First genome-wide analysis of the endangered, endemic lichen Cetradonia linearis reveals isolation by distance and strong population structure

American Journal of Botany
Jessica L AllenS Elizabeth Alter

Abstract

Lichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes that drive their diversification and genetic differentiation. Distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, although asexual and sexual reproductive structures are observable, the lack of information about recombination rates makes inferences about reproductive strategies difficult. We investigated the population genomics of Cetradonia linearis, a federally endangered lichen in the southern Appalachians of eastern North America, to test the relative contributions of environmental and geographic distance in shaping genetic structure, and to characterize the mating system and genome-wide recombination. Whole-genome shotgun sequencing was conducted to generate data for 32 individuals of C. linearis. A reference genome was assembled, and reads from all samples were aligned to generate a set of single-nucleotide polymorphisms for further analyses. We found evidence for low rates of recombination and for isolation by distance, but not for isolation by environment. The species is putatively unisexual, given that only one mating-type locus was fo...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
May 18, 2004·BMC Bioinformatics·Ian Korf
May 17, 2005·Fungal Genetics and Biology : FG & B·Fabian A SeymourPaul S Dyer
Nov 4, 2005·Fungal Genetics and Biology : FG & B·Sandra ScherrerRosmarie Honegger
Apr 8, 2006·Molecular Ecology·Silke WerthChristoph Scheidegger
Mar 3, 2007·Bioinformatics·Jason S Papadopoulos, Richa Agarwala
Jul 3, 2007·Nature Reviews. Microbiology·Maureen A O'Malley
Aug 3, 2007·Current Biology : CB·Mathieu PaolettiPaul S Dyer
Mar 13, 2008·Current Biology : CB·Paul S Dyer
Mar 18, 2008·Proceedings of the National Academy of Sciences of the United States of America·Isheng J TsaiVassiliki Koufopanou
Feb 13, 2009·Nature·Gianni LitiEdward J Louis
Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
May 29, 2010·Microbiology and Molecular Biology Reviews : MMBR·Soo Chan LeeJoseph Heitman
May 14, 2011·Ecological Applications : a Publication of the Ecological Society of America·Dan L Warren, Stephanie N Seifert
May 28, 2011·American Journal of Botany·Nicolas MagainBernard Goffinet
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Sep 10, 2011·Bioinformatics·Tanja Magoč, Steven L Salzberg
Sep 18, 2013·Algorithms for Molecular Biology : AMB·Rayan Chikhi, Guillaume Rizk
Oct 10, 2013·Evolution; International Journal of Organic Evolution·Gideon S BradburdGraham M Coop
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Sep 10, 2014·Applications in Plant Sciences·Shiva DevkotaChristoph Scheidegger
Sep 10, 2014·Applications in Plant Sciences·Olga NadyeinaChristoph Scheidegger
Mar 3, 2015·Molecular Ecology·Sara BrancoThomas D Bruns

❮ Previous
Next ❯

Citations

Mar 13, 2020·Genome Biology and Evolution·Bastian Greshake TzovarasIngo Ebersberger
Jan 30, 2021·American Journal of Botany·Marta Alonso-GarcíaJuan Carlos Villarreal A

❮ Previous
Next ❯

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.