Summer Goodbyes: Suki

The end of summer meant goodbye to our excellent REU student Saisuki Putumbaka. Suki was here for two months and worked on fungal-bacteria interactions project as part of the UCR Research Experiences for Undergraduates organized through the Center for Plant Cell Biology. Under the guidance of Derreck  she tested ideas about the bacteria harbored by a broad range of zygomycete fungi from our draft genome sequencing projects. She also learned how to take pictures of some of these fungi and observing how they sped up the rotting process in fruit. Alas the best laid plans to compare microbiomes of these samples did not come to fruition but I think there were some lessons in there about how science works some of the time.

It was really a joy having her in the group and we are excited about her finishing her senior year at The College of New Jersey and applying to graduate school next. Many of the lab members helped to make sure Suki was properly introduced her to Southern California delights from Joshua Tree National Park, the Pacific Ocean, and In-n-Out Burger.

Saisuki and some of the lab members
Suki with some of her lab mates and mentors from summer 2019.

Congrats to Yan!

I am delighted to announce that Yan Wang a current postdoc in our group, will be a starting his next position as an Assistant Professor in the Department of Biology at the University of Toronto-Scarborough. Yan has spent the last two years in the lab working on Zygolife and Neocallomastigomycota fungi projects. We are super proud of all he has accomplished in his training and research. This includes multiple publications from his thesis work and several papers submitted from his current projects. The lab has greatly benefited from his phylogenetic and insect-fungi expertise. Luckily we still have ~6 more month together to continue projects and help him prepare for his next step in his career.

Helping Yan celebrate his acceptance of offer at UTSC.

Spring papers news

We enjoyed a wonderful spring flower season here in Southern California
(Harford Springs Riverside County Regional Park)

Several publications were accepted and published in last few months and want to highlight the hard work from lab members and collaborators.

Jinfeng lead article published on the localized burst of Rice Transposable Elements Ping and Pong in only a subset of the domesticated lineages and clues to what changed to drive their increased activity.

Variation of mPing, Ping, and Pong element copy number in rice subgroups https://www.nature.com/articles/s41467-019-08451-3/figures/2

A fun collaboration lead by Adam Bewick and Bob Schmitz we called #MycoMeth explored diversity of Cytosine DNA Methylation in Fungi looking at the 5-methylcytosine (5mC) marks and evolution of the fungal 5mC methyltransferases .

Genomewide 5mC profiles https://www.nature.com/articles/s41559-019-0810-9/figures/2

Two Zygolife project papers. One on genome evolution and phylogenic position of Endogone – a truffle forming Mucoromycotina fungus. This was quite challenging but interesting project to tackle, lead by Ying Chang in the Spatafora Lab. Dr Chang took a metagenomics approach to capture these unculturable fungi followed by bioinformatic analyses to isolate the fungal and Mucoromycotina component of the dataset.

Phylogenetic placement and divergence time estimation of Endogonales, and the evolution of fungal plant‐cell‐wall‐degrading enzymes (PCWDEs)

A second paper lead by William Davis from Tim James lab on the genomes and phylogeny of Zoopagomycotina fungi which include nematophagous and mycoparasites.

Fig 5. Ancestral state reconstructions of trophic state on the best ML tree (A) and the ASTRAL consensus tree (B) using maximum likelihood. Pie graphs at nodes show the proportional likelihood of each character state.

Jason participated in a Marine Fungi workshop on the unexplored diversity in the marine environments and co-authored this perspective on the opportunities and challenges in characterizing and studying these fungi.

Morphological diversity of fungi collected from a biotic host. Fungal collection isolated from a marine sponge, Ircinia variabilis (formerly Psammocinia sp.).

Former postdoc Ousmane Cissé developed FGMP, a tool for assessing completeness of fungal genomes which uses both conserved protein coding markers that can include multicopy gene families and conserved non-coding DNA regions. This was published this month as well, congrats Ousmane!

Fig 2. Estimation of genome completeness in fungal genomes. A comparison of genome completeness by multiple software tools using initial and latest genome assembly versions of 45 fungi. Genome completeness expressed as a percentage of expected markers (y-axis) is plotted against assembly size in megabases (x-axis).

