Comparative phylotranscriptomics reveals putative sex differentiating genes across eight diverse bivalve species

The gene-rich genome of the scallop Pecten maximus

(2020) Nathan J Kenny et al.   GigaScience

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

(2020) Chengjie Chen et al.   Molecular Plant

Restriction site-associated DNA sequencing (RAD-seq) analysis in Pacific oyster Crassostrea gigas based on observation of individual sex changes

(2020) Chenyang Yue et al.   Scientific Reports

MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca

(2020) Fuyun Liu et al.   NUCLEIC ACIDS RESEARCH

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(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis)

(2019) Liqing Zhou et al.   BMC GENOMICS

Independent evolution for sex determination and differentiation in the DMRT family in animals

(2019) Shuuji Mawaribuchi et al.   Biology Open

Transcription of the Sox30 Gene Is Positively Regulated by Dmrt1 in Nile Tilapia

(2019) Yaohao Tang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

(2019) Li-Gen Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptomic and Network Analyses Reveal Mechanistic-Based Biomarkers of Endocrine Disruption in the Marine Mussel, Mytilus edulis

(2018) Bonnie J. Blalock et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Deciphering the Link between Doubly Uniparental Inheritance of mtDNA and Sex Determination in Bivalves: Clues from Comparative Transcriptomics

(2018) Charlotte Capt et al.   Genome Biology and Evolution

Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows

(2018) Nidhi Shah et al.   BIOINFORMATICS

FOXL2 and DMRT1L Are Yin and Yang Genes for Determining Timing of Sex Differentiation in the Bivalve Mollusk Patinopecten yessoensis

(2018) Ruojiao Li et al.   Frontiers in Physiology

Gametogenesis and Spawning of the Ribbed Mussel (Geukensia demissa) near the Northern Limit of its Range (Maritime Canada)

(2017) Spencer D.S. Virgin et al.   Estuaries and Coasts

Sry and SoxE genes: How they participate in mammalian sex determination and gonadal development?

(2017) Zhen-Yu She et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

SOX30 is required for male fertility in mice

(2017) Chun-Wei Allen Feng et al.   Scientific Reports

The pearl oyster Pinctada fucata martensii genome and multi-omic analyses provide insights into biomineralization

(2017) Xiaodong Du et al.   GigaScience

Scallop genome provides insights into evolution of bilaterian karyotype and development

(2017) Shi Wang et al.   Nature Ecology & Evolution

Transcriptome Sequencing and Comparative Analysis of Ovary and Testis Identifies Potential Key Sex-Related Genes and Pathways in Scallop Patinopecten yessoensis

(2016) Yangping Li et al.   MARINE BIOTECHNOLOGY

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

De novotranscriptome sequencing to identify the sex-determination genes inHyriopsis schlegelii

(2015) Jianwu Shi et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

Molecular Signatures Discriminating the Male and the Female Sexual Pathways in the Pearl Oyster Pinctada margaritifera

(2015) Vaihiti Teaniniuraitemoana et al.   PLoS One

Correlation of transcriptomic responses and metal bioaccumulation in Mytilus edulis L. reveals early indicators of stress

(2014) Helen C. Poynton et al.   AQUATIC TOXICOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes

(2014) Vaihiti Teaniniuraitemoana et al.   BMC GENOMICS

Pan-metazoan phylogeny of the DMRT gene family: a framework for functional studies

(2014) Judith R. Wexler et al.   DEVELOPMENT GENES AND EVOLUTION

Genomic Analysis of the Pacific Oyster ( Crassostrea gigas ) Reveals Possible Conservation of Vertebrate Sex Determination in a Mollusc

(2014) Na Zhang et al.   G3-Genes Genomes Genetics

Identification of Male Gametogenesis Expressed Genes from the Scallop Nodipecten subnodosus by Suppressive Subtraction Hybridization and Pyrosequencing

(2013) Raúl Llera-Herrera et al.   PLoS One

Sex determination

(2012) Tony Gamble et al.   CURRENT BIOLOGY

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Dmrt genes in the development and evolution of sexual dimorphism

(2012) Artyom Kopp   TRENDS IN GENETICS

Mating Systems and Reproductive Success in Hermaphroditic Bay Scallop, Argopecten irradians irradians (Lamarck 1819), Inferred by Microsatellite-based Parentage Analysis

(2011) Ronghua Li et al.   JOURNAL OF THE WORLD AQUACULTURE SOCIETY

De Novo Assembly of the Manila Clam Ruditapes philippinarum Transcriptome Provides New Insights into Expression Bias, Mitochondrial Doubly Uniparental Inheritance and Sex Determination

(2011) F. Ghiselli et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Molecular Phylogeny of Bivalve Mollusks: Ancient Radiations and Divergences as Revealed by Mitochondrial Genes

(2011) Federico Plazzi et al.   PLoS One

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Identification and characterization of Sox genes in the silkworm, Bombyx mori

(2010) Ling Wei et al.   MOLECULAR BIOLOGY REPORTS

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Evolution of the insect Sox genes

(2008) Megan J Wilson et al.   BMC EVOLUTIONARY BIOLOGY