Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales

Evolutionary Bioinformatics Online
Lu ZhangXue-Jun Ge

Abstract

Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.

References

Oct 6, 1999·Genome Research·X Huang, A Madan
Feb 27, 2001·American Journal of Botany·R G OlmsteadP A Reeves
Nov 25, 2003·Journal of Evolutionary Biology·T BorschW Barthlott
Feb 18, 2004·Systematic Biology·Johan A A NylanderJosé Luis Nieves-Aldrey
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Oct 1, 2005·Systematic Biology·Alexandra H WortleyRobert W Scotland
Nov 16, 2006·PLoS Biology·Antonis Rokas, Sean B Carroll
Mar 17, 2007·Systematic Biology·Laura Salter Kubatko, James H Degnan
Mar 30, 2007·Proceedings of the National Academy of Sciences of the United States of America·Scott V EdwardsDennis K Pearl
Apr 11, 2007·Genome Research·Matthew J OliverOscar M Schofield
Sep 22, 2007·Genome Biology·Hidenori NishiharaMasami Hasegawa
Feb 16, 2008·Systematic Biology·Shuguang JianDouglas E Soltis
Feb 27, 2008·Systematic Biology·Noah A Rosenberg, Randa Tao
May 1, 2008·Nucleic Acids Research·Stefan GötzAna Conesa
Jun 24, 2008·Systematic Biology·John C Avise, Terence J Robinson
Sep 5, 2008·Annual Review of Genomics and Human Genetics·Bruce Rannala, Ziheng Yang
Oct 15, 2008·Systematic Biology·Alexandros StamatakisJacques Rougemont
Jul 10, 2009·BMC Evolutionary Biology·Ingo EbersbergerArndt von Haeseler
May 5, 2010·Proceedings of the National Academy of Sciences of the United States of America·Ziheng Yang, Bruce Rannala
Aug 11, 2010·The Journal of Heredity·Christopher Blair, Robert W Murphy
Oct 13, 2010·BMC Evolutionary Biology·Liang LiuScott V Edwards
Nov 20, 2010·Systematic Biology·Adam D Leaché, Bruce Rannala
Apr 1, 1996·Trends in Ecology & Evolution·J P HuelsenbeckC W Cunningham
Mar 12, 2011·Molecular Biology and Evolution·Benoit NabholzHans Ellegren
May 27, 2011·American Journal of Botany·Douglas E SoltisPamela S Soltis
Dec 1, 2003·American Journal of Botany·Khidir W HiluLars W Chatrou
Feb 1, 2004·American Journal of Botany·Charles C Davis, Mark W Chase
Jun 17, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Anuj SrivastavaRussell L Malmberg
Jul 12, 2011·Nature·UNKNOWN Potato Genome Sequencing ConsortiumRichard G F Visser
Oct 22, 2011·Genome Biology and Evolution·Bojian ZhongPeter James Lockhart
Dec 24, 2011·PLoS Genetics·Ernest K LeeRob Desalle
Feb 10, 2012·Molecular Biology and Evolution·Robert LanfearStephane Guindon
Jun 12, 2012·BMC Genomics·Zhenxiang XiCharles C Davis
Aug 30, 2012·Proceedings of the National Academy of Sciences of the United States of America·Sen SongShaoyuan Wu
Oct 10, 2012·Proceedings of the National Academy of Sciences of the United States of America·Zhenxiang XiCharles C Davis
May 11, 2013·Nucleic Acids Research·Timothy I ShawLiang Liu

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRX1037980

Methods Mentioned

BETA
454 sequencing

Software Mentioned

BLAST
GS assembler
HaMStR
MCcoal
Angiosperm Phylogeny Group system
GAMMA
HMM
SeqClean
MP
Blast2GO

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.