Nature Biotechnology 28, 10 (2010) doi:10.1038/nbt0110-10b

Plant genomics’ ascent

Emily Waltz

Introduction

Grants supporting plant genome research in the US have reached an all-time high. Over 2009, the National Science Foundation (NSF) doled out nearly $102 million, the largest sum since the annual grant program began in 1998. The funding aims to increase understanding of plant gene function and the interaction of plant genomes and the environment. “This funding lets you tackle bigger problems,” says David Salt, a former grant recipient and plant biologist at Purdue University. “It lets you devise more integrated and collaborative projects.” The NSF chose 32 projects focused on “economically important crop plants” ranging from West African cultivated rice to poplar trees, according to the foundation. The largest award, worth more than $10.4 million over four years, went to a proposal to help complete the international effort to sequence the tomato genome. James Giovannoni at Cornell University’s Boyce Thompson Institute for Plant Research in Ithaca, New York, leads the project. The NSF also chose for the first time a switchgrass research project. With a grant worth more than $4.5 million, Thomas Juenger and his team at the University of Texas at Austin will explore over the next four years how switchgrass responds to drought and other stresses caused by climate change, to expand the knowledge needed to develop switchgrass as a biofuel crop.

When you drink, enzymes in the liver known as alcohol dehydrogenases (ADHs) convert alcohol to an organic compound called acetaldehyde; another enzyme then converts acetaldehyde to acetic acid. But about 50% of Asians and 5% of Europeans have mutations in these enzymes that can increase the rate of alcohol metabolism up to 100-fold. This leads to a rapid accumulation of acetaldehyde, which can cause capillaries in the face to dilate�–and the face to turn red. Other unpleasant symptoms can include nausea and headaches. In 2008, a team led by geneticist Kenneth Kidd of Yale University found that one of these mutations–known as ADH1B*47His–may have been favored by natural selection in many East Asian populations.

The researchers searched for the ADH1B*47His mutation in 2275 people across China representing 38 ethnic groups. They found that it was highly prevalent, up to 99%, in ethnic groups from southeast China; a bit less prevalent, 60% to 70%, in western China; and relatively uncommon, 14%, among Tibetans. Moreover, the team found a strong geographical correlation between regions with a high prevalence of the mutation and archaeological sites in China where rice had been domesticated thousands of years ago.

When Su and his colleagues calculated the age of the mutation, it came out at between 7000 and 10,000 years ago. That corresponds roughly to the earliest known evidence for rice farming, the team reports online this week in BMC Evolutionary Biology. "The [mutation] rose to extremely high frequency in a relatively short time, implying that the selective force was quite strong," Su says.

As for what the selective pressure was, the team concludes that the mutation was favored because it protected early farmers from the potentially fatal harms of drinking too much. The researchers cite two additional pieces of evidence for this hypothesis. First, recent archaeological evidence suggests that Chinese farmers concocted an alcoholic brew of rice, honey, and grape or hawthorn as early as 9000 years ago. Second, the drug disulfiram, which causes acetaldehyde to accumulate in the body, discourages alcoholics from drinking by causing nausea, vomiting, and other severe alcohol flush reaction symptoms.

This study is the latest in a growing body of research showing just how important human culture has been as a transformational force in human evolution," says Darren Curnoe, an anthropologist at the University of New South Wales in Sydney, Australia. Indeed, the rise of farming has been linked to evolutionary changes in genes for other enzymes, such as amylase, which breaks down starch, and lactase, which breaks down lactose in milk.

Other researchers are not entirely convinced. Kidd says that the hypothesis is "quite reasonable" but that it’s still speculation at this point. He also questions whether the team has determined the age of the mutation correctly, because the estimates range over at least 3000 years. And Dorian Fuller, an archaeologist at University College London, argues that the team may be wrong to pin the mutation’s origins solely on rice cultivation. The archaeological sites the researchers chose, he says, included settlements where rice had just begun to be farmed and those where rice farming was in full flower. Fuller adds that if the team had restricted its analysis to those later sites where rice had become a predominant crop, beginning about 8000 years ago, then alcoholic beverages could also have been made from grapes–and rice might not be solely responsible for the Asian Flush.

