4.7 Article

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

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Genetics & Heredity

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

Yongqi Li et al.

Summary: The deleterious effects of sterile genes or cytoplasms on anther development and main economy traits are hindrances to the large-scale application of three-line hybrids in cotton. This study created four isonuclear-alloplasmic cotton male sterile lines and identified mitochondrial DNA diversities using mitochondrial simple sequence repeat (mtSSR) markers. The mtSSR59 marker effectively classified the CMS-D2, CMS-(AD)1, and CMS-(AD)2 into one category and the CMS-D8 into another category. The marker was also successfully used in marker-assisted selection (MAS) for breeding new male sterile lines and precise differentiation of different CMS-based three-line and conventional cotton hybrids.

FUNCTIONAL & INTEGRATIVE GENOMICS (2023)

Article Biochemistry & Molecular Biology

CPGView: A package for visualizing detailed chloroplast genome structures

Shengyu Liu et al.

Summary: CPGView is a software package that can draw distribution maps of chloroplast genomes and identify annotation errors. It can draw maps of genes, variable sites, and repetitive sequences, adjust exon-intron boundary positions, and plot the structure of specific genes. The software has shown high accuracy and reliability in testing and will become an important tool for studying chloroplast genome structure.

MOLECULAR ECOLOGY RESOURCES (2023)

Article Plant Sciences

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

Shuo Zhang et al.

Summary: This study assembled seven sorghum mitochondrial and plastid genomes and revealed complex structures of mitochondrial genomes. The findings provide an important foundation for future research and improvement of sorghum traits.

BMC PLANT BIOLOGY (2023)

Article Biochemistry & Molecular Biology

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

Xue Zhang et al.

Summary: In this study, the mitochondrial genome of Pereskia aculeata was sequenced and analyzed. The circular mitogenome was found to be 515,187 bp in length, with a GC content of 44.05%. It contains 52 unique genes, including protein-coding genes, tRNA genes, and rRNA genes. The research also identified SSRs and dispersed repeats in the mitogenome, as well as homologous fragments between the mitochondrial genome and the chloroplast genome.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

Article Plant Sciences

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

Mei Jiang et al.

Summary: We reported the first mitochondrial genome of Taraxacum mongolicum, in which five pairs of repetitive sequences were validated to mediate recombination, resulting in multiple conformations of the genome. This genome can provide crucial information for molecular breeding of T. mongolicum and serve as a reference genome for other species of the genus Taraxacum.

PLANT CELL REPORTS (2023)

Review Plant Sciences

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

Zhi-Qiang Wu et al.

Summary: Since their origin from alpha-Proteobacteria, mitochondrial genomes in plants have undergone divergent evolutionary trajectories, leading to unique features such as complex genomic arrangements and varying sizes. However, research on plant mitochondrial genomes is still limited, especially on the inheritance patterns and architectural variation of multichromosomal structures at different taxonomic levels.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2022)

Article Biotechnology & Applied Microbiology

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

Yingfeng Niu et al.

Summary: Among the Mangifera species, mango (Mangifera indica) is an important commercial fruit crop. This study sequenced and compared the mitochondrial genomes of three Mangifera species, and found that the gene content and the codon usage pattern of Mangifera mitochondrial genomes is similar across various species. Gene transfer from the chloroplast genome to the mitochondrial genome was also identified.

BMC GENOMICS (2022)

Article Food Science & Technology

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

Juan Pablo Carreon-Hidalgo et al.

Summary: Betalains are plant pigments primarily used as food dyes, but they are prone to instability due to environmental factors. Various extraction methods and stabilization techniques have been developed to increase shelf life, as well as diverse biological properties that make betalains suitable for applications in various industries such as food, cosmetics, textiles, and solar cells.

FOOD RESEARCH INTERNATIONAL (2022)

Article Plant Sciences

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

Weishu Fan et al.

Summary: Plant mitochondrial DNA evolves rapidly in structure but slowly in sequence. The noncoding portions of plant mitogenomes are not homologous among species, which raises questions about the rate and spectrum of mutations in noncoding regions. The study shows that plant mitogenomes have low point mutations genome-wide but exceptionally high structural variations, supporting a gain-and-loss model for the rapid loss of homology among plant mitogenomes.

NEW PHYTOLOGIST (2022)

Article Plant Sciences

Deciphering the Multi-Chromosomal Mitochondrial Genome of Populus simonii

Changwei Bi et al.

Summary: This study focuses on the mitochondrial genome of Populus simonii and successfully assembles the complete genome sequence. The study reveals the differences between P. simonii and other Populus species in terms of mitochondrial genome. Additionally, the study also finds that Populus mitochondrial genomes have stable repeat sequences.

