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Leafcutter ants farm a fungal cultivar (Leucoagaricus gongylophorus) that converts inedible vegetation into food that sustains colonies with millions of workers. Like fruits of crops domesticated by humans, L. gongylophorus has evolved specialized nutritional rewards -tiny swollen hyphal cells called gongylidia that package metabolites eaten by ant...
Symbiosis between insects and fungi arose multiple times during the evolution of both groups, and some of the most biologically diverse and economically important are mutualisms in which the insects cultivate and feed on fungi. Among these are bark beetles, whose ascomycetous cultivars are better known and studied than their frequently-overlooked a...
The taxonomy of Polyporales is complicated by the variability in key morphological characters across families and genera, now being gradually resolved through molecular phylogenetic analyses. Here a new resupinate species, Crystallicutis damiettensis sp. nov. found on the decayed trunks of date palm (Phoenix dactylifera) trees in the fruit orchards...
Pterulaceae was formally proposed to group six coralloid and dimitic genera: Actiniceps (=Dimorphocystis), Allantula, Deflexula, Parapterulicium, Pterula, and Pterulicium. Recent molecular studies have shown that some of the characters currently used in Pterulaceae do not distinguish the genera. Actiniceps and Parapterulicium have been removed, and...
The taxonomy of Polyporales is complicated by the variability in key morphological characters across families and genera, now being gradually resolved through molecular phylogenetic analyses. Here a new resupinate species, Flavoceraceomyces damiettense (NOM. PROV.) found on the decayed trunks of date palm (Phoenix dactylifera) trees in the fruit or...
Pterulaceae was formally proposed to group six coralloid and dimitic genera [Actiniceps (=Dimorphocystis), Allantula, Deflexula, Parapterulicium, Pterula and Pterulicium]. Recent molecular studies have shown that some of the characters currently used in Pterulaceae Corner do not distinguish the genera. Actiniceps and Parapterulicium have been remov...
The genus Parapterulicium was first introduced to accommodate two Brazilian species of coralloid fungi with affinities to Pterulaceae (Agaricales). Despite the coralloid habit and the presence of skeletal hyphae, other features, notably the presence of gloeocystidia, dichophyses and papillate hyphal ends, differentiate this genus from Pterulaceae s...
I have a column like the one in the image attached that I've used with sepharose.
I would like to know how to clean them to reuse (with sepharose again).
I'm trying to clean up some DNA for genomic sequencing (Nanopore and Illumina), but i'm still struggling with the purity of my DNA.
My 260/280 ration is ok, that is not an issue, however my 260/230 is always lower than 1.6.
Firstly I thought it could be contaminants carryover from my extract, but I just ran some tests on Lambda phage DNA and got the same problem.
I got some lambda DNA and run some tests with addition of different volumes of my homemade Ampure beads (https://openwetware.org/wiki/SPRI_bead_mix).
I tried 1:1, 1:2 and 1:9 and my 230 ratios were again lower than 1.5.
Is it possible the beads are carrying some PEG? If so it wont be a problem for the libraries preps since the ligation buffers uses peg as well, right?
Can you see other source of 230nm contamination?
Thank you in advance,
I have extracted DNA from fungal mycelia but when I checked on Nanodrop, most of my samples have a 260/230 ratio < 2.
I think the contamination might be from polysaccharides, since some of the media might have been input in the extraction.
I would like to find the best method for not loose much DNA in the process.
Is it possible to cleanup with Ampure Beads? what would be the ratio sample:beads?
Precipitation of polysaccharides with KAc is a possible option?
Domestication provides one of the greatest illustrations of the power of selective forces in shaping organisms. Most of domesticated diversity is found in human agriculture, which has been selecting desirable traits over the last 10.000 years. However, agriculture first evolved in colonies of neotropical ants 50mya. The fungus-farming ants and their fungal crop represent one of the most classic examples of mutualism and coevolution, in which, it was thought, both parts were obligately dependent of the other, the fungi cannot live without ants and vice versa, the ants being responsible for the clonal propagation of fungi and the fungi providing food for the ants. However recent studies have called these mandatory associations into question, showing that the fungi can survive outside some symbiosis. In turn, Pterulaceae fungi grown by Apterostigma ants were never registered independently from ants. This condition has opened the way for this project that will try to answer questions about the selection of beneficial features in the ants' fungi-cultivars. With the key research question being: Do the genomes of fungus-farming ant-cultivated Pterulaceae exhibit features of domestication? Two hypotheses will be worked to try to resolve this issue: 1) Domestication of coral mushroom crops has caused changes in the cultivars’ genetic machinery underpinning enzymatic capacity to degrade garden substrate; 2) Long-term domestication of coral mushroom cultivars has resulted in loss-of-function mutations in genes no longer critical to fungal fitness outside of the symbiosis, e.g., genes involved in basidiome formation and/or the mating type loci. To carry out the project samples Apterostigma cultivars and its free-living relatives will be collected and grown axenically on agar media, analysed in optical microscope for correct identification, and vouchers of each individual shall be deposited in local herbaria. The collections will be target on where the species were previously collected: Belize, Costa Rica, Venezuela and Brazil, and coinciding with the rainy season, when the majority of free-living Pterulaceae are in the reproductive phase. The molecular phylogenetic approaches will be based on next generation sequencing techniques (NGS), which will analyse the whole genomes. Genes related to decomposition, reproduction and the mushroom formation will be the target of the analysis, which will look for duplication, synteny and gene cluster composition. The comparison between cultivars and free-living relatives will allow to discuss the selection of specific traits and domestication.