Monthly Archives: August 2011

How Many Species Are There On Earth And In The Ocean?

This week, it’s been hard to miss the new paper, “How many species are there on Earth and in the Ocean?” published by Mora et al. in the August 2011 issue of the journal PLOS Biology.  There have been commentaries or news articles printed in the New York Times, The Economist, The Guardian, Damian Carrington’s Guardian Blog, National Geographic, Yahoo News, AlterNet, MSNBC, Reuters, UNEP, NewsDaily and Ed Yong has posted a commentary on his Google+ page.  Furthermore, some well respected scientists who study biological diversity have joined the debate too: Jonathan Eisen has devoted two blog posts to the paper (one about the actual paper in PLOS Biology and another on the National Geographic commentary) and there is a commentary from Robert May in PLOS Biology about the study and its significance.  Since there is ample information on the study elsewhere, let me communicate a brief summary of the study and some of my feelings about the paper.

It’s quite embarrassing that we have really no clue how much biological diversity is found on this planet.  Adding insult to injury is the fact that we have no concept of the current magnitude of the loss of diversity due to human induced mass extinctions.  This paper seeks to predict total global biological diversity by documenting current taxonomic numbers and extrapolating consistent patterns to estimate the number of species that have yet to be identified.

The methods of the authors essentially consisted of three parts.  First, the authors compiled a list of approximately 1.2 million species pulled from numerous biological databases.  Second, they surveyed a little over 500 taxonomists who were asked to identify the validity of current scientific names and comment on the intensity of current taxonomic efforts to describe new species.  Third, the authors analyzed this data to find the estimated global numbers of biological taxa for each phylum.

The authors show a predictable pattern in the classification of species (at the phylum, class, order, family, and genus level) at least consistently for animals.  By evaluating these patterns using regression, the authors validated this by closely examining 18 taxonomic groups that we think we understand their total biological diversity.  By doing this, the authors come up with a total estimate of 7.7 million species of animals (mostly insects), close to 300,000 species of plants, more than 600,000 species of fungi, and a total estimate of roughly 9 million eukaryotes on Earth.  The authors estimate that 86% of species on Earth and 91% of species in the oceans still have not been formally described.  Previous estimates of species diversity have been wide: anywhere between 3 million to a 100 million species.

This paper is a novel and worthwhile attempt to determine the total amount of species diversity on this planet.  Despite this, I think – and the authors have their own reservations – that there are some serious problems with some of their calculations.

One problem is that the study is based mainly on using animals, and vertebrates for that matter – which are the best described of any phylum, as the baseline for measuring the completeness of species diversity.  I would argue that plants and fungi, and obviously bacteria, archaea, and “the protists” are clearly not well known enough to extrapolate any serious estimate species numbers especially when considering vertebrate animals as a baseline and whose numbers are largely skewed.

Another problem is in our collective definition of species, as well as taxonomic subjectivity of the categorization of other taxonomic hierarchies, which are based on the on the homology of shared characters and, I would argue, are largely incomparable outside of each phylum.  For example, what one taxonomist calls an order in one grouping may not be equivalent to what another taxonomist calls a completely different order in another completely different grouping.

I should point out that the authors don’t ignore these caveats, but they still exist in their study.  In any event, this paper is important because it adds to the dialogue concerning species diversity, the need to estimate, inventory and preserve the massive amount of diversity we share on the planet.

UPDATE: More commentaries in the news can be found here, here, and here.

Online Courses in Plant Genomics and Breeding from eXtension

The recently established website is a agricultural cooperative extention collective of 74 land grant universities which seeks to serve the public though education and service.

This fall there will be a plant breeding and genomics webinar series for plant breeders, breeding assistants, lab personnel, post docs, and graduate students.  These webinars will focus on how to use specific tools, such as software for genetics and mapping techniques, and on laboratory techniques across various topics of genomics and plant breeding.  For more information or to sign up to view a webinar go here or here.  Join the Plant Breeding and Genomics eXtension community of practice this fall for a webinar series to learn how to use tools, software, and techniques.

Potato Genome Sequence and Analysis

With next-generation sequencing technologies dropping in price and increasing in throughput, it’s not surprising to find multiple genomes published every week in scientific journals.  Most of these articles don’t qualify for publication in the top tier of journals like they did at the onset of the next-generation sequencing boom, but some genome sequencing projects, such as the potato genome, are high profile enough to warrant publication in top tier journals.

