Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena

Database : the Journal of Biological Databases and Curation
Wentao YangJie Xiong

Abstract

Ciliates are a large and diverse group of unicellular organisms characterized by having the following two distinct type of nuclei within a single cell: micronucleus (MIC) and macronucleus (MAC). Although the genomes of several ciliates in different groups have been sequenced, comparative genomics data for multiple species within a ciliate genus are not yet available. Here we collected the genome information and comparative genomics analysis results for 10 species in the Tetrahymena genus, including the previously sequenced model organism Tetrahymena thermophila and 9 newly sequenced species, and constructed a genus-level comparative analysis platform, the Tetrahymena Comparative Genomics Database (TCGD). Genome sequences, transcriptomic data, gene models, functional annotation, ortholog groups and synteny maps were built into this database and a user-friendly interface was developed for searching, visualizing and analyzing these data. In summary, the TCGD (http://ciliate.ihb.ac.cn) will be an important and useful resource for the ciliate research community.

References

Mar 10, 1999·Chemosphere·M P SauvantE Piccinni
Sep 30, 1999·Methods in Cell Biology·D L Nanney, E M Simon
Oct 9, 2002·Genome Research·Lincoln D SteinSuzanna Lewis
Jan 5, 2007·Nucleic Acids Research·Donald G Gilbert
Jul 31, 2007·Systematic Biology·Sina M AdlFrederick Spiegel
Oct 30, 2008·Nucleic Acids Research·Cristina AurrecoecheaHaiming Wang
Jan 6, 2012·Nucleic Acids Research·Yupeng WangAndrew H Paterson
Mar 27, 2012·Methods in Cell Biology·Denis H Lynn, F Paul Doerder
Aug 4, 2012·BMC Bioinformatics·Kashi V RevannaQunfeng Dong
Jun 22, 2014·Genome Biology and Evolution·Samuel H AeschlimannEstienne C Swart
Nov 28, 2014·Nucleic Acids Research·Alex MitchellRobert D Finn
Feb 14, 2017·Current Biology : CB·Mark M SlabodnickPranidhi Sood
Jan 21, 2018·BMC Genomics·Ruan-Lin WangAi-Hua Liang

❮ Previous
Next ❯

Citations

Apr 27, 2021·Computational and Structural Biotechnology Journal·Guangying WangJie Xiong

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
scanning electron microscopy
pull-down

Software Mentioned

PANTHER
SMART
OrthoMCL
MCScanX
GBrowse
BLAST
Linux
TCGD
PROSITE
InterProScan

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.