Three undergraduates, Sara Waldman, Dorothy Tang, and Jiaqi Mei, joined our lab for the summer. Two other undergraduates associated with our lab, Vanessa Carrasco and Sam Kovaka, had off-campus summer research experiences. Except for Jiaqi, all of these students have worked with us previously in 2013 and 2014. Scroll down to read about what they did last summer.
Sara worked with Alfredo Justo on molecular systematics of Stiptophyllum erubescens. This is an odd fungus with a lateral stipe and gills that has anatomical similarities to members of the Gloeophyllales. Stiptophyllum erubescens is morphologically intermediate between forms that have a cap, but no stalk those with a cap and central stalk in the Gloeophyllales, like Gloeophyllum and Neolentinus (respectively). With Fredo’s guidance, Sara generated sequence data from multiple genes for Stiptophyllum and combined them with data for other Gloeophyllales, much of it generated by a former post-doc, Ricardo Garcia-Sandoval. The resulting phylogenies support the view that Stiptophyllum is closely related to pileate-stipitate agarics in the Gloephyllales, including Neolentinus.
Dorothy continued our work on development in Lentinus tigrinus, in consultation with PhD student Alicia Knudson. Dorothy’s work focused on light-induced pileus formation and the genetic basis of the secotioid phenotype. The latter work involved generating and genotyping haploid progeny (single spore isolates) for use in bulked segregant analysis. This is labor-intensive, time-consuming work. Thanks to Dorothy’s efforts we now have over 100 genotyped ssi’s and we should soon be in a position to start generating DNA for the BSA.
Jiaqi is a student at Smith College, where she works with our Open Tree of Life colleague Laura Katz. At Clark, Jiaqi worked with post-doc Romina Gazis on data collection for Open Tree. Jiaqi combed through recent mycological literature seeking phylogenies and TreeBase accession numbers. With her help, we are now mostly caught up on our inventory of the fungal phylogenetic literature going back to the late 1990s.
Our next step in the Open Tree project is to obtain trees from the major phylogenetic studies that establish the backbone of the fungal tree of life, which we will synthesize as part of a planned update of the “AFTOL classification” of fungi. To that end, Jiaqi and Romina conducted an e-mail campaign seeking phylogenies that are not available in GenBank. Jiaqi distributed 200 e-mails to authors, and as of this writing we have received over 50 responses (that’s pretty good for this sort of thing, reflecting the supportive, collaborative nature of the mycological community).
Vanessa received a NOAA Fellowship to conduct bacterial screening on cultured macro algae raised in intensive land-based systems, at the North West Fisheries Science Center in Seattle, WA. This project allowed Vanessa to pursue her interests in agroecology, in an aquaculture setting.
Sam was accepted to the Summer Undergraduate Laboratory Internship (SULI) program of the US Department of Energy. He spent the summer at the Joint Genome Institute in Walnut Creek, CA, working with our collaborators Igor Grigoriev and Bobby Otillar, where he developed a semi-automated approach to construction of large-scale fungal phylogenies based on genomes. This work grew out of a directed study project that Sam completed at Clark last year. Eventually, it is hoped that this tool will be accessible through the JGI MycoCosm portal.