The ADH1B Arg47His polymorphism in East Asian populations and expansion of rice domestication in history

Yi Peng, Hong Shi, Xue-bin Qi, Chun-jie Xiao, Hua Zhong, Run-lin Z Ma  and Bing Su

BMC Evolutionary Biology 2010, 10:15 doi:10.1186/1471-2148-10-15

Abstract

Background

The emergence of agriculture about 10,000 years ago marks a dramatic change in human evolutionary history. The diet shift in agriculture societies might have a great impact on the genetic makeup of Neolithic human populations. The regionally restricted enrichment of the class I alcohol dehydrogenase sequence polymorphism (ADH1BArg47His) in southern China and the adjacent areas suggests Darwinian positive selection on this genetic locus during Neolithic time though the driving force is yet to be disclosed.

Results

We studied a total of 38 populations (2,275 individuals) including Han Chinese, Tibetan and other ethnic populations across China. The geographic distribution of the ADH1B*47His allele in these populations indicates a clear east-to-west cline, and it is dominant in south-eastern populations but rare in Tibetan populations. The molecular dating suggests that the emergence of the ADH1B*47His allele occurred about 10,000~7,000 years ago.

Conclusion

We present genetic evidence of selection on the ADH1BArg47His polymorphism caused by the emergence and expansion of rice domestication in East Asia. The geographic distribution of the ADH1B*47His allele in East Asia is consistent with the unearthed culture relic sites of rice domestication in China. The estimated origin time of ADH1B*47His allele in those populations coincides with the time of origin and expansion of Neolithic agriculture in southern China.

When searching for specific genes in a tissue sample, there may be thousands of genes that perform simple housekeeping functions, whereas others expressed in smaller numbers are charged with more complex and important functions. The difficulty is sorting through thousands of genes to find the ones that have unique functions.

“These housekeeping genes are highly expressed, often hundreds or thousands of times more than other genes,” DeWoody said.

Through normalization, scientists heat up DNA to a point in which its two component strands split, or denature. As it is cooled, matching strands randomly find each other and reattach. Those that reunite quickly are typically the most numerous. By adding specific enzymes, many of the overabundant genes are decreased in number, while the few that reunite slowly are amplified until the genes are equal in number, making it easier to sort through them.

DeWoody and Hale believe normalization is not necessary given the vast amount of data that can be obtained through modern DNA sequencers.

“Normalization used to be required because commonly expressed genes would swamp the signal of rare genes,” DeWoody said. “But normalization also discards valuable information about the relative levels of gene expression in a tissue sample.”

Another key aspect of the paper is the novel use of analytical rarefaction in gene discovery.

In rarefaction, a species is selected at random from that ecosystem. Those selections are charted, with each selection considered one unit of effort. Once selections yield only previously selected species – or in this case, genes – the amount of effort needed to find all the species or genes has been determined. Scientists then know how much effort to use when searching for other genes.

“When it plateaus, you can give up. You’ve put in as much effort as you need,” DeWoody said.

DeWoody and Hale tested the theory on samples from the reproductive organs of lake sturgeon while trying to find the genes responsible for determining fish sex. Hale said the work is important to conserve species by understanding their biological functions.

“Few studies have been done on threatened and endangered species. They’re usually done on models such as mice and Arabidopsis,” Hale said. “This species, the lake sturgeon, is a perfect example of a conservation concern.”

The Great Lakes Fishery Trust and the Indiana Department of Natural Resources funded the research. DeWoody said the next step is to continue the process of finding the genes responsible for determining sex in sturgeon.

ABSTRACT

Next-Generation Pyrosequencing of Gonad Transcriptomes in the Polyploid
Lake Sturgeon (Acipenser Fulvescens): The Relative Merits of Normalization and Rarefaction in Gene Discovery

Matthew C. Hale, Cory R. McCormick, James R. Jackson and J. Andrew DeWoody

Background: Next-generation sequencing technologies have been applied most often to model organisms or species closely related to a model. However, these methods have the potential to be valuable in many wild organisms, including those of conservation concern. We used Roche 454 pyrosequencing to characterize gene expression in polyploid lake sturgeon (Acipenser fulvescens) gonads.

