Michael Freeling

The Sorghum bicolor genome and the diversification of grasses

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the ∼75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization ∼70 million years ago, most duplicated gene sets lost one member before the sorghum–rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum’s drought tolerance.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica’s distinguishing morpho-physiological, medicinal and nutritional properties.

The maize handbook

This book brings together information and techniques for working with maize (com), a plant of enormous significance as a crop and as a model system for studies in plant genetics, biochemistry, and molecular biology. A distinguished editorial board has coordinated the compilation of protocols on maize cell biology, genetic methods and maps, tissue culture, and molecular biology. This book should be useful to those involved in maize research and scienitists working on other plants.

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon–eudicotyledon divergence.

The anaerobic proteins of maize

Anaerobic treatment drastically alters the pattern of protein synthesized by maize primary roots. During the first hour of anaerobiosis, aerobic protein synthesis is halted and there is an increase in the synthesis of a class of polypeptides with approximate molecular weights of 33,000 daltons. During the second hour of anaerobic treatment, the synthesis of another small group of polypeptides is initated. This group, the anerboic polypeptides (ANPs), accounts for > 70% of total protein synthesis after 5 hr of anaerobiosis, and is synthesized in basically the same ratio until root death (approximately 70 hr). The alcohol dehydrogenase polypeptides are major ANPs. RNA isolated from roots treated anaerobically for at least 24 hr directs the translation of only the anaerobic polypeptides. However, RNA from roots treated anaerobically for only 5 hr directs translation of both anaerobic and aerobic polypeptides. Thus an early response to anaerobic treatment is the suppression of aerobic message translation. Although the anaerobic polypeptides share a formal similarity to heat-shock proteins in animals, it is probable that the anaerobic genes are an adaptation to flooding.

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

Ancient tetraploidies are found throughout the eukaryotes. After duplication, one copy of each duplicate gene pair tends to be lost (fractionate). For all studied tetraploidies, the loss of duplicated genes, known as homeologs, homoeologs, ohnologs, or syntenic paralogs, is uneven between duplicate regions. In maize, a species that experienced a tetraploidy 5–12 million years ago, we show that in addition to uneven ancient gene loss, the two complete genomes contained within maize are differentiated by ongoing fractionation among diverse inbreds as well as by a pattern of overexpression of genes from the genome that has experienced less gene loss. These expression differences are consistent over a range of experiments quantifying RNA abundance in different tissues. We propose that the universal bias in gene loss between the genomes of this ancient tetraploid, and perhaps all tetraploids, is the result of selection against loss of the gene responsible for the majority of total expression for a duplicate gene pair. Although the tetraploidy of maize is ancient, biased gene loss and expression continue today and explain, at least in part, the remarkable genetic diversity found among modern maize cultivars.

Grasses as a single genetic system: genome composition, collinearity and compatibility.

The best-known grasses are the cereals, of which three speciesrice, wheat and maizeaccount for about half of total world food production. These and other domesticated grasses (including barley, millet, oats, rye, sorghum and sugar-cane) are among the 10-11 thousand species that comprise the grass (Gramineae) family of monocotyledonous flowering plantsL Because of their unrivaled economic importance and relative ease of genetic manipulation, the cereals and forage grasses have been major targets for basic and applied plant science. Each grass species has unique agronomic properties, particularly with respect to environmental preferences and tolerances, and this variation has led to an array of independent research programs for the study and improvement of each grass. Although many individual species have been investigated intensively, the information and materials acquired have not often been used in the full range of grass species. Recent results from genome mapping and intergeneric sexual hybridization experiments suggest that we can now overcome the barriers that have traditionally isolated these systems. These studies show that the various grasses can best be viewed as different manifestations of one tractable genome, and that research priorities should be set to reflect this rich biological potential. Phylogenies based on morphology, molecular sequences and fossils argue that there is a relatively close evolutionary relationship among grass species. The first grass fossils appear in paleocene-eocene deposits some 50-60 million years old z, at a time when modem orders of mammals are known to have existed, and crops were domesticated from their wild progenitors only a few thousand years ago. Grasses are morphologically welldifferentiated from other families and have a single (monophyletic) origin3. Given the close relatedness of the grasses, it is not surprising that many cross-species sexual hybrids have been documented. Moreover, the movement of chromosome segments from one grass species to another has been a powerful tool in both basic and applied plant research. Very wide-ranging crosses between grasses have recently been made, producing transient allodiploidy or chromosomal addition line#. These interspecies and intergeneric hybrids can now be used in traditional mendelian analyses of segregants to identify the genes, mechanisms and designs that underlie the morphological and physiological differences that have evolved in the Gramineae5. Until recently the quality of genetic maps for grasses, including the cereal crops, ranged from fair to non-existent. This general deficiency was rapidly overcome with the advent of maps based on DNA markers. Now, maps have been constructed for all the major cereals, with restriction fragment length polymorphisms (RFLP) and/or randomly amplified polymorphic DNA (RAPD) probes providing anywhere from hundreds to thousands of markers. The first extensive use of DNA markers for the grasses was in studies of maize, and these programs generated large libraries of mapped probes 6-8. The fwst detailed genetic map of sorghum was generated using probes from maize9: when maize probes were hybridized to sorghum DNA, single-o,!?y sequences hybridized well (>95°/6 detected similarly low copy number bands in sorghum under standard high-stringency conditions), while most repetitive sequences hybridized poorly, or not at all. This suggests that the discrepancy in size between the maize and sorghum genomes l°.l~ (the maize genome is 3.5 times larger than that of sorghum) is due, not to differences in the number or types of genes, but rather to differences in the amount of repetitive DNA. Most interestingly,

How to usefully compare homologous plant genes and chromosomes as DNA sequences

There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non-coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text.

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

In addition to the genomes of Arabidopsis (Arabidopsis thaliana) and poplar (Populus trichocarpa), two near-complete rosid genome sequences, grape (Vitis vinifera) and papaya (Carica papaya), have been recently released. The phylogenetic relationship among these four genomes and the placement of their three independent, fractionated tetraploidies sum to a powerful comparative genomic system. CoGe, a platform of multiple whole or near-complete genome sequences, provides an integrative Web-based system to find and align syntenic chromosomal regions and visualize the output in an intuitive and interactive manner. CoGe has been customized to specifically support comparisons among the rosids. Crucial facts and definitions are presented to clearly describe the sorts of biological questions that might be answered in part using CoGe, including patterns of DNA conservation, accuracy of annotation, transposability of individual genes, subfunctionalization and/or fractionation of syntenic gene sets, and conserved noncoding sequence content. This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically.

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

Following genome duplication and selfish DNA expansion, maize used a heretofore unknown mechanism to shed redundant genes and functionless DNA with bias toward one of the parental genomes.