The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

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Phytozome: a comparative platform for green plant genomics

Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

/pdf/the-tomato-genome-sequence-provides-insights-into-fleshy-7a55qpnrdm.pdf

The tomato genome sequence provides insights into fleshy fruit evolution

The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oyster's adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.

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The oyster genome reveals stress adaptation and complexity of shell formation

Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.

https://www.csie.ntu.edu.tw/~kmchao/bioinformatics12spr/presentation/Report_20120604%236.pdf

Repetitive DNA and next-generation sequencing: computational challenges and solutions.

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

The exposure of plants to drought conditions inhibits shoot growth, increases production of toxic reactive oxygen species (ROS), and negatively affects photosynthesis and carbohydrate metabolism. Drought susceptibility in potato impacts all stages of the crop, from emergence to tuber initiation. Although there have been various studies of the global changes in gene expression profiles during drought conditions in potatoes, few studies have been based on native potato species. Because of their high genetic diversity, native potatoes from the Andean regions of Peru, Ecuador and Bolivia, are well adapted to the harsh environmental conditions that prevail in the Andes, including drought. This makes them ideal candidates for gene expression studies associated with drought tolerance. The identification of drought tolerance traits and genes for potato will facilitate breeding for high yield stability under drought conditions. The first phase of this study consisted on a comparative RNA sequencing analysis between drought-tolerant and drought-susceptible native potato cultivars. During the second phase, a drought experiment with both tolerant and susceptible native potato species, using an aeroponics growth system was conducted. Selected drought-associated candidate genes from the RNA sequence analysis were used in primer design and quantitative RT-PCR analysis. Differential gene expression in tolerant vs. susceptible cultivars has been confirmed for two heat shock proteins and for a triacyl glycerol lipase. Additional candidate genes are being tested. In conclusion, native potatoes are providing important information on genes affected by drought conditions.

Differential expression of native potatoes genes in response to drought conditions

/pdf/characterization-of-native-plants-with-phytoremediation-3ta13js2lt.pdf

Characterization of Native Plants with Phytoremediation Potential in Ancash - Peru Respect to their Capacity of Propagation and Accumulation of Heavy Metals

Olga Ponce

Papers

Differential expression of native potatoes genes in response to drought conditions

Characterization of Native Plants with Phytoremediation Potential in Ancash - Peru Respect to their Capacity of Propagation and Accumulation of Heavy Metals