Plastid Genome Degradation in the Endangered, Mycoheterotrophic, North American Orchid Hexalectris warnockii

Genome Biology and Evolution
Craig F Barrett, Aaron H Kennedy

Abstract

Heterotrophic plants provide evolutionarily independent, natural experiments in the genomic consequences of radically altered nutritional regimes. Here, we have sequenced and annotated the plastid genome of the endangered mycoheterotrophic orchid Hexalectris warnockii. This orchid bears a plastid genome that is ∼80% the total length of the leafy, photosynthetic Phalaenopsis, and contains just over half the number of putatively functional genes of the latter. The plastid genome of H. warnockii bears pseudogenes and has experienced losses of genes encoding proteins directly (e.g., psa/psb, rbcL) and indirectly involved in photosynthesis (atp genes), suggesting it has progressed beyond the initial stages of plastome degradation, based on previous models of plastid genome evolution. Several dispersed and tandem repeats were detected, that are potentially useful as conservation genetic markers. In addition, a 29-kb inversion and a significant contraction of the inverted repeat boundaries are observed in this plastome. The Hexalectris warnockii plastid genome adds to a growing body of data useful in refining evolutionary models in parasites, and provides a resource for conservation studies in these endangered orchids.

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·K H WolfeJ D Palmer
Jan 1, 1985·Annual Review of Genetics·J D Palmer
Nov 20, 2001·Nucleic Acids Research·S KurtzR Giegerich
Jun 8, 2004·Bioinformatics·Stacia K WymanJeffrey L Boore
Apr 2, 2010·The New Phytologist·Vincent Merckx, John V Freudenstein
Mar 23, 2011·Plant Molecular Biology·Susann WickeDietmar Quandt
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jul 28, 2016·Proceedings of the National Academy of Sciences of the United States of America·Susann WickeGerald M Schneeweiss
Jan 10, 2017·The New Phytologist·Sean W GrahamVincent S F T Merckx
Mar 5, 2017·The Plant Journal : for Cell and Molecular Biology·Choun-Sea LinMing-Che Shih
Jul 22, 2017·The New Phytologist·Thomas W A BraukmannJohn V Freudenstein

❮ Previous
Next ❯

Citations

Sep 11, 2019·Molecular Biology and Evolution·Brandon T Sinn, Craig F Barrett
Mar 11, 2020·Frontiers in Plant Science·Young-Kee KimKi-Joong Kim
Oct 22, 2020·PeerJ·Yanqiong ChenJunwen Zhai
May 7, 2019·Molecular Biology and Evolution·Craig F BarrettAaron H Kennedy

❮ Previous
Next ❯

Datasets Mentioned

BETA
JF719062
GU811709
JX08866

Software Mentioned

OGDraw
R
NOVOPlasty
Trimmomatic
PAST
Phobos
Geneious
MAUVE
R Core Development
REPuter

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.