In the July 14th issue of the journal Nature, a draft of the potato (Solanum tuberosum) genome was described in a paper authored by the Potato Genome Sequencing Consortium – a huge group of researchers from 26 institutions.

The potato is the world’s fourth most consumed food crop, the most commonly grown vegetable crop, and a member of the economically important Solanaceae family –otherwise known as the nightshades – which include tomato, peppers, aubergine (eggplant if you live in the United States), tobacco, and petunia.  Widely distributed in western South America, tuber forming Solanum species are highly morphologically diverse and easily cross with other varieties for breeding purposes.

It’s been a bumpy road sequencing the potato genome since the project was started in 2006.  The potato genome is an extremely heterozygous autotetraploid, which translates to four highly variable copies of each of the 12 chromosomes.  It’s also the first sequenced Eudicot genome in the Asterid clade, so there are no close genetic relatives to provide the basis for a guided genome assembly.

The consortium began the sequencing by creating a bacterial artificial chromosome (BAC) library of 78,000 clones from a well studied diploid line providing high quality potatoes, named RH89-039-16.  The group used the BAC library and 10,000 AFLP markers to create more than 7000 contigs which were constructed into a physical map.  The group then identified up to 150 BACs for every chromosome on the potato genome, and verified their locations using fluorescent in situ hybridization.

Heterozygosity was so high in the RH line that after thorough sequencing the group hit an impasse with the assembly of the genome.  In an attempt to complement the sequencing of the RH line, the consortium began sequencing a doubled monoploid potato clone, DM1-3 516R44, derived from a diploid wild South America accession.  The DM line has a simpler genome than the RH line and is highly homozygous.

Using both the Illumina Genome Analyzer II and Roche 454 pyrosequencing platforms, and supplementing this data with traditional Sanger sequencing, approximately 96 Gb of data was acquired for the DM line.  The group then used the SOAPdenovo computer program to assemble the reads with a final assembly of 727 Mb for the DM line and a final estimation of 844 Mb for the genome.

The consortium generated more than 31 Gb of transcriptome data from both the DM and RH line libraries.  These 48 libraries represented major tissue types, developmental stages, and included various responses to abiotic and biotic stresses.  All the reads from the RNA-Seq libraries were mapped to the assembled DM genome.  Using gene prediction methods, along with protein and EST data, the potato genome was predicted to contain 39,000 protein coding genes, an amount which is in agreement with other plant genomes.  Within these genes, there were an estimated 2,642 asterid-specific and 3,372 potato-lineage-specific genes.  Some of the predicted asterid-specific genes include many novel transcription factors, self-incompatibility factors, and defence-related proteins. The draft assembly of the genome consists of more than 60% repeated elements.  The largest class of the transposable elements is the long terminal repeat retrotransposons (LTRs) which are estimated at 30% of the potato genome.

The potato is notorious for being susceptible to many pathogens and pests.  This well known susceptibility was one of the priorities for sequencing the genome and determining genes responsible for disease resistance and pathogen defense.  The DM genome assembly contains more than 800 putative R genes, responsible for conferring disease resistance, including 408 NBS-LRR-encoding genes, 57 Toll/interleukin-1 receptor (TIR) domains, and 351 non-TIR type resistance genes.  An extreme number of pseudogenes – attributed to indels, frameshift mutations, and misplaced stop codons –were identified within known R gene motifs, which possibly explains the potato’s inability to fight off some specific diseases.

One such well known disease, Late Blight, caused by Phytophthora infestans, was responsible for the Irish Potato Famine in the 1840s..  Using information from this genome sequencing project and other studies, we now know the variety brought to Europe in the late 16th century happens to lack specific disease resistance genes for Phytophthora infestans.  One could speculate that unbridled transposon jumping caused the inactivation of many R genes in this potato variety.

Unique for the potato is the formation of tubers (the actual potatoes) through the modification of a stolon.  The tomato is very closely related to potato, but does not produce stolons or modified tubers.  The group used transcript data from both potato and tomato to address genetic regulation of the formation of stolons and the transition of stolons to tubers.  Quite interestingly, the formation of stolons and tubers coincides with an up-regulation of genes associated with starch biosynthesis, protein storage, and Kunitz protease inhibitor genes associated with pests and pathogens.

