GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP

The suppression of tomato defence response genes upon potato cyst nematode infection indicates a key regulatory role of miRNAs

Potato cyst nematode Globodera rostochiensis is an obligate parasite of solanaceous plants, triggering metabolic and morphological changes in roots which may result in substantial crop yield losses. Previously, we used the cDNA-AFLP to study the transcriptional dynamics in nematode infected tomato roots. Now, we present the rescreening of already published, upregulated transcript-derived fragment dataset using the most current tomato transcriptome sequences. Our reanalysis allowed to add 54 novel genes to 135, already found as upregulated in tomato roots upon G. rostochiensis infection (in total - 189). We also created completely new catalogue of downregulated sequences leading to the discovery of 76 novel genes. Functional classification of candidates showed that the 'wound, stress and defence response' category was enriched in the downregulated genes. We confirmed the transcriptional dynamics of six genes by qRT-PCR. To place our results in a broader context, we compared the tomato data with Arabidopsis thaliana, revealing similar proportions of upregulated and downregulated genes as well as similar enrichment of defence related transcripts in the downregulated group. Since transcript suppression is quite common in plant-nematode interactions, we assessed the possibility of miRNA-mediated inverse correlation on several tomato sequences belonging to NB-LRR and receptor-like kinase families. The qRT-PCR of miRNAs and putative target transcripts showed an opposite expression pattern in 9 cases. These results together with in silico analyses of potential miRNA targeting to the full repertoire of tomato R-genes show that miRNA mediated gene suppression may be a key regulatory mechanism during nematode parasitism.

Identification of imprinted genes subject to parent-of-origin specific expression in Arabidopsis thaliana seeds

BACKGROUND

Epigenetic regulation of gene dosage by genomic imprinting of some autosomal genes facilitates normal reproductive development in both mammals and flowering plants. While many imprinted genes have been identified and intensively studied in mammals, smaller numbers have been characterized in flowering plants, mostly in Arabidopsis thaliana. Identification of additional imprinted loci in flowering plants by genome-wide screening for parent-of-origin specific uniparental expression in seed tissues will facilitate our understanding of the origins and functions of imprinted genes in flowering plants.

RESULTS

cDNA-AFLP can detect allele-specific expression that is parent-of-origin dependent for expressed genes in which restriction site polymorphisms exist in the transcripts derived from each allele. Using a genome-wide cDNA-AFLP screen surveying allele-specific expression of 4500 transcript-derived fragments, we report the identification of 52 maternally expressed genes (MEGs) displaying parent-of-origin dependent expression patterns in Arabidopsis siliques containing F1 hybrid seeds (3, 4 and 5 days after pollination). We identified these MEGs by developing a bioinformatics tool (GenFrag) which can directly determine the identities of transcript-derived fragments from (i) their size and (ii) which selective nucleotides were added to the primers used to generate them. Hence, GenFrag facilitates increased throughput for genome-wide cDNA-AFLP fragment analyses. The 52 MEGs we identified were further filtered for high expression levels in the endosperm relative to the seed coat to identify the candidate genes most likely representing novel imprinted genes expressed in the endosperm of Arabidopsis thaliana. Expression in seed tissues of the three top-ranked candidate genes, ATCDC48, PDE120 and MS5-like, was confirmed by Laser-Capture Microdissection and qRT-PCR analysis. Maternal-specific expression of these genes in Arabidopsis thaliana F1 seeds was confirmed via allele-specific transcript analysis across a range of different accessions. Differentially methylated regions were identified adjacent to ATCDC48 and PDE120, which may represent candidate imprinting control regions. Finally, we demonstrate that expression levels of these three genes in vegetative tissues are MET1-dependent, while their uniparental maternal expression in the seed is not dependent on MET1.

