Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints

BMC Genomics
De-Long GuanJuan-Ying Xie

Abstract

Hirudinaria manillensis is an ephemeral, blood-sucking ectoparasite, possessing anticoagulant capacities with potential medical applications. Analysis of codon usage patterns would contribute to our understanding of the evolutionary mechanisms and genetic architecture of H. manillensis, which in turn would provide insight into the characteristics of other leeches. We analysed codon usage and related indices using 18,000 coding sequences (CDSs) retrieved from H. manillensis RNA-Seq data. We identified four highly preferred codons in H. manillensis that have G/C-endings. Points generated in an effective number of codons (ENC) plot distributed below the standard curve and the slope of a neutrality plot was less than 1. Highly expressed CDSs had lower ENC content and higher GC content than weakly expressed CDSs. Principal component analysis conducted on relative synonymous codon usage (RSCU) values divided CDSs according to GC content and divided codons according to ending bases. Moreover, by determining codon usage, we found that the majority of blood-diet related genes have undergone less adaptive evolution in H. manillensis, except for those with homologous sequences in the host species. Codon usage in H. manillensis had an over...Continue Reading

References

Feb 1, 1991·Blood Coagulation & Fibrinolysis : an International Journal in Haemostasis and Thrombosis·A ElectricwalaT Atkinson
Nov 1, 1991·Journal of Molecular Evolution·A C Eyre-Walker
Nov 25, 1993·Nucleic Acids Research·S L Fennoy, J Bailey-Serres
Dec 11, 1999·Nucleic Acids Research·R L TatusovE V Koonin
Jan 30, 2002·Gene·Irene T RombelStephen Albert Johnston
Nov 16, 2002·Current Opinion in Genetics & Development·Laurent Duret
Dec 19, 2003·Nucleic Acids Research·Minoru KanehisaMasahiro Hattori
Dec 17, 2009·BMC Bioinformatics·Christiam CamachoThomas L Madden
Dec 17, 2010·The Journal of Parasitology·Gi-Sik MinMark E Siddall
Sep 4, 2012·Nucleic Acids Research·Hila GingoldYitzhak Pilpel
Dec 27, 2012·Biochemical and Biophysical Research Communications·Lin ChenGuangyou Yang
Nov 30, 2013·Nucleic Acids Research·Robert D FinnMarco Punta
Apr 4, 2015·Journal of Molecular Evolution·Jeffrey R Powell, Kirstin Dion
Apr 19, 2015·BMC Genomics·Marcelo BaezaVíctor Cifuentes
Dec 5, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Arif Uddin, Supriyo Chakraborty
Feb 7, 2016·Methods : a Companion to Methods in Enzymology·Kok Siong AngDong-Yup Lee
Jun 14, 2017·Acta Tropica·Snawar Hussain, Sahibzada Tasleem Rasool
Jun 19, 2017·Virology Journal·Matías CastellsJuan Cristina

❮ Previous
Next ❯

Citations

Jan 28, 2020·Genome Génome / Conseil National De Recherches Canada·Aasim MajeedPankaj Bhardwaj
Jan 27, 2019·Journal of Cellular Biochemistry·Muhammad Salabat KhanSheng-Quan Xu
Feb 7, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Thi Hung NguyenShiheng Tao
Dec 31, 2020·Briefings in Bioinformatics·Yashpal Singh MalikKam Y J Zhang
May 11, 2021·International Journal of Biological Macromolecules·Jianke YangXianzhao Kan
Jul 29, 2021·Veterinary World·Sharanagouda S PatilBibek Ranjan Shome

❮ Previous
Next ❯

Datasets Mentioned

BETA
SRX2735687
SRX2735688

Methods Mentioned

BETA
PCA
protein folding

Software Mentioned

BLAST
CodonW
SPSS
DAMBE
Excel
blastx

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.

© 2022 Meta ULC. All rights reserved