FRONTIERS IN PLANT SCIENCE (2022)

Review Biochemistry & Molecular Biology

Metabolism and Signaling of Plant Mitochondria in Adaptation to Environmental Stresses

Pedro Barreto et al.

Summary: The interaction between mitochondria and cellular components differs between plants and mammals. In plants, proteins like AOXs and UCPs allow bypassing of canonical oxidative phosphorylation (OXPHOS) and are linked with new mechanisms of mitochondrial retrograde signaling. This retrograde signaling affects plant responses to abiotic stress and chloroplast function. Mitochondrial inner membrane transporters mediate communication with other organelles. Utilizing mitochondrial metabolism can enhance crop resilience to environmental stresses. Brazilian research groups have made significant contributions to mitochondrial metabolism and signaling.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Multidisciplinary Sciences

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

Nan Wang et al.

Summary: This study investigates the evolutionary conflicts between cytoplasmic and nuclear genomes in citrus plants. The researchers constructed a pan-mitogenome and identified chimeric open reading frames generated by extensive structural variations. They also analyzed the variations in the nuclear, mitochondrial, and chloroplast genomes of 184 citrus accessions. The findings suggest discordant interactions between the cytoplasmic and nuclear genomes due to mutation rate and levels of heteroplasmy. The study provides important implications for genetics and breeding in citrus plants.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

Article Plant Sciences

Transcriptomics-based identification and characterization of genes related to sugar metabolism in 'Hongshuijing' pitaya

Zhike Zhang et al.

Summary: This study investigated the changes in sugar content and sugar-metabolizing enzymes in different sections of pitaya fruit during various developmental phases. Genes related to sugar metabolism were screened using transcriptome analysis. The results revealed that sugar accumulation varied in different sections of pitaya fruit, and vacuolar acid invertase and sucrose synthase played crucial roles in sugar metabolism. HpVAI1 was found to have a key regulatory role in fruit development. These findings provide important information for improving fruit quality and breeding new pitaya cultivars.

HORTICULTURAL PLANT JOURNAL (2022)

Article Plant Sciences

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

Laura E. Garcia et al.

Summary: The holoparasite Lophophytum has undergone extensive functional replacement of native genes by foreign genes in its mitochondrial DNA, with most foreign genes being highly transcribed, accurately spliced, and efficiently RNA edited. There is no evidence of functional gene transfer to the nucleus or loss of mitochondrial functions in Lophophytum. This raises questions about the population-genetic and molecular mechanisms underlying such a high level of foreign gene takeover.

NEW PHYTOLOGIST (2021)

Review Chemistry, Applied

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

Fabio Fernandes de Araujo et al.

Summary: Representatives of the Cactaceae family are good sources of nutrients and phytochemicals, showing potential in preventing diseases and in various technological applications. They have great potential in food production and other technological domains.

FOOD CHEMISTRY (2021)

Review Genetics & Heredity

RNA Editing and Its Roles in Plant Organelles

Wei Hao et al.

Summary: RNA editing serves as a vital supplement to the central dogma by producing genetic information different from DNA templates. C-to-U conversion is the main type of RNA editing in plant organelles, with various factors and mechanisms involved. Deep sequencing has revealed numerous RNA editing events in plant organelles, playing essential roles in plant development and stress responses.

FRONTIERS IN GENETICS (2021)

Article Biochemistry & Molecular Biology

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

Patricia P. Chan et al.

Summary: tRNAscan-SE, a tool for predicting transfer RNA genes, has been widely used for over twenty years. Recent updates have greatly improved its ability to identify and classify tRNAs by creating nearly one hundred specialized isotype- and Glade-specific models.

NUCLEIC ACIDS RESEARCH (2021)

Review Plant Sciences

Plant mitochondria - past, present and future

Ian Max Moller et al.

Summary: The study of plant mitochondria began in the 1950s, focusing on establishing basic properties and unique characteristics compared to mammalian mitochondria. With advancements in molecular biology and genomics, further unique features were discovered, including the large size of plant mtDNA, unique mRNA maturation process, and a large proteome with many unique proteins.

PLANT JOURNAL (2021)

Article Plant Sciences

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

Jian-ye Chen et al.

Summary: The genome sequencing of pitaya revealed a whole-genome triplication and recent whole-genome duplication, providing a valuable resource for molecular breeding programs and shedding new light on the regulation of betalain biosynthesis in edible fruits.

