Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications

CPGView : A package for visualizing detailed chloroplast genome structures

(2023) Shengyu Liu et al.   Molecular Ecology Resources

Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution

(2023) Shuo Zhang et al.   BMC PLANT BIOLOGY

Assembly of the Complete Mitochondrial Genome of Pereskia aculeata Revealed That Two Pairs of Repetitive Elements Mediated the Recombination of the Genome

(2023) Xue Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Characterisation of the complete mitochondrial genome of Taraxacum mongolicum revealed five repeat-mediated recombinations

(2023) Mei Jiang et al.   PLANT CELL REPORTS

Complete mitochondrial genomes of three Mangifera species, their genomic structure and gene transfer from chloroplast genomes

(2022) Yingfeng Niu et al.   BMC GENOMICS

Fragaria mitogenomes evolve rapidly in structure but slowly in sequence and incur frequent multinucleotide mutations mediated by microinversions

(2022) Weishu Fan et al.   NEW PHYTOLOGIST

Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii

(2022) Changwei Bi et al.   Frontiers in Plant Science

Metabolism and Signaling of Plant Mitochondria in Adaptation to Environmental Stresses

(2022) Pedro Barreto et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification

(2022) Nan Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of mitochondrial simple sequence repeat markers to simultaneously distinguish cytoplasmic male sterile sources in cotton

(2022) Yongqi Li et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

(2021) Patricia P Chan et al.   NUCLEIC ACIDS RESEARCH

Plant Mitochondria – Past, present and future

(2021) Ian Max Møller et al.   PLANT JOURNAL

A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis

(2021) Jian-ye Chen et al.   Horticulture Research

Underutilized plants of the Cactaceae family: Nutritional aspects and technological applications

(2021) Fábio Fernandes de Araújo et al.   FOOD CHEMISTRY

Betalain plant sources, biosynthesis, extraction, stability enhancement methods, bioactivity, and applications

(2021) Juan Pablo Carreón-Hidalgo et al.   FOOD RESEARCH INTERNATIONAL

RNA Editing and Its Roles in Plant Organelles

(2021) Wei Hao et al.   Frontiers in Genetics

DNA Repair and the Stability of the Plant Mitochondrial Genome

(2020) Nicolas Chevigny et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic architectural variation of plant mitochondria—A review of multichromosomal structuring

(2020) Zhi‐Qiang Wu et al.   Journal of Systematics and Evolution

Pitaya, an Attractive Alternative Crop for Mediterranean Region

(2020) Alice Trivellini et al.   Agronomy-Basel

Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria

(2020) Lu Fan et al.   Nature Ecology & Evolution

HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis

(2020) Tiziano Flati et al.   BMC BIOINFORMATICS

Siberian larch (Larix sibirica Ledeb.) mitochondrial genome assembled using both short and long nucleotide sequence reads is currently the largest known mitogenome

(2020) Yuliya A. Putintseva et al.   BMC GENOMICS

Horizontal gene transfers dominate the functional mitochondrial gene space of a holoparasitic plant

(2020) Laura E. Garcia et al.   NEW PHYTOLOGIST

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

CPGAVAS2, an integrated plastome sequence annotator and analyzer

(2019) Linchun Shi et al.   NUCLEIC ACIDS RESEARCH

A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour

(2019) Liyi Zhang et al.   Nature Communications

Diversity in genome size and GC content shows adaptive potential in orchids and is closely linked to partial endoreplication, plant life-history traits and climatic conditions

(2019) Pavel Trávníček et al.   NEW PHYTOLOGIST

PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies

(2019) Dong Zhang et al.   Molecular Ecology Resources

A novel maize dwarf mutant generated by Ty1-copia LTR-retrotransposon insertion in Brachytic2 after spaceflight

(2019) Chuan Li et al.   PLANT CELL REPORTS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Genus Hylocereus : Beneficial phytochemicals, nutritional importance, and biological relevance-A review

(2018) Sabrin Ragab Mohamed Ibrahim et al.   JOURNAL OF FOOD BIOCHEMISTRY

Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria

(2018) Alejandro A. Edera et al.   PLANT MOLECULAR BIOLOGY

Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution

(2018) Emily L. Wynn et al.   G3-Genes Genomes Genetics

Archaea and the origin of eukaryotes

(2017) Laura Eme et al.   NATURE REVIEWS MICROBIOLOGY

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Genetic diversity among germplasms of Pitaya based on SSR markers

(2017) Limei Pan et al.   SCIENTIA HORTICULTURAE

A phylogenetic framework for the Hylocereeae (Cactaceae) and implications for the circumscription of the genera

(2017) NADJA KOROTKOVA et al.   Phytotaxa

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

(2017) Yuxin Chen et al.   GigaScience

The role of mitochondria in plant development and stress tolerance

(2016) Katie L. Liberatore et al.   FREE RADICAL BIOLOGY AND MEDICINE

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

High speed BLASTN: an accelerated MegaBLAST search tool

(2015) Ying Chen et al.   NUCLEIC ACIDS RESEARCH

Miniaturized mitogenome of the parasitic plantViscum scurruloideumis extremely divergent and dynamic and has lost allnadgenes

(2015) Elizabeth Skippington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes

(2014) Jeffrey L. Bennetzen et al.   Annual Review of Plant Biology

RNA Editing in Plants and Its Evolution

(2013) Mizuki Takenaka et al.   Annual Review of Genetics

RCircos: an R package for Circos 2D track plots

(2013) Hongen Zhang et al.   BMC BIOINFORMATICS

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

(2013) Aaron O Richardson et al.   BMC BIOLOGY

Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes

(2013) David E. McCauley   NEW PHYTOLOGIST

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Intraspecific variation in mitochondrial genome sequence, structure, and gene content inSilene vulgaris, an angiosperm with pervasive cytoplasmic male sterility

(2012) Daniel B. Sloan et al.   NEW PHYTOLOGIST

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Genetic mapping of paternal sorting of mitochondria in cucumber

(2012) Claudia I. Calderon et al.   THEORETICAL AND APPLIED GENETICS

Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes

(2011) Jeffrey P Mower et al.   BMC BIOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

Paternal inheritance of mitochondria in Chlamydomonas

(2010) Soichi Nakamura   JOURNAL OF PLANT RESEARCH

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE

Angiosperm mitochondrial genomes and mutations

(2007) Tomohiko Kubo et al.   MITOCHONDRION