Tag Archives: Genomics

Summer 2013 Bioinformatics Workshop Roundup Part Two

Here’s a couple more promising bioinformatics workshops taking place in the summer of 2013:

Metagenomics: From The Bench To Data Analysis, Heidelberg, Germany, April 14th to April 20th, 2013

EMBO course header

Joint EU-US Training in Marine Bioinformatics, Newark, Delaware, USA, June 16th to June 29th, 2013

EU-US Course Header

Summer 2013 Bioinformatics Workshop Roundup Part One

The summer is a great time to learn some new skills and really hone data analysis techniques.  I think it’s best to learn some topics — bioinformatic tools and data analysis scripting in particular — as intense multi-day workshops or a week- or two-week long short courses.  Here’s a few courses that are being held this summer that may be of interest to you.  I’ll be sure to post more as I hear about them.

Programming for Evolutionary Biology, Leipzig, Germany, April 3rd to April 19th, 2013

course one

Informatics for RNA-sequence Analysis, Toronto, Canada, June 3rd to June 4th, 2013

course two

Pathway & Network Analysis of -Omics Data, Toronto, Canada, June 10th to June 12th, 2013

course two

The Draft Genome Of Watermelon: Citrullus lanatus

The Cucurbitaceae is an agriculturally important family of plants (think melons, pumpkins, cucumbers, squashes, etc.) and one of the most popular species in this family is Watermelon.  Watermelon has been cultivated for more than 4,000 years and was most probably spread by nomadic people as a portable source of both water and pre-packaged nutrients.  The estimated center of diversity of the Cucurbits is in Southern Africa.  Watermelon has many cultivars – more than 200 in production worldwide – with a wide range of phenotypic diversity and a wide area of production that accounts for 7% of land grown for vegetables.

Watermelons

Unfortunately, Curcubits are generally susceptible to pathogens – most typically in the form of bacterial and fungal pathogens.  The genomes in this group are starting to pile up which makes the family an interesting group for comparative genomics studies –particularly in the development of model species for plant pathogen studies.

watermelon genome paper header

The recently published paper “The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions” by Guo et al. in the journal Nature Genetics, described the draft genome for the Citrullus lanatus East Asian cultivar 97103 and then re-sequenced 20 different watermelon accessions – representing three different sub-species – in order to observe genetic diversity in wild.

Almost 47 Gb of sequence data was generated using Illumina’s sequencing platforms to give 108X coverage on the relatively small estimation of 426 Mb C. lanatus genome, while the draft is approximately 353 Mb or 83.2% of the estimated genome size.  Unmapped reads, totaling almost 20% of the sequencing data, could not accurately be constructed into contigs because of explicit regions of genome duplication.

watermelon figure 1

The authors estimated 23,440 genes in the watermelon genome – very close to both the cucumber genome (no surprise) and the human genome (surprise).  About 85% of the genes from watermelon could be predicted on the basis of homology to other plant genes.  The authors did a throughout assessment of transposable elements, various repeats, and classified functional RNAs from ribosomal RNA subunits to microRNAs.  Like other plants, watermelon shows gene enrichment in subtelomeric regions.  On the basis of comparison to other genome sequences, watermelon possesses the seven paleotriplications shared with the eudicots.

watermelon paper figure 2

The authors assessed genetic diversity across varieties of C. lanatus by sequencing 20 representative accessions anywhere between 5X and 16X coverage.  The estimated diversity of these accessions was considerably lower than similar arrays of accessions in maize, soybean, and rice.  One explanation of the disease susceptibility of the Cucurbitaceae is this low level of genetic diversity.  As a result, one objective of breeding programs for watermelon is to introduce more diversity from wild accessions.

watermelon paper figure 3

Lastly, the authors assessed a number of key features of the C. lanatus genome (along with the other Cucurbitaceae): vascular transport of water and nutrients along vine-like stems, sugar content and accumulation, and the presence of an interesting non-essential amino acid – originally described from watermelons – called Citrulline.

