Everything You Wanted to Know about the Lake Arrowhead Microbial Genomes meeting #LAMG14

The Lake Arrowhead Microbial Genomes meeting, which happens every other year, is starting tonight.  I love this meeting.  No bias here since I am now a co-organizer.  But I really love this meeting.  I am posting here some background information about the meeting for those interested.  We will be live tweeting the meeting using the hashtag #LAMG14.  This years program is here.

Posts of mine about previous meetings

• March 02, 2014: Save the dates / preliminary program for Lake Arrowhead Microbial Genomes Meeting
• July 11, 2012: Lake Arrowhead Microbial Genomes 2012 #Genomes #Microbes #Mountains #Lake #Fun #Wine #MustGo
• September 22, 2012: Lake Arrowhead Microbial Genomes Meeting 2012 Speaker Gender Ratio #LAMG12
• September 22, 2012: Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting
• October 28, 2010: The Story behind the Meeting: Lake Arrowhead Microbial Genomes 2010 
• September 14, 2008: It's Miller Time - Lake Arrowhead Microbial Genomes Conference -- about to begin
• September 16, 2008: Lake arrowhead notes - UPDATED
• September 29, 2006: Genomics Education highlighted at 14th Annual International Meeting on Microbial Genomics

Blog posts by others

• December 23, 2012: Srijak Bhatnagar: Lessons from 2012: Lake Arrowhead Microbial Genomes
• September 21, 2008: Morgan Langille Review of Arrowhead Conference

Programs and notes from past meetings

• 1998_LakeArrowhead notes
• 1998_Arrowhead
• 2000_Arrowhead
• 2002 Lake_Arrowhead
• 2004  meeting notes and booklet
• 2006_Arrowhead
• 2008_Arrowhead
• 2010_Arrowhead
• 2012 Lake Arrowhead Booklet

Meeting Web Sites

• Microbial Genomics - ARROWHEAD 2012

I have uploaded slides from my previous presentations at the meeting

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Jonathan Eisen @phylogenomics talk for #LAMG12 from Jonathan Eisen

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Jonathan Eisen talk on "The Importance of History" at Lake Arrowhead Small Genomes Meeting 2010 from Jonathan Eisen

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Jonathan Eisen talk on "Genomic Encyclopedia" at Lake Arrowhead Small Genomes Meeting 2008 from Jonathan Eisen

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Jonathan Eisen talk on "Enodsymbiont Genomics" at Lake Arrowhead Small Genomes Meeting 2006 from Jonathan Eisen

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Jonathan Eisen talk on "Phylogenomics of Microbes" at Lake Arrowhead Small Genomes Meeting 2004 from Jonathan Eisen

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Jonathan Eisen talk on "Phylogenomics of Microbes" at Lake Arrowhead Small Genomes Meeting 2002 from Jonathan Eisen

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Jonathan Eisen talk on "Phylogenomics of DNA repair" at Lake Arrowhead Small Genomes Meeting 2000 from Jonathan Eisen

Question - anyone having issues w/ delays/difficulty in the process of getting genomes / metagenomes into Genbank?

DNA sequencing continues to go crazy in terms of lower cost, higher speed, and spread of technology. Alas, some aspects of doing a genome project are not necessarily keeping up. So I am posting here to ask a simple question about one of these steps. What do people out there think about the steps of getting genome / metagenome data into Genbank. Without wanting to bias answers too much - we are having some challenges in this area. Storify of Twitter responses below the fold

Nice timing: Our paper on the Darwin's Finch genome is out today on Darwin's birthday

Birthday party for Darwin in 2009

Well, I assume this was on purpose from the folks at Biomed Central but not sure.  Our paper on the genome of one of Darwin's Finches is out today in BMC Genomics: BMC Genomics | Abstract | Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.

Abstract of the paper:

Background
A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris.
Results
13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins.
Conclusions
These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches.

Figure 1

There is a long long long story behind this paper.  Too long for me to write up right now.  I wrote up some of the story for a Figshare posting of the genome data last year.

“Darwin’s Finches” are a model system for the study of various aspects of evolution and development.  In 2008 we commenced on a project to sequence the genomes of some of these species – inspired by the (then) upcoming celebration of the 200th anniversary of the birth of Charles Darwin (which was in February 2009).  The project started with a brief discussion at the AGBT meeting in 2008 and then via an email conversation between Jonathan Eisen and Jason Affourtit about the possibility of a collaboration involving the 454 company (which was looking for projects to highlight the power of it’s then relatively new 454 sequencing machines).  After further discussions between Jonathan Eisen, his brother Michael Eisen (who separately had become interested in Darwin’s finches) and people from 454 it was decided that this was a potentially good project for a scientific and marketing collaboration.  