Results: Titration runs on a Roche 454 GS-FLX produced more than 47,000 sequencing reads. These reads represented 20,741 unique sequences that passed quality control (mean length = 186 bp). These were assembled into 1,831 contigs (mean contig depth = 4.1 sequences). Over 4,000 sequencing reads (~19%) were assigned gene ontologies, mostly to protein, RNA, and ion binding. A total of 877 candidate SNPs were identified from >50 different genes. We employed an analytical approach from theoretical ecology (rarefaction) to evaluate depth of sequencing coverage relative to gene discovery. We also considered the relative merits of normalized versus native cDNA libraries when using next-generation sequencing platforms. Not surprisingly, fewer genes from the normalized libraries were rRNA subunits. Rarefaction suggests that normalization has little influence on the efficiency of gene discovery, at least when working with thousands of reads from a single tissue type.

Conclusion: Our data indicate that titration runs on 454 sequencers can characterize thousands of expressed sequence tags which can be used to identify SNPs, gene ontologies, and levels of gene expression in species of conservation concern. We anticipate that rarefaction will be useful in evaluations of gene discovery and that next-generation sequencing technologies hold great potential for the study of other non-model organisms.

The international research team found an unexpected level of genetic variation between the two strains, which followed different evolutionary paths. The researchers also identified signatures of important cellular machinery and processes, such as gene silencing and thiamine biosynthesis. One strain appears to be an important source of the distinctive transposable elements previously found in a “metagenome” study of the Sargasso Sea. As John Archibald writes in a related Perspective, these results should help shed light on the genetic “toolkit” that may have been present in the ancestors of today’s land plants and green algae.

Via: Science 10 April 2009: DOI: 10.1126/science.1167222

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

Alexandra Z. Worden,1* Jae-Hyeok Lee,2 Thomas Mock,3 Pierre Rouzé,4 Melinda P. Simmons,1 Andrea L. Aerts,5 Andrew E. Allen,6 Marie L. Cuvelier,1,7 Evelyne Derelle,8 Meredith V. Everett,7 Elodie Foulon,9 Jane Grimwood,5,10 Heidrun Gundlach,11 Bernard Henrissat,12 Carolyn Napoli,13 Sarah M. McDonald,1 Micaela S. Parker,3 Stephane Rombauts,4 Aasf Salamov,5 Peter Von Dassow,9 Jonathan H. Badger,6 Pedro M. Coutinho,11 Elif Demir,1 Inna Dubchak,5 Chelle Gentemann,14 Wenche Eikrem,15 Jill E. Gready,16 Uwe John,17 William Lanier,18 Erika A. Lindquist,5 Susan Lucas,5 Klaus F. X. Mayer,10 Herve Moreau,8 Fabrice Not,9 Robert Otillar,5 Olivier Panaud,19 Jasmyn Pangilinan,5 Ian Paulsen,20 Benoit Piegu,19 Aaron Poliakov,5 Steven Robbens,4 Jeremy Schmutz,5,10 Eve Toulza,21 Tania Wyss,22 Alexander Zelensky,23 Kemin Zhou,5 E. Virginia Armbrust,3 Debashish Bhattacharya,18 Ursula W. Goodenough,2 Yves Van de Peer,4 Igor V. Grigoriev5

Picoeukaryotes are a taxonomically diverse group of organisms less than 2 micrometers in diameter. Photosynthetic marine picoeukaryotes in the genus Micromonas thrive in ecosystems ranging from tropical to polar and could serve as sentinel organisms for biogeochemical fluxes of modern oceans during climate change. These broadly distributed primary producers belong to an anciently diverged sister clade to land plants. Although Micromonas isolates have high 18S ribosomal RNA gene identity, we found that genomes from two isolates shared only 90% of their predicted genes. Their independent evolutionary paths were emphasized by distinct riboswitch arrangements as well as the discovery of intronic repeat elements in one isolate, and in metagenomic data, but not in other genomes. Divergence appears to have been facilitated by selection and acquisition processes that actively shape the repertoire of genes that are mutually exclusive between the two isolates differently than the core genes. Analyses of the Micromonas genomes offer valuable insights into ecological differentiation and the dynamic nature of early plant evolution.