The watermelon genome database is located both here and here.

Book Review: Cryptococcus – From Human Pathogen To Model Yeast

I wrote the following book review for the Mycological Society of America‘s Inoculum newsletter and I think the book is a great resource if you study Cryptococcus — so I am reproducing my review here.  You can also find a copy of the review here.

cryptococcus book cover for web

Cryptococcus: From Human Pathogen To Model Yeast. 2010.  Joseph Heitman, Thomas R. Kozel, Kyung J. Kwon-Chung, John R Perfect, and Arturo Casadevall (Eds.).  ASM Press, Washington, DC.

The yeast-forming basidiomycete genus, Cryptococcus, has emerged as a significant model for both fungal genetics and pathogenicity.  A long history of research compounded with numerous laboratory resources, as well as two sequenced genomes, have yielded a great deal of information on this enigmatic fungus.  The new book Cryptococcus: From Human Pathogen To Model Yeast, edited by Heitman, Kozel, Kwon-Chung, Perfect, and Casadevall, features contributions from 123 authors and summarizes a vast amount of data as well as synthesizes disparate concepts on the biology of Cryptococcus.  If you consider Casadevall & Perfect’s 1998 tome Cryptococcus neoformans as the groundwork for this book, then these 646 pages are evidence for the explosive advance of knowledge on Cryptococcus that has accrued over the last 12 years.

Cryptococcus species, arguably the most important fungal pathogen of mammals, are common in immuno-compromised hosts; HIV-associated cryptococcosis alone infects more than 1 million people per year.  For example, Cryptococcus has been laboratory confirmed in Sub-Saharan African countries to be responsible for anywhere from 10 to 70% of fatal meningitis cases over the last two decades.  A well-publicized outbreak of a particularly virulent strain of C. gattii was determined to be the causative agent of more than 200 cases of human meningitis in non-immuno compromised individuals within the Pacific Northwest over the last decade.  A concerted global consortium of medical mycology researchers ­ the majority of whom are authors of chapters in this book ­have provided the foundation for establishing Cryptococcus as the model system for understanding fungal pathogenesis in both a medical and veterinary setting.

Species of Cryptococcus entered my personal radar when they kept turning up in plant-associated environmental samples.  Wanting to get up to speed with natural history, population genetics, and methods for typing Cryptococcal diversity, this book was an obvious entry point for me.  Chapters here are dedicated to identification from environmental niches – such as the description of avian- or plant-associated vectors – as well as population biology to phylogeography, and species complexes to hybridization.

Copiously illustrated throughout, notable figures include those documenting Cryptococcus morphology, cell and molecular biological networks, secondary metabolite chemistry, and gene and genome structure.  Chapters devoted to phylogeography and species complexes have detailed phylogenetic trees and distribution maps.  Additionally, this wouldn’t be a clinical textbook if it didn’t include a series of color and monochrome plates of human and animal infections that remind you why you have – or haven’t – studied medical mycology.

Mycologists aren’t the only ones who will find this resource useful.  Geared toward a wide array of specialists, this book is equally applicable to the interests of clinicians and physicians, microbiologists and immunologists, disease ecologists and epidemiologists, and, to a lesser extent, public health and policy administrators.  The book succeeds in connecting and interpreting basic research science and applying this knowledge in a clinical context.

The book consists of a whopping 44 chapters separated into seven sections.  These sections are devoted to general biology; genetics and genomics; virulence; environmental interactions and population biology; immune host responses; pathogenesis; and diagnosis, treatment, and prevention.  Each of the sections consist of five to eight chapters and each informative chapter stands on its own – concise enough to allow for discrete chunks of reading without overwhelming the reader.  In fact, I would argue that the book’s greatest strength is cohesive breadth blended with factual depth.  My only criticism ­ and this is an extremely minor one ­ is that the book as a whole is slightly overwhelming in scope.  This by no means indicates a lack of vision from the authors or editors, but reflects their desire to take into consideration the complete state of knowledge relating to Cryptococcus and its biology.  As a result, the contributors have not only provided a truly fascinating and utterly comprehensive collection of everything Cryptococcus, but have set the bar high for the best treatise on fungal biology at the genus level.  I would consider this book essential for anyone working directly with Cryptococcus ­ or wanting to get up to speed ­ and for mycologists looking for a framework to fully grasp the biology of an important model fungus.

ICOM7 – The 7th International Conference on Mycorrhiza, January 2013

ICOM7

Perhaps because I study mycorrhizae the ICOM meetings have a special place in my heart, so I’m excited to tell you that the next ICOM — the 7th International Conference on Mycorrhiza (ICOM7) — is open for registration.  The meeting will be held in New Dehli in January of 2013.  Here is the call for abstracts.  Here’s some more information from the meeting website:

The Organizing Committee cordially invites you to the 7th International Conference on Mycorrhiza (ICOM7) to be held from 6th to 11th January’ 2013 in New Delhi, the capital Republic of India. Organized by TERI under the auspices of the International Mycorrhiza Society and in collaboration with the Mycorrhiza Network, this 6 day gala event would bring the ICOM legacy to Asia for the first time.

The theme of this conference, “Mycorrhiza for all – An Under Earth Revolution” is wisely chosen so that it may prove to be the epicenter of a new revolution that our planet is in dire need of. A change that would help minimise the usage of chemical fertilizer on soil and hence leave the least environmental footprint.

Carbohydrate binding gene family expansion in the amphibian pathogen Batrachochytrium dendrobatidis

You’d have to be living under a rock – as some amphibians do – to not be aware of the massive extinction facing our vertebrate friends living within aquatic habitats.  Researchers still don’t fully understand what is causing the amphibian mass-extinction – stress from habitat loss, increased chemical concentrations in the environment, and an auto-immune degrading infection have all been proposed.  What is known is that the chytrid fungus Batrachochytrium dendrobatidis – opportunistic or not – is infecting and killing a large number of amphibians.

What is not fully understood about B. dendrobatidis is its pathogenicity and what mechanisms it employs to cause infection.  A recent paper, “Species-Specific Chitin-Binding Module 18 Expansion in the Amphibian Pathogen Batrachochyrium dendrobatidis”, published in the mBio journal by John Abramyam & Jason Stajich at UC Riverside, begins to address this pathogenicity.  As the authors point out – more than 100,000 species of fungi have been described to date and very few of them are pathogenic.  This means that the ability to be pathogenic is derived from somewhere: genome expansion events, gene family duplication and diversification events – and we’re only starting to understand horizontal gene transfer events in fungi. This paper addresses the expansion of a gene family across two B. dendrobatidis genomes that are associated with pathogenicity.

When comparing the genomes of B. dendrobatidis with the genomes from other chytrid fungi there has been an expansion of genes within the family Carbohydrate-Binding Module Family 18 (CBM18).  The CBM18 family is a large group of proteins that have been implicated in other fungal pathogenic infections on both plants and animals.  The authors here question whether this interesting lineage specific expansion of CBM18 in B. dendrobatidis could be associated with the virulence of its pathogenicity on amphibians.

The authors used the CBM18 protein family domain HMM to search across the B. dendrobatidis genomes and found an increase in the number of domains when comparing it to genome of its closest relative.  When constructing phylogenetic trees of the CBM18 gene family, three monophyletic and strongly supported clades emerged.  When focusing on divergence of the protein domains, the authors determined that individual domain groups were monophyletic and showed a general pattern with regards to their genome locations.

More specifically, clades of the CBM18 family appears to possess different gene functions, some of which appear to be similar to lectins (LL), tyrosinase/catechol oxidases (TL), and chitin deacetylases (DL).  The function of these genes has yet to be experimentally determined, but the authors make some deductions based on DNA sequences.  The lectin-like genes may be involved in the sequestering of chitin, which could then be disrupting the amphibian immune response.  The tyrosinase/catechol oxidase gene family is associated with melanin synthesis, which could be disrupting the electron transport of the infected amphibians.  Lastly, chitin deacetylases may be involved in suppressing defense mechanisms in place to suppress the fungal infection of the host.  The authors plan to continue to elucidate the pathogenicity of B. dendrobatidis in an attempt to understand the ecology and evolution of its infection on amphibians.

A Genome Sequence for Tomato

The average person in the United States eats more than 10 kilograms of tomatoes a year – underscoring the fact that the fruit is one of the most important plant crops in cultivation.  To improve taste, texture, and disease resistance – just to name a few traits – a large consortium of researchers has initiated and provided a draft tomato genome.  In fact, the research consortium has published the genome sequence from two varieties of tomatoes: the domesticated inbred Solanum lycopersicum strain Heinz 1706 – the variety famous for ketchup – and the wild breeding Peruvian ancestor, Solanum pimpinellifolium.

The consortium published the draft genome sequences with a paper entitled “The tomato genome sequence provides insights into fleshy fruit evolution” in the journal Nature.  The consortium started sequencing the genome officially in 2003, but heterozygosity and duplication events made assembling the genome difficult.  The tomato genome is approximately 900 Mb – smaller than the Human genome – but certainly not small by eukaryotic standards.  Genetically and phenotypically diverse, the genus Solanum is one of the largest in the angiosperms.

The genomes of Solanum lycopersicum and S. pimpinellifolium only show 0.6% divergence and there is evidence of recent hybridization between the two species.  Both species show approximately 8% genome divergence compared against close relative potato, Solanum tuberosum.  Across the genus Solanum there has been two genome triplications with subsequent gene loss: one genome triplication is ancient and shared with all the rosid clade and another triplication is shared within the Solanaceae, which appear to be highly syntenic across the family.  The genomes were completed with both Sanger- and Illumina-derived sequences and assembled with the help of physical and genetic maps developed from a long history of tomato breeding efforts.

There are 34,727 and 35,004 genes identified across the genomes of Solanum lycopersicum and S. pimpinellifolium respectively.  These findings are similar to other plant genomes as 8,615 of these genes are found to be common to tomato, potato, rice, grape, and Arabidopsis.  Expression was assessed by replicated RNA-Seq of root, leaf, flower, and fruit tissues.  A total of 18,320 orthologous gene pairs were found in tomato and potato indicating diversifying selection between the two species of Solanum.

The consortium specifically compared tomato to grape in this study, as grape and tomato shared a common ancestor at approximately 100 million years ago, before the first whole genome triplication event that preceded the rosid-asterid divergence.  Additionally, both grape and tomato have similar molecular fruit maturation mechanisms.  When comparing the genomes of tomato and grape, approximately 73% of gene models are orthologous.  By estimating genome triplication events, the researchers conclude that the genome duplication event within the Solanaceae occurred roughly 71 million years ago and approximately 7 million years prior to the tomato-potato divergence.

Having a draft genome sequence is an important mechanism to understanding the molecular biology of the tomato plant.  Genome duplication events gave rise to the diversification of genes responsible for enhanced fruit physiological and chemical development – such as lycopene synthesis – and include photoreceptors and transcription factors that influence fruit ripening.  Additionally, tomato has had a contraction in the number of gene families associated with toxic alkaloid synthesis – the chemical hallmarks of many members of the Solanaceae.  One interesting question not answered by this research is the genomic mechanism by which the tomato regulates nutrient investment in above-ground fruits while the potato regulates starch investment in below-ground tubers.

These two tomato genomes, along with the genomes of fellow Nightshades completed or in the works (potato, pepper, tobacco, petunia, eggplant, etc.), will help breeders to develop traits desired by producers, like long shelf life, and fruit quality traits desired by tomato-consumers, such as taste, color, and texture.  In addition to these benefits, the draft tomato genomes will provide insights into the biology and nutrition of the Solanaceous plants, and provide more information for comparative genomics within this important economic group of plants.