Prevalence of isomeric plastomes and effectiveness of plastome super-barcodes in yews (Taxus) worldwide

Scientific Reports
Chao-Nan FuLian-Ming Gao

Abstract

Taxus (yew) is both the most species-rich and taxonomically difficult genus in Taxaceae. To date, no study has elucidated the complexities of the plastid genome (plastome) or examined the possibility of whole plastomes as super-barcodes across yew species worldwide. In this study, we sequenced plastomes from two to three individuals for each of the 16 recognized yew species (including three potential cryptics) and Pseudotaxus chienii. Our comparative analyses uncovered several gene loss events that independently occurred in yews, resulting in a lower plastid gene number than other Taxaceous genera. In Pseudotaxus and Taxus, we found two isomeric arrangements that differ by the orientation of a 35 kb fragment flanked by "trnQ-IRs". These two arrangements exist in different ratios within each sampled individual, and intraspecific shifts in major isomeric arrangements are first reported here in Taxus. Moreover, we demonstrate that entire plastomes can be used to successfully discriminate all Taxus species with 100% support, suggesting that they are useful as super-barcodes for species identification. We also propose that accD and rrn16-rrn23 are promising special barcodes to discriminate yew species. Our newly developed Taxus plas...Continue Reading

References

Aug 26, 2000·Molecular Biology and Evolution·Y TsumuraK Yoshimura
Sep 30, 2004·PLoS Biology·Paul D N HebertCharles M Francis
Dec 11, 2008·Molecular Ecology·Nolan C Kane, Quentin Cronk
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra
Aug 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN CBOL Plant Working Group
Aug 28, 2010·Plant Biotechnology Journal·Catherine J NockRobert J Henry
Mar 23, 2011·Plant Molecular Biology·Susann WickeDietmar Quandt
Jun 4, 2011·PloS One·Peter M HollingsworthDamon P Little
Nov 22, 2011·Proceedings of the National Academy of Sciences of the United States of America·UNKNOWN China Plant BOL GroupGuang-Wen Duan
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anton BankevichPavel A Pevzner
May 3, 2012·Proceedings of the National Academy of Sciences of the United States of America·Kangshan MaoSusanne S Renner
Aug 1, 2012·Nature Methods·Diego DarribaDavid Posada
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Sep 7, 2013·PloS One·Jun-Bo YangDe-Zhu Li
Mar 29, 2014·Biological Reviews of the Cambridge Philosophical Society·Xiwen LiShilin Chen
Aug 3, 2014·Genome Biology and Evolution·Chih-Yao HsuShu-Miaw Chaw
Jan 23, 2015·Molecular Ecology Resources·Markus RuhsamPeter M Hollingsworth
Jul 25, 2015·Trends in Plant Science·Steven Dodsworth
Sep 12, 2015·Molecular Ecology Resources·Pasquale L CurciGabriella Sonnante
Nov 8, 2015·American Journal of Botany·Joseph F WalkerNancy C Emery
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
May 14, 2016·Nucleic Acids Research·Todd M Lowe, Patricia P Chan
Jun 9, 2016·Genome Biology and Evolution·Chih-Yao HsuShu-Miaw Chaw
Aug 3, 2016·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Peter M HollingsworthAlex D Twyford

❮ Previous
Next ❯

Citations

May 28, 2020·Scientific Reports·Morgan R GostelCaroline Puente-Lelievre
Nov 30, 2019·International Journal of Molecular Sciences·Xinbo PangBin Li
Aug 1, 2020·Frontiers in Genetics·Ruo-Nan WangZeng-Yuan Wu
Apr 14, 2020·Genome Biology and Evolution·Chaehee LeeRobert K Jansen
Nov 28, 2020·Scientific Reports·Chung-Shien WuShu-Miaw Chaw
Nov 4, 2020·The Journal of Eukaryotic Microbiology·Sarah RussellAdrian Reyes-Prieto
Jan 10, 2021·BMC Plant Biology·Chung-Shien WuShu-Miaw Chaw
Dec 1, 2020·Annals of Botany·Yunheng JiJiahui Chen
Mar 5, 2021·Mitochondrial DNA. Part B, Resources·Ningning ZhangZhenqiang Zhang

❮ Previous
Next ❯

Datasets Mentioned

BETA
MH390441
MH390489

Methods Mentioned

BETA
PCR
PCRs

Software Mentioned

SPAdes
MEGA
SE
RAxML
Sciadopitys
jModelTest2
Geneious
tRNAscan
progressMavus
clpP

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.