We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis, ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

/pdf/the-genome-of-black-cottonwood-populus-trichocarpa-torr-gray-uje0c9fwz6.pdf

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Lignin is the generic term for a large group of aromatic polymers resulting from the oxidative combinatorial coupling of 4-hydroxyphenylpropanoids ([Boerjan et al., 2003][1]; [Ralph et al., 2004][2]). These polymers are deposited predominantly in the walls of secondarily thickened cells, making them

Lignin Biosynthesis and Structure

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

/pdf/genome-sequence-and-analysis-of-the-tuber-crop-potato-3bzwxev7ko.pdf

Genome sequence and analysis of the tuber crop potato.

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.

http://science.sciencemag.org/content/sci/345/6199/950.full.pdf

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

Extraction and analysis of phenolics in food

In the last years, the spread of wilt and dieback diseases in olive trees (Olea europaea), caused by the soilborne pathogens, has often been related to intensive modern farming of highly productive cultivars, planted at high densities, usually in an irrigated system. Plants have developed different strategies to trigger defense signaling to defend themselves and to maintain surveillance against pathogens. However, the response of olive tree to pathogen infections is not well studied yet. The present work is aimed at studying the response of olive tree to soilborne fungi isolated from different affected areas in Tunisia, such as Fusarium spp., Verticillium dahliae, Cylindrocarpon sp. and Rhizoctonia solani. Artificial inoculation on young olive trees cv. ‘Chemlali’ confirmed the pathogenicity of all these pathogens by reproducing typical symptoms of root rot with varied degrees. Biochemical analysis realized after 21 days of inoculation has shown that chlorophyll pigments, solubles sugar, total polyphenols and proline contents were highly detected in plants infected by V. dahliae and F. solani. The expression of four genes Olest 06, Olest 47, Olest 73 and Olest 30 involved in the signaling biotic and abiotic stress and transcriptional activation of pathogenesis-related proteins was analyzed by reverse transcription-PCR after 21 days of inoculation. The transcript level of Olest 73 was relatively constant in all tested fungi. The expression of gene Olest 47 was observed in the leaves of olive in vitro plants infected by V. dahliae and Fusarium spp., and the gene expression of Olest 30 was detected only in plants infected by V. dahliae. No PCR product was detected for Olest 06 in all inoculated olive trees. In conclusion, according to results obtained by biochemical and molecular analysis, the olive trees develop variable responses to pathogenic soil fungi attack.

Response of olive tree (Olea europaea L.cv. Chemlali) to infection with soilborne fungi

This study investigates the impact of the alteration of the monolignol biosynthesis pathway on the establishment of the in vitro interaction of poplar roots either with a mutualistic ectomycorrhizal fungus or with a pathogenic root-knot nematode. Overall, the five studied transgenic lines downregulated for caffeoyl-CoA O-methyltransferase (CCoAOMT), caffeic acid O-methyltransferase (COMT), cinnamoyl-CoA reductase (CCR), cinnamyl alcohol dehydrogenase (CAD) or both COMT and CAD displayed a lower mycorrhizal colonisation percentage, indicating a lower ability for establishing mutualistic interaction than the wild-type. The susceptibility to root-knot nematode infection was variable in the five lines, and the CAD-deficient line was found to be less susceptible than the wild-type. We discuss these phenotypic differences in the light of the large shifts in the metabolic profile and gene expression pattern occurring between roots of the CAD-deficient line and wild-type. A role of genes related to trehalose metabolism, phytohormones, and cell wall construction in the different mycorrhizal symbiosis efficiency and nematode sensitivity between these two lines is suggested. Overall, these results show that the alteration of plant metabolism caused by the repression of a single gene within phenylpropanoid pathway results in significant alterations, at the root level, in the response towards mutualistic and pathogenic associates. These changes may constrain plant fitness and biomass production, which are of economic importance for perennial industrial crops such as poplar.

/pdf/alterations-in-the-phenylpropanoid-pathway-affect-poplar-28k1lz5hvx.pdf

Marie Baucher

Papers

Response of olive tree (Olea europaea L.cv. Chemlali) to infection with soilborne fungi

Alterations in the phenylpropanoid pathway affect poplar ability for ectomycorrhizal colonisation and susceptibility to root-knot nematodes.

Genetic engineering in forest trees

Transgenic poplar trees with altered lignin and improved pulping

Transgenic poplar trees with altered lignin and improved pulping characteristics