4.7 Article

Comparative chloroplast genome and transcriptome analysis on the ancient genus Isoetes from China

Related references

Note: Only part of the references are listed.
Article Forestry

Structural characterization and comparative analysis of the chloroplast genome ofGinkgo bilobaand other gymnosperms

Xiaoming Yang et al.

Summary: The study of the Ginkgo biloba chloroplast genome revealed high divergence in gene content and organization compared to other gymnosperms, with the two typical IR regions relatively shorter due to the ycf2 gene. Phylogenetic analysis showed G. biloba to be sister to cycads. Overall, the genomic characteristics of G. biloba will be helpful for further research on the taxonomy, species identification, and evolutionary history of gymnosperms.

JOURNAL OF FORESTRY RESEARCH (2021)

Article Plant Sciences

Comprehensive transcriptome analyses of two Oocystis algae provide insights into the adaptation to Qinghai-Tibet Plateau

Zhen-Hua Zhang et al.

Summary: Studying the adaptive strategies of Oocystis algae in the Qinghai-Tibet Plateau revealed positively selected genes associated with antioxidative response, DNA repair mechanisms, translation, and post-translational modifications. Cold-responsive and UV-B-responsive genes were identified, along with transcriptional regulation strategies under stress conditions, shedding light on the adaptive strategies of green algae living in the QTP.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2021)

Article Plant Sciences

Chloroplast genomes of key species shed light on the evolution of the ancient genus Isoetes

Jovani B. S. Pereira et al.

Summary: Phylogenetic analysis and genomic comparison have revealed the deep relationships and recent radiations in Isoetes, while also uncovering the conservation of genomic traits across different clades. These findings contribute to understanding the diversification of Isoetes and provide a better framework for exploring the evolutionary history of the genus.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2021)

Article Multidisciplinary Sciences

Underwater CAM photosynthesis elucidated by Isoetes genome

David Wickell et al.

Summary: Despite the extensive characterization of crassulacean acid metabolism (CAM) in terrestrial angiosperms, little attention has been given to aquatics and early diverging land plants. Here, the authors assemble the genome of Isoetes taiwanensis and investigate the genetic factors driving CAM in this aquatic lycophyte. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, several key differences are identified, including the recruitment of 'bacterial-type' PEPC and diverged circadian control of key CAM pathway genes in Isoetes.

NATURE COMMUNICATIONS (2021)

Article Genetics & Heredity

Transcriptome and Comparative Chloroplast Genome Analysis of Vincetoxicum versicolor: Insights Into Molecular Evolution and Phylogenetic Implication

Xiaolei Yu et al.

Summary: The study assembled and functionally annotated the transcriptome and chloroplast genome of V. versicolor, revealing abundant transcription factor families and highly conserved chloroplast genomes. Phylogenetic analysis supported the separate genera status of Vincetoxicum and Cynanchum.

FRONTIERS IN GENETICS (2021)

Review Plant Sciences

Evolutionary origin of species diversity on the Qinghai-Tibet Plateau

Kang-Shan Mao et al.

Summary: The Qinghai-Tibet Plateau has exceptional species diversity, with various studies exploring the reasons for species formation in the region and the environmental adaptation of high-altitude species. Despite disputes, research has shown that the uplift of the plateau is heterogeneous and supported by abundant fossils for an asynchronous upheaval model. Genomic evidence has identified numerous candidate genes for high-altitude adaptation.

JOURNAL OF SYSTEMATICS AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

Plastome-based phylogenomics elucidate relationships in rare Isoetes species groups from the Neotropics

Jovani B. S. Pereira et al.

Summary: The study investigated the phylogenetic and biogeographic patterns of the genus Isoetes in the Neotropics, using plastome and rDNA sequences to analyze potential sources of phylogenetic incongruence and detail the populations of Isoetes in the Neotropics. By estimating node ages and ancestral range distributions, the study revealed the timing and geographical processes of evolution within the genus in the region.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2021)

Article Ecology

Variation of the adaptive substitution rate between species and within genomes

Ana Filipa Moutinho et al.

EVOLUTIONARY ECOLOGY (2020)

Article Biotechnology & Applied Microbiology

Evolutionary dynamics of chloroplast genomes in subfamily Aroideae (Araceae)

Claudia L. Henriquez et al.

GENOMICS (2020)

Article Multidisciplinary Sciences

Phylogenomics indicates the living fossilIsoetesdiversified in the Cenozoic

Daniel Wood et al.

PLOS ONE (2020)

Article Multidisciplinary Sciences

Origin and adaptation to high altitude of Tibetan semi-wild wheat

Weilong Guo et al.

NATURE COMMUNICATIONS (2020)

Article Genetics & Heredity

Chloroplot: An Online Program for the Versatile Plotting of Organelle Genomes

Shuyu Zheng et al.