Possibly due to extremely high levels of heterozygosity, it has been difficult to improve the potato through traditional breeding efforts.  It’s estimated that there is a worldwide economic loss of 4.5 billion US dollars to potato crops from diseases each year.  Just to attempt to suppress these diseases copious amounts of pesticides and fungicides are applied to potato crop land each year.  The potato cyst nematode, for example, is an important pest that researchers hope to improve resistance to via breeding initiatives.  Having this draft potato genome sequence will aid in the characterization of existing germplasm collections and description of allelic variance in breeding efforts to avoid diseases.  The potato genome will also serve as a resource for breeders wanting to improve the quality of other economically important Solanaceous plants such as tomato, pepper, eggplant, and tobacco.

The 7th International Symbiosis Congress, Poland, July 2012

The International Symbiosis Society hosts a congress every three years at different locations.   It’s been announced that the 7th International Symbiosis Congress will convene in the city of Kraków (Poland) on July 22nd to the 28th, 2012 (Poster).  This international meeting is held every three years and this cycle is being held at Jagiellonian University.

It is expected that several hundred scientists will present new research both in the form of talks and posters.  Registration is now open and is located here.  A confirmed list of speakers will address areas of research such as dinoflagellates, mycorrhizas, lichens, insect symbioses, and nitrogen fixing plant associated bacteria.  Quite fittingly, this Congress is dedicated to the memory of Gopi Podilla.

UPDATE (September 22nd, 2011):

Genome Sequence of the Date Palm

Published in the June 2011 issue of the journal Nature Biotechnology was a paper reporting on the genome sequence of the data palm, Phoenix dactylifera.  This paper, authored by Al-Dous et al., addressed the genome sequencing and de novo assembly of this agriculturally important monocot tree, along with comparative genomics with other plants.

Dates have been found in the tombs of pharaohs estimated at 8,000 years old.  Fields of agriculturally planted trees, estimated to be older than 5,000 years, suggest the date palm is one of the oldest cultivated plants in the world.  Dates are the most important agricultural crop in the hot and arid regions surrounding the Arabian Gulf and their global production is close to 7 million tons yearly.

Despite a prolonged emphasis on their agriculture, there are a few problems to deal with if you are a date grower.  Typical of tree crops, there is a long generation time from seedling to fruit harvesting.  Additionally, only the female date palm provides fruit and it takes at least 5 years after seed germination to tell if you have a male or female plant.  To make it even harder for a date grower, there are more than 2000 date varieties, each exhibiting its own color, flavor, size, shape, and ripening schedule, and they are all really hard to keep track of based on conventional techniques.

In an effort to provide genetic resources for date growers and breeders, the authors of this study – who were mainly located in Qutar – sequenced and assembled 380 Mb of the estimated 658 Mb genome of the Khalas cultivar, which is known for high fruit quality.  Generated using short reads from the Illumina Genome Analyzer IIx platform, this partial sequence excluded numerous large repeated regions, includes a predicted 28,890 genes, and represented 18 pairs of chromosomes.  The authors estimate that this draft genome represents roughly 90% of the total genes and 60% of the total genome.

This genome resource also serves a comparative genomics purpose by being the first member of the widespread monocot order Arecales.  To this date, the only Monocots with sequenced genomes – for example: Corn, Rice, and Sorghum – have all been in the grass order, the Poales.

This report is missing some vital information: in addition to an incomplete genome assembly, there is no metabolic, developmental, or gene network pathway reconstruction for the date palm provided in this paper (and unfortunately this paper also includes some glaring typos in the citation section).  In place of these expected analyses, the authors conducted a throughout survey of SNPs in this Khalas cultivar, along with eight additional cultivars common in breeding programs for the date palm.  Within these nine cultivars, 3,518,029 SNPs were determined, but quite interestingly, a total of 32 SNPs could be used to differentiate the cultivars.

In addition to the throughout SNP analysis, the researchers then did a full parentage analysis of the cultivars used in this study, which includes the famous date varieties such as Deglet Noor, Dayri, and Medjool.  Here‘s an article in Nature Middle East on the importance of understanding this parentage and gender analysis.

Although this is a draft genome still being completed and undergoing resequencing, namely the tools provided by the authors, the SNP and parentage analysis, should provide date palm breeders with many resources for improved fruit quality and this genome represents an exciting piece of the monocot evolutionary puzzle.