HORTICULTURE RESEARCH (2021)

Review Biochemistry & Molecular Biology

DNA Repair and the Stability of the Plant Mitochondrial Genome

Nicolas Chevigny et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Article Biochemistry & Molecular Biology

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

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Agronomy

Pitaya, an Attractive Alternative Crop for Mediterranean Region

Alice Trivellini et al.

AGRONOMY-BASEL (2020)

Article Biochemical Research Methods

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

Tiziano Flati et al.

BMC BIOINFORMATICS (2020)

Article Biotechnology & Applied Microbiology

GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes

Jian-Jun Jin et al.

GENOME BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

CPGAVAS2, an integrated plastome sequence annotator and analyzer

Linchun Shi et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

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

Liyi Zhang et al.

NATURE COMMUNICATIONS (2019)

Article Genetics & Heredity

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

Emily L. Wynn et al.

G3-GENES GENOMES GENETICS (2019)

Article Biochemical Research Methods

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Correction Microbiology

Archaea and the origin of eukaryotes (vol 15, pg 711, 2017)

Laura Eme et al.

NATURE REVIEWS MICROBIOLOGY (2018)

Article Biochemical Research Methods

NanoPack: visualizing and processing long-read sequencing data

Wouter De Coster et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen et al.

BIOINFORMATICS (2018)

Review Biochemistry & Molecular Biology

Genus Hylocereus: Beneficial phytochemicals, nutritional importance, and biological relevanceA review

Sabrin Ragab Mohamed Ibrahim et al.

JOURNAL OF FOOD BIOCHEMISTRY (2018)

Article Biochemistry & Molecular Biology

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

Alejandro A. Edera et al.

PLANT MOLECULAR BIOLOGY (2018)

Article Biochemistry & Molecular Biology

GeSeq - versatile and accurate annotation of organelle genomes

Michael Tillich et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Horticulture

Genetic diversity among germplasms of Pitaya based on SSR markers

Limei Pan et al.

SCIENTIA HORTICULTURAE (2017)

Article Biochemical Research Methods

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

Ryan R. Wick et al.

PLOS COMPUTATIONAL BIOLOGY (2017)

Article Biochemical Research Methods

MISA-web: a web server for microsatellite prediction

Sebastian Beier et al.

BIOINFORMATICS (2017)

Review Biochemistry & Molecular Biology

The role of mitochondria in plant development and stress tolerance

Katie L. Liberatore et al.

FREE RADICAL BIOLOGY AND MEDICINE (2016)

Article Biochemistry & Molecular Biology

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Biochemical Research Methods

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

Ryan R. Wick et al.

BIOINFORMATICS (2015)

Article Biochemistry & Molecular Biology

High speed BLASTN: an accelerated MegaBLAST search tool

Ying Chen et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes

Elizabeth Skippington et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Review Plant Sciences

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

Jeffrey L. Bennetzen et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 65 (2014)

Review Genetics & Heredity

RNA Editing in Plants and Its Evolution

Mizuki Takenaka et al.

ANNUAL REVIEW OF GENETICS, VOL 47 (2013)

Article Biochemical Research Methods

RCircos: an R package for Circos 2D track plots

Hongen Zhang et al.

BMC BIOINFORMATICS (2013)

Review Genetics & Heredity

How important are transposons for plant evolution?

Damon Lisch

NATURE REVIEWS GENETICS (2013)

Article Biotechnology & Applied Microbiology

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

Daehwan Kim et al.

GENOME BIOLOGY (2013)

Article Biochemistry & Molecular Biology

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

Yupeng Wang et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Agronomy

Genetic mapping of paternal sorting of mitochondria in cucumber

Claudia I. Calderon et al.

THEORETICAL AND APPLIED GENETICS (2012)

Article Biochemical Research Methods

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

Heng Li et al.

BIOINFORMATICS (2010)

Article Plant Sciences

Paternal inheritance of mitochondria in Chlamydomonas

Soichi Nakamura

JOURNAL OF PLANT RESEARCH (2010)

Article Cell Biology

Angiosperm mitochondrial genomes and mutations

Tornohiko Kubo et al.

MITOCHONDRION (2008)

Review Genetics & Heredity

Horizontal gene transfer in eukaryotic evolution

Patrick J. Keeling et al.

NATURE REVIEWS GENETICS (2008)

Review Biochemistry & Molecular Biology

Evolution of mitochondrial gene content: gene loss and transfer to the nucleus

KL Adams et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)

Article Biochemistry & Molecular Biology

REPuter: the manifold applications of repeat analysis on a genomic scale

S Kurtz et al.

NUCLEIC ACIDS RESEARCH (2001)