FRONTIERS IN GENETICS (2020)

Article Plant Sciences

Genetic Diversity of Phyllanthus emblica From Two Different Climate Type Areas

Xiongfang Liu et al.

FRONTIERS IN PLANT SCIENCE (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 Plant Sciences

The hornwort genome and early land plant evolution

Jian Zhang et al.

NATURE PLANTS (2020)

Article Multidisciplinary Sciences

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

Ticao Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Multidisciplinary Sciences

Comparative transcriptomics of 3 high-altitude passerine birds and their low-altitude relatives

Yan Hao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Chloroplast genome analysis of box-ironbark Eucalyptus

Khawla G. Alwadani et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2019)

Review Plant Sciences

New Light on Chloroplast Redox Regulation: Molecular Mechanism of Protein Thiol Oxidation

Keisuke Yoshida et al.

FRONTIERS IN PLANT SCIENCE (2019)

Article Biochemical Research Methods

IRscope: an online program to visualize the junction sites of chloroplast genomes

Ali Amiryousefi et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Mt-rps3 is an ancient gene which provides insight into the evolution of fungal mitochondrial genomes

Artemis Korovesi et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Plastome organization, genome-based phylogeny and evolution of plastid genes in Podophylloideae (Berberidaceae)

Wen-Qing Ye et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

RNF138-mediated ubiquitination of rpS3 is required for resistance of glioblastoma cells to radiation-induced apoptosis

Wanyeon Kim et al.

EXPERIMENTAL AND MOLECULAR MEDICINE (2018)

Review Genetics & Heredity

RNA Editing and Its Molecular Mechanism in Plant Organelles

Mizuho Ichinose et al.

GENES (2017)

Article Biochemistry & Molecular Biology

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Jaime Huerta-Cepas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

GeSeq - versatile and accurate annotation of organelle genomes

Michael Tillich et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Rps3/uS3 promotes mRNA binding at the 40S ribosome entry channel and stabilizes preinitiation complexes at start codons

Jinsheng Dong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Plant Sciences

Origin and biogeography of the ancient genus Isoetes with focus on the Neotropics

Jovani B. S. Pereira et al.

BOTANICAL JOURNAL OF THE LINNEAN SOCIETY (2017)

Article Plant Sciences

DISENTANGLING THE PHYLOGENY OF ISOETES (ISOETALES), USING NUCLEAR AND PLASTID DATA

Eva Larsen et al.

INTERNATIONAL JOURNAL OF PLANT SCIENCES (2016)

Article Multidisciplinary Sciences

Large-scale identification of human protein function using topological features of interaction network

Zhanchao Li et al.

SCIENTIFIC REPORTS (2016)

Article Biochemical Research Methods

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis

BIOINFORMATICS (2014)

Review Genetics & Heredity

RNA Editing in Plants and Its Evolution

Mizuki Takenaka et al.

ANNUAL REVIEW OF GENETICS, VOL 47 (2013)

Article Biochemistry & Molecular Biology

Nuclear DYW-Type PPR Gene Families Diversify with Increasing RNA Editing Frequencies in Liverwort and Moss Mitochondria

Mareike Ruedinger et al.

JOURNAL OF MOLECULAR EVOLUTION (2012)

Article Evolutionary Biology

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Fredrik Ronquist et al.

SYSTEMATIC BIOLOGY (2012)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Review Plant Sciences

Chloroplast genomes of photosynthetic eukaryotes

Beverley R. Green

PLANT JOURNAL (2011)

Review Cell Biology

Organellar RNA editing

Anne-Laure Chateigner-Boutin et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2011)

Review Plant Sciences

Chloroplast RNA Metabolism

David B. Stern et al.

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 61 (2010)

Article Biochemical Research Methods

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

Heng Li et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal

Mareike Ruedinger et al.

MOLECULAR GENETICS AND GENOMICS (2009)

Article Biochemistry & Molecular Biology

Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts

Mareike Ruedinger et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Biochemical Research Methods

Choosing BLAST options for better detection of orthologs as reciprocal best hits

Gabriel Moreno-Hagelsieb et al.

BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

PAML 4: Phylogenetic analysis by maximum likelihood

Ziheng Yang

MOLECULAR BIOLOGY AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

The evolution of chloroplast RNA editing

Michael Tillich et al.

MOLECULAR BIOLOGY AND EVOLUTION (2006)

Article Biochemistry & Molecular Biology

The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs

P Schattner et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins

S Moelbert et al.

PROTEIN SCIENCE (2004)

Article Biochemistry & Molecular Biology

MUSCLE: multiple sequence alignment with high accuracy and high throughput

RC Edgar

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

VISTA: computational tools for comparative genomics

KA Frazer et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

RNA editing in hornwort chloroplasts makes more than half the genes functional

M Kugita et al.

NUCLEIC ACIDS RESEARCH (2003)