The genome of Theobroma cacao

Cell death mediated by the N-terminal domains of a unique and highly conserved class of NB-LRR protein

Plant genomes encode large numbers of nucleotide-binding, leucine-rich repeat (NB-LRR) proteins, many of which are active in pathogen detection and defense response induction. NB-LRR proteins fall into two broad classes: those with a Toll and interleukin-1 receptor (TIR) domain at their N-terminus and those with a coiled-coil (CC) domain at the N-terminus. Within CC-NB-LRR-encoding genes, one basal clade is distinguished by having CC domains resembling the Arabidopsis thaliana RPW8 protein, which we refer to as CCR domains. Here, we show that CCR-NB-LRR-encoding genes are present in the genomes of all higher plants surveyed, and that they comprise two distinct subgroups: one typified by the Nicotiana benthamiana N-required gene 1 (NRG1) protein and the other typified by the Arabidopsis activated disease resistance gene 1 (ADR1) protein. We further report that, in contrast to CC-NB-LRR proteins, the CCR domains of both NRG1- and ADR1-like proteins are sufficient for the induction of defense responses, and that this activity appears to be SGT1-independent. Additionally, we report the apparent absence of both NRG1 homologs and TIR-NB-LRR-encoding genes from the dicot Aquilegia coerulea and the dicotyledonous order Lamiales as well as from monocotyledonous species. This strong correlation in occurrence is suggestive of a functional relationship between these two classes of NB-LRR proteins.

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing

Polyploidy complicates genomics-based breeding of many crops, including wheat, potato, cotton, oat and sugarcane. To address this challenge, we sequenced leaf transcriptomes across a mapping population of the polyploid crop oilseed rape (Brassica napus) and representative ancestors of the parents of the population. Analysis of sequence variation and transcript abundance enabled us to construct twin single nucleotide polymorphism linkage maps of B. napus, comprising 23,037 markers. We used these to align the B. napus genome with that of a related species, Arabidopsis thaliana, and to genome sequence assemblies of its progenitor species, Brassica rapa and Brassica oleracea. We also developed methods to detect genome rearrangements and track inheritance of genomic segments, including the outcome of an interspecific cross. By revealing the genetic consequences of breeding, cost-effective, high-resolution dissection of crop genomes by transcriptome sequencing will increase the efficiency of predictive breeding even in the absence of a complete genome sequence.

The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants

Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.

Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

Background

BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library.

Results

This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight.

Conclusions

Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

An introduction to the medicinal plant genome project

In recent years, genomics has developed rapidly with the application of next-generation sequencing technology. However, very few studies have been carried out on genomics for medicinal plants. This paper introduces the genome research of medicinal plants, including genome sequencing, assembly, annotation, and functional genomics, to set up the foundation for the development of natural medicines and the selection of cultivars with good agricultural traits. This study places the study on traditional Chinese medicine into the frontier field of life science.

Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

BACKGROUND

Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited.

RESULT

We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences.

CONCLUSION

The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns.