Plastid and mitochondrial genomes of Coccophora langsdorfii (Fucales, Phaeophyceae) and the utility of molecular markers

PloS One
Louis GrafHwan Su Yoon

Abstract

Coccophora langsdorfii (Turner) Greville (Fucales) is an intertidal brown alga that is endemic to Northeast Asia and increasingly endangered by habitat loss and climate change. We sequenced the complete circular plastid and mitochondrial genomes of C. langsdorfii. The circular plastid genome is 124,450 bp and contains 139 protein-coding, 28 tRNA and 6 rRNA genes. The circular mitochondrial genome is 35,660 bp and contains 38 protein-coding, 25 tRNA and 3 rRNA genes. The structure and gene content of the C. langsdorfii plastid genome is similar to those of other species in the Fucales. The plastid genomes of brown algae in other orders share similar gene content but exhibit large structural recombination. The large in-frame insert in the cox2 gene in the mitochondrial genome of C. langsdorfii is typical of other brown algae. We explored the effect of this insertion on the structure and function of the cox2 protein. We estimated the usefulness of 135 plastid genes and 35 mitochondrial genes for developing molecular markers. This study shows that 29 organellar genes will prove efficient for resolving brown algal phylogeny. In addition, we propose a new molecular marker suitable for the study of intraspecific genetic diversity that...Continue Reading

References

Apr 1, 1991·Journal of Bioenergetics and Biomembranes·B KadenbachD Steverding
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Dec 10, 2000·The Journal of Biological Chemistry·X Pérez-MartínezD González-Halphen
Aug 2, 2001·Journal of Molecular Evolution·M P Oudot-Le SecqS Loiseaux-De Goër
Dec 14, 2002·Science·Soledad FunesDiego González-Halphen
Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Jun 8, 2004·Bioinformatics·Stacia K WymanJeffrey L Boore
Apr 2, 2005·Proceedings of the National Academy of Sciences of the United States of America·Marie VoisinFrédérique Viard
Jun 28, 2005·Nucleic Acids Research·Peter SchattnerTodd M Lowe
Sep 22, 2006·Gene·Ross F Waller, Patrick J Keeling
Apr 25, 2007·Nucleic Acids Research·Karin LagesenDavid W Ussery
Jan 25, 2008·BMC Bioinformatics·Yang Zhang
Jan 30, 2008·Bioinformatics·Gavin C Conant, Kenneth H Wolfe
Nov 10, 2009·BMC Genomics·Rob M de GraafJohannes H P Hackstein
May 4, 2010·Nucleic Acids Research·Federico AbascalMaximilian J Telford
Jul 14, 2010·Bioinformatics·Lionel GuySiv G E Andersson
Mar 23, 2011·Plant Molecular Biology·Susann WickeDietmar Quandt
Aug 10, 2011·BMC Genomics·Nabil-Fareed AlikhanScott A Beatson
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Feb 19, 2013·Molecular Biology and Evolution·Bui Quang MinhArndt von Haeseler
Jul 2, 2014·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Feng Liu, Shaojun Pang
Aug 28, 2014·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Feng LiuWeizhou Chen
Sep 5, 2014·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Feng Liu, Shaojun Pang
Nov 6, 2014·Molecular Biology and Evolution·Lam-Tung NguyenBui Quang Minh
Dec 31, 2014·Nature Methods·Jianyi YangYang Zhang
Apr 15, 2015·Genome Biology and Evolution·David Roy Smith
May 23, 2015·Mitochondrial DNA
Jun 24, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Yanhui Bi, Zhigang Zhou
Jul 15, 2015·Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis·Shuai WangNaihao Ye

❮ Previous
Next ❯

Citations

May 14, 2020·F1000Research·Rafael Zardoya
Nov 4, 2020·The Journal of Eukaryotic Microbiology·Sarah RussellAdrian Reyes-Prieto
Jun 2, 2021·Genome Biology and Evolution·Samuel StarkoPatrick T Martone
Nov 23, 2021·Frontiers in Plant Science·Ruoran LiXumin Wang

❮ Previous
Next ❯

Datasets Mentioned

BETA
KU255795
KU255794

Methods Mentioned

BETA
PCR

Software Mentioned

SequenceMatrix
DOGMA
TranslatorX
BLAST
RNAmmer
MIRA assembler
Geneious Pro
R
BLASTp
R library

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.

Related Papers

Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Shuai WangNaihao Ye
Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Zheng GuanNaihao Ye
Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Xiao FanNaihao Ye
Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Le XuNaihao Ye
© 2022 Meta ULC. All rights reserved