Congrats Derreck on CCSTS fellowship

Derreck Carter-HouseCongrats Derreck! He was selected by the California Council on Science and Technology (CCST) to give a presentation and represent Dept of Microbiology and Plant Pathology and UCR at the California Science Translators Showcase. He will be giving a talk about his research at the California State Capitol to legislators/state senators, agency managers, and senior policy leaders. He was chosen out of a pool of California PhD students, post-docs, and career scientists from all different STEM fields and universities to talk about plant pathology/fungi.

Fall lab news

Nat visited New Mexico State University several times this summer to complete work at the Jornada LTER site working with Nicole Pietrasiak (@drylandalgae) on the micro- and myco-biomes of biological crusts. Visits to Anza Borrego and Boyd Deep Canyon for Tania to scope out UCNRS research sites to explore desert rock varnish and rock or crust associated black fungi. Julia continued to develop her Joshua Tree research sites for lichen studies and has collected and sequenced new accessions for a reference library of lichens from Joshua Tree NP.

Congrats to Jesús (IG: variety_hour) who passed his qualifying exam has continued to explore zygomycete diversity focusing on sexual reproduction.  Derreck has been working on bacteria-fungal interactions via volatiles and new work with N. crassa sensing of these. Yan has submitted a manuscript on his postdoc work on phylogenomics and dating the emergence of the the anaerobic gut fungi. Jinfeng has submitted and is revising work on characterizing the transposition and burst of the Ping, Pong, and mPing transposable elements across 3000 Rice accessions. Sawyer generated and analyzed whole genome sequence from strains of Rhizopus stolonifer in his population genomics project which he presented at the IMC11 conference.

New publications including population genomic diversity of Candida lusitaniae, Entomophthorales proteases, space fungi!, and fungal & bacteria communities in Antarctic rocks came out in the last few months.

Hopefully another update before the end of 2018 but check out pictures and tweets for shorter updates.

Summer conference season

The lab is back from conferences this summer. The Cellular and Molecular Fungal Biology Gordon Research Conference in Holderness, NH and the 11th International Mycological Congress in Puerto Rico. Tania also gave her first talk  at the Black Yeast workshop held in Amsterdam as part of the ISHAM meeting.

Many tweets were had … #FungalGRC2018 and #IMC11 or #IMC11pr. Posters and talks were given by everyone in the lab who attended and it was a great chance to mix with fungal friends new and old!

Recent Lab Papers

There have been several manuscripts are now out from work that was done over the last few years. It has been great to be able to collaborate with many research teams as part of this work.

Been slow to mention these but wanted to make sure and call out the hard work from everyone. A long term collaboration lead by Cene Gostinčar on population genomics in Hortaea, a ascomycete black yeast, complemented some reference genome work we published last year [1].  Former postdoc Ousmane Cissé published his work on Pneumocystis at the NIH in his current postdoc [2]. Current postdoc Yan Wang published part of his thesis work and we worked on these data a bit as part of the zygolife project here [3].  Graduate students Nat Pombubpa collaborated with Plant Sciences and Jeff Diez lab graduate student Courtney Collins  on her thesis work looking at the mycobiome differences of soils in an alpine gradient with and without invasive shrub introduction [4].  Andrii Gryganskyi’s work on Rhizopus phylogeny with some of the first multi-genome work on this genus that was one of the earliest collaborations on some ZyGoLife questions questions [5].  Work exploring whether Transposable elements have a role in stage-specific gene expression in Coccidioides with Theo Kirkland and Anna Muszewska [6].  A collaboration lead by Tom Richard’s lab and Guy Leonard sequence and assembled and annotated a genome of a ‘pseudofungus’ hyphochytriomycete called Hyphochytrium catenoides [7]. I think I forgot to also call out that last year postdoc Jinfeng Chen published work collaboratively with postdocs Lu Lu and Sofia Robb on the active Rice transposable element system mPing and Ping [8].

Good work all!