CONCLUSIONS

Using a cDNA-AFLP transcriptome profiling approach, we have identified three genes, ATCDC48, PDE120 and MS5-like which represent novel maternally expressed imprinted genes in the Arabidopsis thaliana seed. The extent of overlap between our cDNA-AFLP screen for maternally expressed imprinted genes, and other screens for imprinted and endosperm-expressed genes is discussed.

ESTs from Seeds to Assist the Selective Breeding of Jatropha curcas L. for Oil and Active Compounds

We report here on the characterization of a cDNA library from seeds of Jatropha curcas L. at three stages of fruit maturation before yellowing. We sequenced a total of 2200 clones and obtained a set of 931 non-redundant sequences (unigenes) after trimming and quality control, ie, 140 contigs and 791 singlets with PHRED quality ≥10. We found low levels of sequence redundancy and extensive metabolic coverage by homology comparison to GO. After comparison of 5841 non-redundant ESTs from a total of 13193 reads from GenBank with KEGG, we identified tags with nucleotide variations among J. curcas accessions for genes of fatty acid, terpene, alkaloid, quinone and hormone pathways of biosynthesis. More specifically, the expression level of four genes (palmitoyl-acyl carrier protein thioesterase, 3-ketoacyl-CoA thiolase B, lysophosphatidic acid acyltransferase and geranyl pyrophosphate synthase) measured by real-time PCR proved to be significantly different between leaves and fruits. Since the nucleotide polymorphism of these tags is associated to higher level of gene expression in fruits compared to leaves, we propose this approach to speed up the search for quantitative traits in selective breeding of J. curcas. We also discuss its potential utility for the selective breeding of economically important traits in J. curcas.

Amplified fragment length homoplasy: in silico analysis for model and non-model species

BACKGROUND

AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species.

RESULTS

In this study we performed in silico AFLPs on the complete genome of three model species to predict intra-individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti. Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species.

CONCLUSIONS

These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and population genetic estimation bias. ISIF (In SIlico Fingerprinting) program is freely available at http://www-leca.ujf-grenoble.fr/logiciels.htm.

Identification of genes involved in stem rust resistance from wheat mutant D51 with the cDNA-AFLP technique

Wheat (Triticum aestivum L.) stem rust caused by Puccinia graminis f. sp. tritici is one of the main diseases of wheat worldwide. Wheat mutant line D51, which was derived from the highly susceptible cultivar L6239, shows resistance to the prevailing races 21C3CPH, 21C3CKH, and 21C3CTR of P. graminis f. sp. tritici in China. In this study, we used the cDNA-AFLP technology to identify the genes that are likely involved in the stem rust resistance. EcoRI/MseI selective primers were used to generate approximately 1920 DNA fragments. Seventy five differentially transcribed fragments (3.91%) were identified by comparing the samples of 21C3CPH infected D51 with infected L6239 or uninfected D51. Eleven amplified cDNA fragments were sequenced. Eight showed significant similarity to known genes, including TaLr1 (leaf rust resistance gene), wlm24 (wheat powdery mildew resistance gene), stress response genes and ESTs of environment stress of tall fescue. These identified genes are involved in plant defense response and stem rust resistance and need further research to determine their usefulness in breeding new resistance cultivars.

Components of variance in transcriptomics based on electrophoretic separation of cDNA fragments (cDNA-AFLP)

The sources of variance and errors in transcriptomics based on the electrophoretic separation of amplified cDNA fragments were investigated using cDNA-amplified fragment length polymorphism (AFLP). Transcriptome profiles of the plant-pathogenic fungus Verticillium longisporum were generated by a standard cDNA-AFLP protocol followed by electrophoretic separation of amplified DNA fragments in flatbed polyacrylamide gels with fluorescence detection as well as by capillary electrophoresis (DNA sequencer). The total variance was partitioned into contributions of cDNA synthesis, adapter ligation, preamplification, amplification, and electrophoresis. Parameters of computer-aided peak recognition and matching were investigated and strategies improving matching success based on double passage with different signal intensity thresholds were developed. The overall quality of data was similar for cDNA-AFLP and microarray hybridization. Variance of cDNA-AFLP was independent of signal intensity, whereas microarray data showed higher variance for low-intensity signals. Capillary electrophoresis significantly reduced the number of wrongly matched and unmatched signals as compared with flatbed gels. These results are also likely to apply to related electrophoresis-based transcriptome analysis techniques such as mRNA differential display.