In these conversations it was determined that the most likely limiting factor would be access to DNA from the finches.  This was largely an issue due to the fact that the Galapagos Islands (where the finches reside) are a National Park in Ecuador and also a World Heritage site.  Collection of samples there for any type of research is highly regulated.  Thus, Jonathan Eisen made contact with Peter and Rosemary Grant – the most prominent researchers working on the finches – and who Eisen had discussed sequencing the finch genomes in the early 2000s.  In that previous conversation it was determined that the sequencing would be too expensive to carry out without a major fundraising effort.  However, with the advent of “next generation” sequencing methods such as 454 the total costs of such a project would be much lower.   

In the conversations with the Grants, the Grants offered to ask around to see if anyone had sufficient amounts of DNA (or access to samples), which would be needed for genome library construction.  Subsequently they identified Arkhat Abzhanov from Harvard as someone who likely had samples as well as permission to do DNA-based work on them, from many of the finch species. Abzhanov offered to provide samples from three key species (large ground finch Geospiza magnirostris, large cactus finch G. conirostris and sharp-billed finch G. difficilis) and DNA was sent to Roche-454 for sequencing in July of 2008.  In August, the first “test” sequence data was provided from Geospiza magnirostris.  A plan was then made to generate additional data and Roche offered to do the sequencing at their center at a steep discount.  Funds were raised by Jonathan Eisen, Greg Wray, Monica Riley, and others to pay for the sequencing and over the next year or so, three sequencing bursts were conducted at Roche-454. "

That is a decent summary of the background.  The details on the science are in the paper.  What the background does not say is that the project languished for years as we did not have funds to support the actual analysis of the genomes and it was kind of out of my normal area of expertise.  Along the way, I did a poor job of communicating with some of the initial parties in the project (e.g., I did a really bad job of communicating with Greg Wray - who had provide some of the funds - and I will forever be trying to make things up to him).  Anyway, thankfully Arhat eventually pulled together a group of people led by Chris Ponting to help analyze the genome and Chris led the way to the paper that is out today.  Only four years after our original goal.

I have been a birder and an evolutionary biologist for many many many years. Thus this is kind of a cool project for me.  When I was in the Galapagos in 2002 I dreamed of doing a project like this - and even started doodling Darwin's finches all over the place - including on some of the styrofoam cups we sent down to the bottom of the ocean on the outside of the Alvin sub as part of a deep sea research cruise I went on.  See below:

Add caption

Some related posts:

From 2002

From 2002

Me, in the Galapagos in 2002

Me in the Galapagos in 2002

Me, today, w/ Darwin's finch art

• Top five metaphors Darwin considered and rejected for "The Tree of Life
• Art-Science Fusion and Darwin's Face at Davis
• 10 simple ways to honor Charlie D (aka Darwin)
• My favorite evolution stuff 2. Charles Darwin Tobacco Card
• Darwin Celebration in Davis
• Open Access Darwin?
• Evolution pumpkins - from Darwin to Woese
• Nice Darwin Art at #UCDavis Evolution/Ecology Dept.
• My favorite evolution stuff 1. 1900 Darwin Post Card

Rhodopsins Rhodopsins everywhere ...

Was browsing through this paper (largely due to my interest in sequencing genomes of novel organisms): Genome Biology | Abstract | Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.

And I found they found something very interesting.  "We identified two rhodopsins both with C-terminal histidine kinase and response regulator domains with homology to the sensory rhodopsins of the green algae that represent candidates for light sensors in Ac (Figure 3)." Seems they found some homologs of the proteorhodopsin / halorhodopsin family of proteins which I have been interested in for years.  Check out Figure 3:

Every couple of months there is a new group of organisms that is found to have a member of this gene family.  See for example: Sequencing of Seven Haloarchaeal Genomes Reveals Patterns of Genomic Flux and Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea for papers in which I was involved where Rhodopsins were part of the story.  Also see the Venter et al. Sargasso paper: PDF.  Anyway - just a quick post for those out there interested in rhodopsins and the like ...

Welcome to the Microbial Earth Project

Map of type strains.

All interested in microbes and their genomes should check out The Microbial Earth Project.  It "is an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains. The name of the project comes from the recognition that Earth is a predominantly a microbial planet, and by effect in order to understand life on our planet, we need to understand how microbial life works."

There are some 10,000 described type strains of bacteria and archaea.  Not really a lot given that there are probably millions upon millions of species of bacteria and archaea.  But it is what we have available to us in terms of the formally described and accepted species for which there is an available cultured strain.

At this site you can do things like "Adopt a Type Strain" or view a cool "Map of the type strains".

The Steering Committee for the project is

• Jonathan Eisen (University of California, Davis)
• George Garrity (Names for Life, USA)
• Philip Hugenholtz (Australian Centre for Ecogenomics Research, Australia)
• Hans-Peter Klenk (DSMZ, Germany)
• Nikos C. Kyrpides (DOE-Joint Genome Institute, USA)
• William B. Whitman (University of Georgia)
• Tanja Woyke (DOE-Joint Genome Institute, USA)

Much of the real work being done by Nikos Kyrpides, George Garrity, and others though I am very pleased to be a member of the Steering Committee.   One of my key jobs will be to get the word out early and often.  Hence this post.

