology …, 2023 - Wiley Online Library
Chloroplast genomes have been widely used in studying plant phylogeny and evolution.
Several chloroplast genome visualization tools have been developed to display the …

OrganellarGenomeDRAW (OGDRAW) version 1.3. 1: expanded toolkit for the graphical visualization of organellar genomes

S Greiner, P Lehwark, R Bock - Nucleic acids research, 2019 - academic.oup.com
Organellar (plastid and mitochondrial) genomes play an important role in resolving
phylogenetic relationships, and next-generation sequencing technologies have led to a …

CPGAVAS2, an integrated plastome sequence annotator and analyzer

L Shi, H Chen, M Jiang, L Wang, X Wu… - Nucleic acids …, 2019 - academic.oup.com
We previously developed a web server CPGAVAS for annotation, visualization and
GenBank submission of plastome sequences. Here, we upgrade the server into CPGAVAS2 …

[HTML][HTML] PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

XJ Qu, MJ Moore, DZ Li, TS Yi - Plant Methods, 2019 - Springer
Background Plastome (plastid genome) sequences provide valuable information for
understanding the phylogenetic relationships and evolutionary history of plants. Although …

GeSeq–versatile and accurate annotation of organelle genomes

M Tillich, P Lehwark, T Pellizzer… - Nucleic acids …, 2017 - academic.oup.com
We have developed the web application GeSeq (https://chlorobox. mpimp-golm. mpg.
de/geseq. html) for the rapid and accurate annotation of organellar genome sequences, in …

From barcodes to genomes: extending the concept of DNA barcoding

E Coissac, PM Hollingsworth, S Lavergne, P Taberlet - 2016 - Wiley Online Library
DNA barcoding has had a major impact on biodiversity science. The elegant simplicity of
establishing massive scale databases for a few barcode loci is continuing to change our …

Plann: a command‐line application for annotating plastome sequences

DI Huang, QCB Cronk - Applications in plant sciences, 2015 - Wiley Online Library
Premise of the study: Plann automates the process of annotating a plastome sequence in
GenBank format for either downstream processing or for GenBank submission by annotating …

[HTML][HTML] The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

JL Olsen, P Rouzé, B Verhelst, YC Lin, T Bayer… - Nature, 2016 - nature.com
Seagrasses colonized the sea on at least three independent occasions to form the basis of
one of the most productive and widespread coastal ecosystems on the planet. Here we …

De novo assembly of a Chinese soybean genome

Y Shen, J Liu, H Geng, J Zhang, Y Liu, H Zhang… - Science China Life …, 2018 - Springer
Soybean was domesticated in China and has become one of the most important oilseed
crops. Due to bottlenecks in their introduction and dissemination, soybeans from different …

What can we do with 1000 plastid genomes?

J Tonti‐Filippini, PG Nevill, K Dixon, I Small - The Plant Journal, 2017 - Wiley Online Library
The plastid genome of plants is the smallest and most gene‐rich of the three genomes in
each cell and the one generally present in the highest copy number. As a result, obtaining …