1 Monterey Bay Aquarium Research Institute, Moss Landing, CA 95039 USA.
2 Department of Biology, Washington University at St. Louis, St. Louis, MO 63130, USA.
3 School of Oceanography, University of Washington, Seattle, WA 98195, USA.
4 Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB) and Department of Molecular Genetics, Ghent University, 9052 Gent, Belgium.
5 U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, CA 94598, USA.
6 J. Craig Venter Institute, San Diego, CA 92121, USA.
7 Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA.
8 Observatoire Océanologique, CNRS–Université Pierre et Marie Curie, 66651 Banyuls sur Mer, France.
9 Station Biologique de Roscoff, CNRS–Université Pierre et Marie Curie, Roscoff Cedex, France.
10 Stanford Human Genome Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
11 Institute of Bioinformatics and System Biology, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
12 Architecture et Fonction des Macromolécules Biologiques, Universities of Aix-Marseille I and II, Marseille 13288, France.
13 Biology Institute, University of Arizona, Tucson, AZ 85719, USA.
14 Remote Sensing Systems, Santa Rosa, CA 95401, USA.
15 Avdeling for Marinbiologi og Limnologi, University of Oslo, Oslo N-0316, Norway.
16 Division of Molecular Bioscience, College of Medicine, Biology and the Environment, Australian National University, Canberra ACT 2601, Australia.
17 Alfred Wegener Institute for Polar and Marine Research, Am Handelshafen, Bremerhaven 27570, Germany.
18 Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
19 Laboratoire Genome et Development des Plantes Université de Perpignan, 66860 Perpignan, France.
20 Department of Chemistry and Biomolecular Sciences, Macquarie University, New South Wales 2109, Australia.
21 Ecosystèmes Lagunaires, Université Montpellier II, F-34095 Montpellier Cedex 05, France.
22 Department of Biology, University of Miami, Miami, FL 33149, USA.
23 Department of Genetics, Erasmus Medical Center, Rotterdam 3015 CE, Netherlands.

The most costly is bacterial blight of rice, which is caused by a bacterium called Xanthomonas oryzae pathovar oryzae, and can diminish yield by up to 50 percent.

The team is also studying bacterial leaf streak of rice caused by the closely related bacterium Xanthomonas oryzae pathovar oryzicola. Bacterial leaf streak is usually not as damaging as bacterial blight, but it is increasing in importance in many areas of the world, particularly Southeast Asia.

These bacteria damage rice by entering the plant and taking control of certain rice cell processes, eventually killing the rice cells. Pathovar oryzae does this in the vascular system of the plant, which typically allows the bacterium to spread faster and cause more damage than is its cousin, oryzicola, which is limited to growth in the tissue between the veins.

Some types of rice are naturally resistant to the Xanthomonas bacteria. Bogdanove and other researchers — Bing Yang, Iowa State assistant professor of genetics development and cell biology; Dan Nettleton, Iowa State professor of statistics; and Frank White, principal investigator and professor of plant pathology at Kansas State University, Manhattan — are researching why some types of rice are naturally resistant to the bacteria.

In rice varieties that are resistant to the diseases, the team is exposing the plants to the two bacteria. They then check to see which plant genes are activated, and to what extent.

By identifying which genes are turned on, Bogdanove believes the team can identify the genes that are making the plants resistant.

“We are looking at genes of successful plants,” he said. “What genes are active and when and how much they are being turned on.”

Bogdanove hopes that this effort will aid in breeding the resistance into cultivated varieties that are currently susceptible to the diseases.

Another aspect of the research is aimed at discovering how the bacteria change gene expression in susceptible rice plants.

“If we understand which genes are being manipulated by the pathogens in disease, we can look into different varieties and wild relatives of rice for variants of these genes that are immune to manipulation and bring these genes into cultivated varieties,” said Bogdanove. “The idea is to reduce or eliminate susceptibility altogether.”

Rice is the major food staple for more than half the world’s population. In the United States, rice is planted on almost 3 million acres with yields of around 7,000 pounds per acre in 2007, according the U.S. Department of Agriculture.

American producers grow 95 percent of the rice eaten in this country and the United States is a major exporter as well, according to Bogdanove.

In addition to the benefits to rice, the research should be helpful in understanding and controlling diseases in other cereal crops.

Professor David Twell and colleagues in the Department of Biology at the University of Leicester reported the discovery of a gene that has a critical role in allowing precursor reproductive cells to divide to form twin sperm cells. The study takes to a new level understanding of the genes needed for successful plant reproduction and seed production.

