4.5 Article

Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex

Related references

Note: Only part of the references are listed.
Review Cell Biology

Zygnematophycean algae: Possible models for cellular and evolutionary biology

Kinuka Ohtaka et al.

Summary: Plant terrestrialization was an important event in the history of Earth. Charophytes, particularly the class Zygnematophyceae, have been extensively studied due to their phylogenetic proximity to land plants. Within Zygnematophyceae, the genera Mougeotia, Penium, and Closterium are representative model organisms for studying chloroplast photorelocation movement, cell wall characteristics, and sexual reproduction, respectively.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2023)

Article Plant Sciences

A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium

Hiroyuki Sekimoto et al.

Summary: This study investigated the mating type determination in Closterium and identified CpMinus1 as the major determinant for mt- phenotype. Functional analysis showed that CpMinus1 is a divergent transcription factor specifically expressed during gamete differentiation. Introduction of CpMinus1 into mt+ strains converted them to mt- phenotype, while CpMinus1-knockout mt- strains exhibited the mt+ phenotype.

NEW PHYTOLOGIST (2023)

Review Cell Biology

Zygnematophycean algae: Possible models for cellular and evolutionary biology

Kinuka Ohtaka et al.

Summary: Plant terrestrialization was a critical event in Earth's history, and charophytes, especially Zygnematophyceae, have been studied extensively for their phylogenetic relationship with land plants. Zygnematophyceae exhibit isogamous conjugation during sexual reproduction, a characteristic feature of this algal lineage. This study highlights three representative model organisms of Zygnematophyceae, Mougeotia, Penium, and Closterium, which serve as models for studying chloroplast photorelocation movement, cell wall structure, and sexual reproduction, respectively.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2023)

Article Biochemistry & Molecular Biology

Extensive protein dosage compensation in aneuploid human cancers

Klaske M. Schukken et al.

Summary: This study investigates the effect of aneuploidy on protein expression in human cancers. The majority of proteins exhibit dosage compensation, failing to change in proportion to chromosome copy number. Various gene groups, including protein complex subunits and cell cycle genes, are buffered by chromosome gain or loss. Genetic and biophysical factors play a role in protein buffering. Aneuploidy moderately affects the expression of oncogenes and tumor suppressors.

GENOME RESEARCH (2022)

Article Multidisciplinary Sciences

Consequences of aneuploidy in human fibroblasts with trisomy 21

Sunyoung Hwang et al.

Summary: The study reveals that mRNA and protein levels are increased by 1.5-fold on average in trisomy 21 cells, with some proteins enriched for subunits of macromolecular complexes showing signs of post-transcriptional regulation. Additionally, trisomy 21 cells exhibit lower viability and increased dependency on serine-driven lipid synthesis.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Biochemical Research Methods

Sensitive protein alignments at tree-of-life scale using DIAMOND

Benjamin Buchfink et al.

Summary: We are at the beginning of a genomic revolution where all known species are planned to be sequenced. The improved version of DIAMOND allows for quick tree-of-life scale protein alignments.

NATURE METHODS (2021)

Article Biology

Linking genome size variation to population phenotypic variation within the rotifer, Brachionus asplanchnoidis

Claus-Peter Stelzer et al.

Summary: The study found a positive correlation between genome size and body size, egg size, and embryonic development time in a natural population, indicating genetic variation influences the relationship between these traits.

COMMUNICATIONS BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number

Francesca B. Lopez et al.

Summary: In this study, the researchers used Cas9-mediated genome editing in Arabidopsis to reduce the copy number of 45S rRNA genes to around 10%, creating low copy number (LCN) lines. Despite the significant reduction in rDNA copies, the transcriptional rates and steady-state levels of rRNA remained the same as wild-type plants. Furthermore, editing rRNA repeats using Cas9 technology provides insights into the mechanisms of rDNA dosage compensation and the impacts of low rDNA copy number on genome stability, development, and cellular processes.

PLANT CELL (2021)

Article Computer Science, Interdisciplinary Applications

multimode: An R Package for Mode Assessment

Jose Ameijeiras-Alonso et al.

Summary: This paper introduces the utility of the R package multimode, which collects various exploratory and testing non-parametric approaches for determining the number and locations of modes, including graphical tools, formal testing procedures, and classical data examples.

JOURNAL OF STATISTICAL SOFTWARE (2021)

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 Biochemical Research Methods

SonicParanoid: fast, accurate and easy orthology inference

Salvatore Cosentino et al.

BIOINFORMATICS (2019)

Article Biochemical Research Methods

ntEdit: scalable genome sequence polishing

Rene L. Warren et al.

BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution

Shifeng Cheng et al.

