4.5 Article

Genome of the Lord Howe Island Stick Insect Reveals a Highly Conserved Phasmid X Chromosome

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Convergent consequences of parthenogenesis on stick insect genomes

Kamil S. Jaron et al.

Summary: This study investigated the genome evolution of parthenogenetic species in the stick insect genus Timema and found that parthenogenesis leads to a significant reduction in heterozygosity and often results in genetically uniform populations. Additionally, the study revealed that parthenogenetic species experience less effective positive selection, indicating that sex is prevalent in natural populations due to its facilitation of rapid adaptation. The study also observed no increased accumulation of transposable elements in parthenogenetic species, likely due to the low TE activity in the genus. Overall, these findings provide empirical support for the negative consequences of parthenogenesis as predicted by theory.

SCIENCE ADVANCES (2022)

Article Ecology

X chromosomes show relaxed selection and complete somatic dosage compensation across Timema stick insect species

Darren J. Parker et al.

Summary: Sex chromosomes have evolved repeatedly across different species, with similar consequences such as accelerated evolution and increased accumulation of sexually antagonistic alleles. In Timema stick insects, the X chromosome has remained consistent in size and gene content over 30 million years of evolution, showing limited association with sexually biased genes.

JOURNAL OF EVOLUTIONARY BIOLOGY (2022)

Article Biochemistry & Molecular Biology

Phylomitogenomics provides new perspectives on the Euphasmatodea radiation (Insecta: Phasmatodea)

Giobbe Forni et al.

Summary: The study found that the diversity of Phasmatodea species is mainly concentrated in the suborder Euphasmatodea, which has a pantropical distribution and is believed to have originated from a recent rapid evolutionary radiation. By analyzing the mitogenomes of 17 species and other available mitogenomes, researchers sought to uncover the origins and diversification of Euphasmatodea. The divergence time analysis suggested that Euphasmatodea diversification began around 187 million years ago, potentially influenced by the Triassic-Jurassic mass extinction and the breakup of Pangea.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

OrthoDB in 2020: evolutionary and functional annotations of orthologs

Evgeny M. Zdobnov et al.

Summary: OrthoDB provides evolutionary and functional annotations of orthologs for a vast number of organisms, with a wide coverage of species and rich data content. The user interface has been enhanced, and features three views on the data, as well as online tools for interactive exploration and data download.

NUCLEIC ACIDS RESEARCH (2021)

Letter Biochemistry & Molecular Biology

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Mose Manni et al.

Summary: The BUSCO software provides essential methods for assessing the quality of genomic and metagenomic data, offering new functionalities and improvements to streamline the process. It is capable of evaluating both eukaryotic and prokaryotic species, and can be used across various data types including genome assemblies, metagenomic bins, transcriptomes, and gene sets.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biochemical Research Methods

Identifying and removing haplotypic duplication in primary genome assemblies

Dengfeng Guan et al.

BIOINFORMATICS (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 Biochemical Research Methods

Fast and accurate long-read assembly with wtdbg2

Jue Ruan et al.

NATURE METHODS (2020)

Review Genetics & Heredity

Taming the Turmoil Within: New Insights on the Containment of Transposable Elements

Erin S. Kelleher et al.

TRENDS IN GENETICS (2020)

Article Biochemical Research Methods

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis et al.

BIOINFORMATICS (2019)

Letter Biotechnology & Applied Microbiology

Errors in long-read assemblies can critically affect protein prediction

Mick Watson et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Biotechnology & Applied Microbiology

Nanopore sequencing and assembly of a human genome with ultra-long reads

Miten Jain et al.

NATURE BIOTECHNOLOGY (2018)

Article Biochemical Research Methods

Mosdepth: quick coverage calculation for genomes and exomes

Brent S. Pedersen et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

Museum Genomics Confirms that the Lord Howe Island Stick Insect Survived Extinction

Alexander S. Mikheyev et al.

CURRENT BIOLOGY (2017)

Article Biochemical Research Methods

Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes

Malte Petersen et al.

BMC BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

Nicholas H. Putnam et al.

GENOME RESEARCH (2016)

Article Evolutionary Biology

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

Olga Chernomor et al.

SYSTEMATIC BIOLOGY (2016)

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 Multidisciplinary Sciences

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

Victor Soria-Carrasco et al.

SCIENCE (2014)

Article Multidisciplinary Sciences

The locust genome provides insight into swarm formation and long-distance flight

Xianhui Wang et al.

NATURE COMMUNICATIONS (2014)

Article Biochemical Research Methods

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin et al.

BIOINFORMATICS (2013)

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 Biochemistry & Molecular Biology

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

Robert Lanfear et al.

MOLECULAR BIOLOGY AND EVOLUTION (2012)

Review Evolutionary Biology

The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea)

Thomas R. Buckley et al.

SYSTEMATIC ENTOMOLOGY (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 Biology

Extreme convergence in stick insect evolution: phylogenetic placement of the Lord Howe Island tree lobster

Thomas R. Buckley et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2009)

Article Ecology

The recovery programme for the Lord Howe Island Phasmid (Dryococelus australis) following its rediscovery

Nicholas Carlile et al.

ECOLOGICAL MANAGEMENT & RESTORATION (2009)

Article Biochemical Research Methods

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

Mario Stanke et al.

BIOINFORMATICS (2008)

Article Multidisciplinary Sciences

Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata

Steven Lockton et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Biochemical Research Methods

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li et al.

BIOINFORMATICS (2006)

Article Biochemical Research Methods

Gene finding in novel genomes

I Korf

BMC BIOINFORMATICS (2004)

Review Multidisciplinary Sciences

The genome sequence of Drosophila melanogaster

MD Adams et al.

SCIENCE (2000)