Professor Twell said: “Flowering plants, unlike animals require not one, but two sperm cells for successful fertilisation. One sperm cell to join with the egg cell to produce the embryo and the other to join with the central cell to produce the nutrient-rich endosperm tissue inside the seed. A mystery in this ‘double fertilisation’ process was how each single pollen grain could produce the pair of sperm cells needed for fertility and seed production.

“We now report the discovery of a dual role for DUO1, a regulatory gene required for plant sperm cell production. We show that the DUO1 gene is required to promote the division of sperm precursor cells, while at the same time promoting their specialised function as sperm cells. It effectively switches on the essence of male.

“We show that DUO1 is required for the expression of a key protein that controls cell division and for the expression of genes that are critical for gamete differentiation and fertilisation.

“This work provides the first molecular insight into the mechanisms through which cell cycle progression and gamete differentiation are coordinated in flowering plants.

The find will be helpful in understanding the mechanisms and evolution of gamete development in flowering plants and may be useful in the control of gene flow and crossing behaviour in crop plants.

The researchers also report on the presence of genes closely related to DUO1 in a wide variety of flowering plants and even in lowly land plants such as moss, which suggests that DUO1 may be part of an ancient sperm cell regulatory network that evolved even before pollen and flowers appeared on the scene.

Interestingly, DUO1 is also related to a super class of Myb regulator proteins also present in animals that have an important role in controlling cell proliferation and that are implicated in certain human cancers such as leukemias. So like animal cell Myb proteins, DUO1 is needed for control of cell proliferation, but DUO1 is distinguished by its specific role in plant reproduction, namely its dual role in sperm cell production and switching on their ability to fertilize.

Professor Twell added that the study could help to unravel the evolutionary origins of plant sperm cells and provide new molecular tools for the manipulation of plant fertility and hybrid seed production – as well as to control gene flow in transgenic crops where the male contribution may need to be eliminated.

In the end how many genes are there of human? It is generally think there is around 100,000 genes more than 10 years ago, in 2001 the international Human Genome Project published 30,000-40,000 human genes. Then in 2004, Collins, director of “National Human Genome Research Institute,” estimated that only 20,000-25,000. The tiny nematode actually have around 19,500 genes, is also about small Arabidopsis gene 27000.

The formation of this gap reflects the people’s “knowledge” and “idea” of possible errors. If you do not reverse the wrong idea, even further to carry out various “group study” and other major scientific research, may not solve the problem.

Genomics is the study of the complete structure of the genome. It provides information on gene structures and thus a basis for understanding protein structures. As a result, a theoretical model of an organism’s biology may be built from a listing of its genes.

Comparing the relative location of genes on the chromosomes and DNA sequences in different organisms will significantly reduce the time needed to identify and select potentially useful genes. For most types of crops, livestock, and diseases, certain species have been studied as model species because they can be used to understand related organisms. Knowledge of the genome of model species is accumulating rapidly.

Different plant species tend to have a genome structure with very similar gene content and gene order along the chromosomes. This similarity is called “synteny”. This means that the location of a gene which defines particular characteristics can easily be determined by comparing one genome to another. Therefore, it is not critical for our understanding to undertake the complete sequencing of plant genomes for all of crop plants with the great costs that this would entail.

Molecular markers are specific fragments of DNA that can be identified within the whole genome. The markers are found at specific locations of the genome. They are used to ‘flag’ the position of a particular gene or the inheritance of a particular characteristic. In a genetic cross, the characteristics of interest will usually stay linked with the molecular markers. Thus, individuals can be selected in which the molecular marker is present, since the marker indicates the presence of the desired characteristic.

Molecular markers can be used to select individual plants or animals carrying genes that affect economically important traits such as fruit yield, wood quality, disease resistance, milk and meat production, or body fat. Measuring such characteristics by conventional methods is much more difficult, time-consuming, or expensive, since it requires the organism to grow to maturity.

Plants can be obtained from small plant samples grown in test tubes. This is a more sophisticated form of the conventional planting of cuttings from existing plants. Another laboratory technique, in vitro selection, involves growing plant cells under adverse conditions to select resistant cells before growing the full plant.

In conventional breeding half of an individual’s genes come from each parent, whereas in genetic engineering one or several specially selected genes are added to the genetic material. Moreover, conventional plant breeding can only combine closely related plants.