4.6 Article Data Paper

The Draft Genome of Chinese Endemic Species Phascolosoma esculenta (Sipuncula, Phascolosomatidae) Reveals the Phylogenetic Position of Sipuncula

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 Biochemistry & Molecular Biology

Cloning, Functional Characterization and Response to Cadmium Stress of the Thioredoxin-like Protein 1 Gene from Phascolosoma esculenta

Jiajie Meng et al.

Summary: The edible marine worm Phascolosoma esculenta produces a new isoform of Thioredoxin (PeTrxl) in response to cadmium (Cd) stress. PeTrxl exhibits significant antioxidant capacity and can protect P. esculenta from Cd-induced oxidative stress.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Oceanography

Effects of Low Temperature Stress on the Morphology and hsp70 and hsp90 Gene Expression of Phascolosoma esculenta

Shen Weiliang et al.

Summary: Phascolosoma esculenta undergoes morphological and histological damage under low temperature stress, with hsp70 and hsp90 potentially functioning in its adaptability to low temperatures.

JOURNAL OF OCEAN UNIVERSITY OF CHINA (2021)

Review Biodiversity Conservation

How Many Sipunculan Species Are Hiding in Our Oceans?

Anja Schulze et al.

Summary: Sipunculans, once considered a separate phylum, are now commonly included in Annelida based on phylogenomic analyses. They lack chaetae but have proteinaceous hooks on the introvert, along with other external taxonomic characters. Molecular studies have revealed high species diversity in sipunculans, with cryptic species complexes and ongoing changes in internal relationships within the phylogeny.

DIVERSITY-BASEL (2021)

Article Genetics & Heredity

miRNAture-Computational Detection of microRNA Candidates

Cristian A. Velandia-Huerto et al.

Summary: Annotation of short RNAs, including microRNAs, is challenging due to their small size. The miRNAture pipeline automates homology search and validation, yielding good results for typical miRBase families but facing difficulties with atypical cases.
Article Biochemistry & Molecular Biology

Genomic Signatures Supporting the Symbiosis and Formation of Chitinous Tube in the Deep-Sea Tubeworm Paraescarpia echinospica

Yanan Sun et al.

Summary: Vestimentiferan tubeworms are gutless, habitat-forming animals in deep-sea chemosynthetic ecosystems that depend on endosymbiotic bacteria for nutrition. The genome of Paraescarpia echinospica has been remodeled to support symbiosis and includes mechanisms for nutrient transfer, immune response, and stress resistance. The study provides insights into the tubeworms' unique adaptations for survival in deep-sea environments and the formation of chitinous tubes.

MOLECULAR BIOLOGY AND EVOLUTION (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 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)

Article Genetics & Heredity

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP plus and AUGUSTUS supported by a protein database

Tomas Bruna et al.

Summary: The task of eukaryotic genome annotation remains challenging and the new BRAKER2 pipeline is an automatic method that outperforms other pipelines in terms of accuracy and performance, yet further innovations are required to achieve highly accurate annotation.

NAR GENOMICS AND BIOINFORMATICS (2021)

Article Biochemical Research Methods

NextPolish: a fast and efficient genome polishing tool for long-read assembly

Jiang Hu et al.

BIOINFORMATICS (2020)

Article Biochemical Research Methods

Identifying and removing haplotypic duplication in primary genome assemblies

Dengfeng Guan et al.

BIOINFORMATICS (2020)

Article Genetics & Heredity

The first complete mitochondrial genome of Siphonosoma from Siphonosoma cumanense (Sipuncula, Sipunculidae)

Shengping Zhong et al.

MITOCHONDRIAL DNA PART B-RESOURCES (2020)

Article Multidisciplinary Sciences

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

T. Rhyker Ranallo-Benavidez et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

Chengjie Chen et al.

MOLECULAR PLANT (2020)

Review Evolutionary Biology

Recent progress in reconstructing lophotrochozoan (spiralian) phylogeny

Christoph Bleidorn

ORGANISMS DIVERSITY & EVOLUTION (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Review Biochemistry & Molecular Biology

Antioxidant Defence Systems and Oxidative Stress in Poultry Biology: An Update

Peter F. Surai et al.

ANTIOXIDANTS (2019)

Article Biotechnology & Applied Microbiology

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Shujun Ou et al.

GENOME BIOLOGY (2019)

Article Biochemical Research Methods

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

Shifu Chen et al.

BIOINFORMATICS (2018)

Article Biochemical Research Methods

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

Jens Keilwagen et al.

BMC BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

Evolution of mitochondrial gene order in Annelida

Anne Weigert et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2016)

Article Biochemical Research Methods

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Mihaela Pertea et al.

NATURE PROTOCOLS (2016)

Review Evolutionary Biology

Current status of annelid phylogeny

Anne Weigert et al.

ORGANISMS DIVERSITY & EVOLUTION (2016)

Article Biochemistry & Molecular Biology

Articulating Archiannelids: Phylogenomics and Annelid Relationships, with Emphasis on Meiofaunal Taxa

Sonia C. S. Andrade et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

Re-evaluating the phylogeny of Sipuncula through transcriptomics

Sarah Lemer et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2015)

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

Illuminating the Base of the Annelid Tree Using Transcriptomics

Anne Weigert et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

Article Biochemical Research Methods

Infernal 1.1: 100-fold faster RNA homology searches

Eric P. Nawrocki et al.

BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

Mira V. Han et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Multidisciplinary Sciences

The oyster genome reveals stress adaptation and complexity of shell formation

Guofan Zhang et al.

NATURE (2012)

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 Multidisciplinary Sciences

Phylogenomic analyses unravel annelid evolution

Torsten H. Struck et al.

NATURE (2011)

Article Fisheries

Cloning and expression of HSP70 gene of sipuncula Phascolosoma esculenta

Xiurong Su et al.

FISH & SHELLFISH IMMUNOLOGY (2010)

Article Evolutionary Biology

Phylogenetic position of Sipuncula derived from multi-gene and phylogenomic data and its implication for the evolution of segmentation

Janina Dordel et al.

JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH (2010)

Article Biotechnology & Applied Microbiology

The cytochrome P450 (CYP) gene superfamily in Daphnia pulex

William S. Baldwin et al.

BMC GENOMICS (2009)

Article Biology

MicroRNAs resolve an apparent conflict between annelid systematics and their fossil record

Erik A. Sperling et al.

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

Article Biochemistry & Molecular Biology

RNAmmer:: consistent and rapid annotation of ribosomal RNA genes

Karin Lagesen et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Evolutionary Biology

Annelid phylogeny and the status of Sipuncula and Echiura

Torsten H. Struck et al.

BMC EVOLUTIONARY BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology

Anja Schulze et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2007)

Article Marine & Freshwater Biology

Reconstructing the phylogeny of the Sipuncula

A Schulze et al.

HYDROBIOLOGIA (2005)

Article Biology

Early Cambrian sipunculan worms from southwest China

DY Huang et al.

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2004)

Review Multidisciplinary Sciences

Oxidants, oxidative stress and the biology of ageing

T Finkel et al.

NATURE (2000)