  1. Gostinčar C, Stajich JE, Zupančič J, Zalar P, Gunde-Cimerman N. Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast.BMC Genomics. 2018 May 15;19(1):364. doi: 10.1186/s12864-018-4751-5.
  2. Wang Y, Stata M, Wang W, Stajich JE, White MM, Moncalvo JM. Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis. MBio. 2018 May 15;9(3). pii: e00636-18. doi: 10.1128/mBio.00636-18.
  3. Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA. Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis. MBio. 2018 May 8;9(3). pii: e00381-18. doi: 10.1128/mBio.00381-18.
  4. Gryganskyi AP, Golan J, Dolatabadi S, Mondo S, Robb S, Idnurm A, Muszewska A, Steczkiewicz K, Masonjones S, Liao HL, Gajdeczka MT, Anike F, Vuek A, Anishchenko IM, Voigt K, de Hoog GS, Smith ME, Heitman J, Vilgalys R, Stajich JE. Phylogenetic and Phylogenomic Definition of Rhizopus Species.  G3 (Bethesda). 2018 Apr 19. pii: g3.200235.2018. doi: 10.1534/g3.118.200235.
  5. Collins CG, Stajich JE, Weber SE, Pombubpa N, Diez JM. Shrub range expansion alters diversity and distribution of soil fungal communities across an alpine elevation gradient. Mol Ecol.2018 Apr 19. doi: 10.1111/mec.14694.
  6. Kirkland TN, Muszewska A, Stajich JE. Analysis of Transposable Elements in Coccidioides Species. J Fungi (Basel). 2018 Jan 19;4(1). pii: E13. doi: 10.3390/jof4010013.
  7. Leonard G, Labarre A, Milner DS, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bové X, Sebé-Pedrós A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides.  Open Biol. 2018 Jan;8(1). pii: 170184. doi: 10.1098/rsob.170184.
  8. Lu L, Chen J, Robb SMC, Okumoto Y, Stajich JE, Wessler SR. Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. Proc Natl Acad Sci U S A. 2017 Dec 5;114(49):E10550-E10559. doi: 10.1073/pnas.1716459114.

Figure 6 – Overview of the timing and evolution of Pneumocystis and their mammalian hosts.

ZyGoLife visitors

Last week we hosted several visitors from our ZyGoLife collaborative team in sunny California. I wrote a few notes on Nicole Reynolds and Javier Tabima’s visit for the zygolife site on their extended research stay. We also got to host the Zygofornia Zygolife team meeting.  Here are some pictures I took from the desert and mountain visits.

Zygolife team photo, minus Jason, in the UC James Reserve, San Jacinto Mountains, California

Lost in a forest? Or finding fungi? in the James Reserve, San Jacinto Mountains

bees love the water near a wash that had a little bit of moisture in Mojave, in Granite Mountain Desert Research Center

Jessie and Derreck bonded over fungi and bacteria

Lichens and mosses on granite rocks in Granite Mountain Desert Research Center

Sunset over Kelso Dunes in Mojave National Preserve

Lizards in Mojave National Preserve

Blooms among Lava in Mojave National Preserve

Sweeny Granite Mountain Desert Research Center, a University of California, Natural Reserve.

Kelso Dunes, Mojave National Preserve

Desert Adventures, 2018

Nat and Jason headed out to the Mojave National Preserve to meet up with Erik Hom and his StudyUSA class from Univ of Mississippi. We started at the Sweeney Granite Mountains Desert Research Center which is one of 39 Natural Reserves in the University of California.  We were there to teach a bit about cryptogamic crusts, show the Kelso dunes off, and explore some more of the desert crust sampling sites that our collaborator Nicole Pietrasiak (@drylandalgae) and Paul De Ley have collected from. Nothing like seeing sites that previously I only knew from pictures or tubes of soil!

A few pictures from our visit.

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Kelso Dunes
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Crusts symbioses of algae and cyanobacteria with fungi, bacteria, and many uncounted single celled organisms.

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Lichen Crusts galore across from the Kelso dunes
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Moss Crusts are also rich symbioses with a predominant moss.
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Old volcanic flow in the Cima area also has cacti and crusts
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Colorful lichens found on the granite faces. On closer looks, these are often 3 or more species competing for space on the same surface.

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