Storify for Lake Arrowhead Microbial Genomes #LAMG12 Meeting

Meeting went well.  Here is a storification of it:

A blast from the past: Plasmodium, plastids, phylogeny, and reproducibility

A few days ago I got an email from a colleague who I had not seen in many years.  It was from Malcolm Gardner who worked at TIGR when I was there and is now at Seattle Biomed.

His email was related to the 2002 publication of the complete genome sequence of Plasmodium falciparum - the causative agent of most human malaria cases -  for which he was the lead author.   Someone had emailed Malcolm asking if he could provide details about the settings used in the blast searches that were part of the evolutionary analyses of the paper.   The paper is freely available at Nature - at least for now - every once in a while the Nature Publishing Group seems to put it behind a paywall despite their promises not to.

Malcolm was contacting me because I had run / coordinated much of the evolutionary analysis reported in that paper.  I note - as one of the only evolution focused people at TIGR it was pretty common for people to come to me and ask if I could help them with their genome.  I pretty much always said yes since, well, I loved doing that kind of thing and it was really exciting in the early days of genome sequencing to be the first person to ask some evolution related question about the data.

Interesting new paper: "Proving universal common ancestry with similar sequences"

Just discovered an interesting paper by Leonardo de Oliveira Martins and David Posada.  It is titled "Proving universal common ancestry with similar sequences."  It relates to a paper by Douglas Theobald: "A formal test of the theory of universal common ancestry. Nature 2010; 465:219-22." Although the latter paper is not openly available the more recent one is.  


The new paper is worth a look.  Not sure about the Theobald one as I do not have access from home.


Am hoping Leonardo writes more about this in his blog: Bayesian Procedures in Biology ....

Antibiotic use in animals (may) lead to superbugs in people #mBIO

New paper in mBIO of potential interest from Lance Price et al.:  Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock.  For those not in the know, mBIO is a relatively new Open Access journal from the American Society for Microbiology.  The paper discusses genomic studies of MRSA which has led the authors to conclude that antibiotic use in animals may contribute to the rise and spread of superbugs in people.

From here. Maximum-parsimony tree of the 89 CC398 isolates (including ST398SO385) based on 4,238 total SNPs, including 1,102 parsimony-informative SNPs with a CI of 0.9591. Clades and groups of importance are labeled in a hierarchical fashion to facilitate description in the text. The tree was rooted with clade I based on an iterative selection process that identified this group as the most ancestral (see Materials and Methods). COO, country of origin; AT, Austria; BE, Belgium; CA, Canada; CH, Switzerland; CN, China; DE, Germany; DK, Denmark; ES, Spain; FI, Finland; FR, France; GF, French Guiana; HU, Hungary; IT, Italy; NL, The Netherlands; PE, Peru; PL, Poland; PT, Portugal; SI, Slovenia; US, United States; P, pig; H, human; R, horse; T, turkey; B, bovine; MET, methicillin susceptibility; R, resistant; S, susceptible.

Draft blog post cleanup #1: Divide and Conquer to Find Orthologs

OK - I am cleaning out my draft blog post list.  I start many posts and don't finish them and then they sit in the draft section of blogger.  Well, I am going to try to clean some of that up by writing some mini posts.  Here is the first ---

Saw an interesting paper worth checking out:
PLoS ONE: Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach

Coming up on http://phyloseminar.org Jason Stajich (aka @hyphaltip) #fungi #genomics

Upcoming seminar on Phyloseminar.Org

Jason Stajich speaks Wednesday, June 29th at noon PST on "Fungal phylogenomics: Getting lost in the moldy forest."
Fungi occupy diverse ecological niches in roles from nutrient cycling in rainforest floors to aggressive plant and animal pathogens. Molecular phylogenetics has helped resolve many of branches on the Fungal tree of life and enabling studies of evolution across this diverse kingdom. The genome sequences from hundreds of fungi now permit the study of change in genes and gene content in this phylogenetic context and to connect molecular evolution with adaptation to ecological niches or changes in lifestyles. I will describe our work in studies contrasting pathogenic and non-pathogenic fungi and efforts to unravel the evolution of multicellularity in fungi comparing unicellular basal fungi with multicellular mushrooms and molds.
The development of tools for data mining and use of fungal genomics is also driving the pace of molecular biology and genetics of fungi. I will highlight new approaches to make this easier and the ways data integration can inform and transform studies of functional biology of fungi.

Japan	04:00 (04:00 AM) on Thursday, June 30
New Zealand	07:00 (07:00 AM) on Thursday, June 30
West Coast USA	12:00 (12:00 PM) on Wednesday, June 29
East Coast USA	15:00 (03:00 PM) on Wednesday, June 29
England	20:00 (08:00 PM) on Wednesday, June 29
France	21:00 (09:00 PM) on Wednesday, June 29

Learn how to connect ahead of time. To hear about upcoming talks, send an email to phyloseminar+subscribe@googlegroups.com or follow @ematsen.
If you can't make it, don't fret-- you can always watch the recording