Using multi-locus sequence data for addressing species boundaries in commonly accepted lichen-forming fungal species

Zhao, Xin; Fernández-Brime, Samantha; Wedin, Mats; Locke, Marissa C.; Leavitt, Steven D.; Lumbsch, H. Thorsten

doi:10.1007/s13127-016-0320-4

Cited by 25 publications

(19 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA‐sequencing analysis revealed numerous differentially expressed genes in Thellungiella salsuginea under cold treatment . RNA interference lines of the cold‐induced gene TsFtsH8 enhanced Thellungiella salsuginea tolerance to cold . Similarly, the Thellungiella salsuginea salt‐induced gene TsnsLTP4 encodes a non‐specific lipid transfer protein that participates in wax deposition and in plant tolerance against abiotic stresses, including salt, ABA, and high and low temperatures …”

Section: Temperature Changesmentioning

confidence: 99%

“…152,153 RNA interference lines of the cold-induced gene TsFtsH8 enhanced Thellungiella salsuginea tolerance to cold. 28,[154][155][156] Similarly, the Thellungiella salsuginea salt-induced gene TsnsLTP4 encodes a non-specific lipid transfer protein that participates in wax deposition and in plant tolerance against abiotic stresses, including salt, ABA, and high and low temperatures. [157][158][159][160] Distinct pathways mediate stress adaptation…”

Section: Salt Stressmentioning

confidence: 99%

See 1 more Smart Citation

Molecular mechanisms underlying stress response and adaptation

Sun

Zhou

2017

Thoracic Cancer

View full text Add to dashboard Cite

Environmental stresses are ubiquitous and unavoidable to all living things. Organisms respond and adapt to stresses through defined regulatory mechanisms that drive changes in gene expression, organismal morphology, or physiology. Immune responses illustrate adaptation to bacterial and viral biotic stresses in animals. Dysregulation of the genotoxic stress response system is frequently associated with various types of human cancer. With respect to plants, especially halophytes, complicated systems have been developed to allow for plant growth in high salt environments. In addition, drought, waterlogging, and low temperatures represent other common plant stresses. In this review, we summarize representative examples of organismal response and adaptation to various stresses. We also discuss the molecular mechanisms underlying the above phenomena with a focus on the improvement of organismal tolerance to unfavorable environments.

show abstract

Section: Temperature Changesmentioning

confidence: 99%

Section: Salt Stressmentioning

confidence: 99%

Molecular mechanisms underlying stress response and adaptation

Sun

Zhou

2017

Thoracic Cancer

View full text Add to dashboard Cite

show abstract

“…Difficulties during sequencing of the mycobiont and lichenicolous fungi have been reported because universal DNA barcodes do not exist (Schoch et al, ). After testing several recent primer pairs and PCR conditions (Matheny, Liu, Ammirati, & Hall, ; Schmitt et al, ; Schoch et al, ; Westberg, Millanes, Knudsen, & Wedin, ; Williams et al, ; Zhao et al, ), the following final settings were used for the mycobiont: the primer pair ITS1f and LR3 (ITS) and gRPB1‐A and fRPB1‐C (RPB1) after Westberg et al () and Zhao et al () respectively. The lichenicolous fungi were inseparably connected to the lichen thallus and therefore always mixed with DNA of the mycobiont.…”

Section: Methodsmentioning

confidence: 99%

Ecophysiology and phylogeny of new terricolous and epiphytic chlorolichens in a fog oasis of the Atacama Desert

et al. 2019

View full text Add to dashboard Cite

The Atacama Desert is one of the driest and probably oldest deserts on Earth where only a few extremophile organisms are able to survive. This study investigated two terricolous and two epiphytic lichens from the fog oasis “Las Lomitas” within the National Park Pan de Azúcar which represents a refugium for a few vascular desert plants and many lichens that can thrive on fog and dew alone. Ecophysiological measurements and climate records were combined with molecular data of the mycobiont, their green algal photobionts and lichenicolous fungi to gain information about the ecology of lichens within the fog oasis. Phylogenetic and morphological investigations led to the identification and description of the new lichen species Acarospora conafii sp. nov. as well as the lichenicolous fungi that accompanied them and revealed the trebouxioid character of all lichen photobionts. Their photosynthetic responses were compared during natural scenarios such as reactivation by high air humidity and in situ fog events to elucidate the activation strategies of this lichen community. Epiphytic lichens showed photosynthetic activity that was rapidly induced by fog and high relative air humidity whereas terricolous lichens were only activated by fog.

show abstract

“…2,000 bases long mitochondrial ribosomal small subunit (mtSSU). This fragment, as delimited by the primers mtSSU1 and mtSSU3R (Zoller et al, 1999), is frequently used in lichen systematics and for species delimitation (Amo de Paz et al, 2011;Leavitt et al, 2015;Zhao et al, 2017;Kistenich et al, 2018). We designed a set of seven forward and seven reverse primers (Table 2; Figure 2) covering all of the 900 bases using Primer3 v. 2.3 (Untergasser et al, 2012) based on mtSSU sequences for our selected taxa or closely related taxa available from GenBank (Benson et al, 2018).…”

Section: Primer Design and Pcr Amplificationmentioning

confidence: 99%

DNA Sequencing Historical Lichen Specimens

et al. 2019

View full text Add to dashboard Cite

Biological specimens in natural history collections worldwide are increasingly being used in biogeographical, environmental, and taxonomic studies. For their meaningful use, correct species identification is crucial. For example, clarifying if a species is new to science requires an overview of what has already been described. This includes comparisons with existing authoritative specimens (types). Most type specimens are rather old and their DNA expected to be degraded to various extents. Comparative DNA sequence analysis is in regular use in taxonomic research of today and is essential for identifying and delimiting species. In this study, we focus on lichenized fungi (lichens), in which many species groups are highly inconspicuous and impossible to identify to species based on morphology alone. Our aim was to test the non-mutually exclusive hypotheses that DNA quality of lichens depends on (1) time since collection, (2) taxonomic affinity, and/or (3) habitat/ecology. We included two species from each of four different lichen genera (i.e., Cladonia, Nephroma, Peltigera, and Ramalina), each species pair with a different autecology. For each species, we included samples from approximately every 25 years from present to about 150 years back in time. We used a two-step PCR-based approach followed by sequencing on an Ion Torrent PGM to produce target sequences (mtSSU) of degraded DNA. We received satisfactory DNA sequence information for 54 of 56 specimens. We recovered full-length sequences for several more than 100-years-old specimens, including a 127-years-old specimen, and retrieved enough sequence information for species identification of a 150-years-old specimen. As expected, sequencing success was negatively correlated with age of the specimens. It also varied with taxonomic affinity. We found no significant correlation between sequencing success and habitat ecology of the investigated specimens. The herein tested Ion Torrent sequencing approach outperformed Sanger sequencing with regard to sequencing success and efficiency. We find the protocol used herein highly suitable for obtaining sequences from both young and old lichen specimens and discuss potential improvements to it.

show abstract

Using multi-locus sequence data for addressing species boundaries in commonly accepted lichen-forming fungal species

Abstract: Using multi-locus sequence data for addressing species boundaries in commonly accepted lichen-forming fungal species.

Cited by 25 publications

References 67 publications

Molecular mechanisms underlying stress response and adaptation

Molecular mechanisms underlying stress response and adaptation

Ecophysiology and phylogeny of new terricolous and epiphytic chlorolichens in a fog oasis of the Atacama Desert

DNA Sequencing Historical Lichen Specimens

Contact Info

Product

Resources

About