Article Biochemical Research Methods

wgd-simple command line tools for the analysis of ancient whole-genome duplications

Arthur Zwaenepoel et al.

BIOINFORMATICS (2019)

Article Evolutionary Biology

Genome Size Evolution within and between the Sexes

Carl E. Hjelmen et al.

JOURNAL OF HEREDITY (2019)

Article Biochemical Research Methods

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

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization

Tomoaki Nishiyama et al.

Article Multidisciplinary Sciences

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

Floreal Cabanettes et al.

PEERJ (2018)

Article Biochemical Research Methods

ARCS: scaffolding genome drafts with linked reads

Sarah Yeo et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

findGSE: estimating genome size variation within human and Arabidopsis using k-mer frequencies

Hequan Sun et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

VCFR: a package to manipulate and visualize variant call format data in R

Brian J. Knaus et al.

MOLECULAR ECOLOGY RESOURCES (2017)

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

Review Biology

Dosage-sensitive genes in evolution and disease

Alan M. Rice et al.

BMC BIOLOGY (2017)

Letter Genetics & Heredity

Misspecification in Mixed-Model-Based Association Analysis

Willem Kruijer

GENETICS (2016)

Article Biochemistry & Molecular Biology

Global deceleration of gene evolution following recent genome hybridizations in fungi

Sira Sriswasdi et al.

GENOME RESEARCH (2016)

Article Biochemistry & Molecular Biology

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

Jaime Huerta-Cepas et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Biochemistry & Molecular Biology

Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms

Zhen Li et al.

PLANT CELL (2016)

Article Biochemical Research Methods

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Felipe A. Simao et al.

BIOINFORMATICS (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

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

Alexandros Stamatakis

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Wen Huang et al.

GENOME RESEARCH (2014)

Article Multidisciplinary Sciences

Phylotranscriptomic analysis of the origin and early diversification of land plants

Norman J. Wickett et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (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)

Review Genetics & Heredity

Dosage Compensation of the Sex Chromosomes

Christine M. Disteche

ANNUAL REVIEW OF GENETICS, VOL 46 (2012)

Article Agronomy

Genome size variation in three Saccharum species

Jisen Zhang et al.

EUPHYTICA (2012)

Article Biochemical Research Methods

NIH Image to ImageJ: 25 years of image analysis

Caroline A. Schneider et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemical Research Methods

A novel hybrid gene prediction method employing protein multiple sequence alignments

Oliver Keller et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

Guillaume Marcais et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Co-evolution between transposable elements and their hosts: a major factor in genome size evolution?

J. Arvid Agren et al.

CHROMOSOME RESEARCH (2011)

Article Biotechnology & Applied Microbiology

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

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Genetics & Heredity

A copy number variation morbidity map of developmental delay

Gregory M. Cooper et al.

NATURE GENETICS (2011)

Article Multidisciplinary Sciences

The Characterisation of Three Types of Genes that Overlie Copy Number Variable Regions

Cara Woodwark et al.

PLOS ONE (2011)

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

Murray P. Cox et al.

BMC BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Multidisciplinary Sciences

Origins and functional impact of copy number variation in the human genome

Donald F. Conrad et al.

NATURE (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

Fast and accurate short read alignment with Burrows-Wheeler transform

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

flowCore: a Bioconductor package for high throughput flow cytometry

Florian Hahne et al.

BMC BIOINFORMATICS (2009)

Editorial Material Ecology

Within-species variation in genome size

C. Biemont

HEREDITY (2008)

Article Multidisciplinary Sciences

Rare chromosomal deletions and duplications increase risk of schizophrenia

Jennifer L. Stone et al.

NATURE (2008)

Article Multidisciplinary Sciences

A portrait of copy-number polymorphism in Drosophila melanogaster

Erik B. Dopman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Multidisciplinary Sciences

Natural history and evolutionary principles of gene duplication in fungi

Ilan Wapinski et al.

NATURE (2007)

Article Multidisciplinary Sciences

Effects of aneuploidy on cellular physiology and cell division in haploid yeast

Eduardo M. Torres et al.

SCIENCE (2007)

Article Multidisciplinary Sciences

Global variation in copy number in the human genome

Richard Redon et al.

NATURE (2006)

Article Biochemical Research Methods

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

Adrian Alexa et al.

BIOINFORMATICS (2006)

Article Biochemical Research Methods

Automated generation of heuristics for biological sequence comparison

GS Slater et al.

BMC BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

BJ Haas et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Veterinary Sciences

Flow cytometric analysis of nuclear DNA for sex identification in three psittacine species

NR Canon et al.

AMERICAN JOURNAL OF VETERINARY RESEARCH (2000)