Dynamics in the tomato root transcriptome on infection with the potato cyst nematode Globodera rostochiensis

Plant parasitic nematodes infect roots and trigger the formation of specialized feeding sites by substantial reprogramming of the developmental process of root cells. In this article, we describe the dynamic changes in the tomato root transcriptome during early interactions with the potato cyst nematode Globodera rostochiensis. Using amplified fragment length polymorphism-based mRNA fingerprinting (cDNA-AFLP), we monitored 17 600 transcript-derived fragments (TDFs) in infected and uninfected tomato roots, 1-14 days after inoculation with nematode larvae. Six hundred and twenty-four TDFs (3.5%) showed significant differential expression on nematode infection. We employed GenEST, a computer program which links gene expression profiles generated by cDNA-AFLP and databases of cDNA sequences, to identify 135 tomato sequences. These sequences were grouped into eight functional categories based on the presence of genes involved in hormone regulation, plant pathogen defence response, cell cycle and cytoskeleton regulation, cell wall modification, cellular signalling, transcriptional regulation, primary metabolism and allocation. The presence of unclassified genes was also taken into consideration. This article describes the responsiveness of numerous tomato genes hitherto uncharacterized during infection with endoparasitic cyst nematodes. The analysis of transcriptome profiles allowed the sequential order of expression to be dissected for many groups of genes and the genes to be connected with the biological processes involved in compatible interactions between the plant and nematode.

Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA

BACKGROUND

cDNA-AFLP is a transcriptomics technique which does not require prior sequence information and can therefore be used as a gene discovery tool. The method is based on selective amplification of cDNA fragments generated by restriction endonucleases, electrophoretic separation of the products and comparison of the band patterns between treated samples and controls. Unequal distribution of restriction sites used to generate cDNA fragments negatively affects the performance of cDNA-AFLP. Some transcripts are represented by more than one fragment while other escape detection, causing redundancy and reducing the coverage of the analysis, respectively.

RESULTS

With the goal of improving the coverage of cDNA-AFLP without increasing its redundancy, we designed a modified cDNA-AFLP protocol. Immobilized cDNA is sequentially digested with several restriction endonucleases and the released DNA fragments are collected in mutually exclusive pools. To investigate the performance of the protocol, software tool MECS (Multiple Enzyme cDNA-AFLP Simulation) was written in Perl. cDNA-AFLP protocols described in the literature and the new sequential digestion protocol were simulated on sets of cDNA sequences from mouse, human and Arabidopsis thaliana. The redundancy and coverage, the total number of PCR reactions, and the average fragment length were calculated for each protocol and cDNA set.

CONCLUSION

Simulation revealed that sequential digestion of immobilized cDNA followed by the partitioning of released fragments into mutually exclusive pools outperformed other cDNA-AFLP protocols in terms of coverage, redundancy, fragment length, and the total number of PCRs. Primers generating 30 to 70 amplicons per PCR provided the highest fraction of electrophoretically distinguishable fragments suitable for normalization. For A. thaliana, human and mice transcriptome, the use of two marking enzymes and three sequentially applied releasing enzymes for each of the marking enzymes is recommended.

Optimizing automated AFLP scoring parameters to improve phylogenetic resolution

The amplified fragment length polymorphism (AFLP) technique is an increasingly popular component of the phylogenetic toolbox, particularly for plant species. Technological advances in capillary electrophoresis now allow very precise estimates of DNA fragment mobility and amplitude, and current AFLP software allows greater control of data scoring and the production of the binary character matrix. However, for AFLP to become a useful modern tool for large data sets, improvements to automated scoring are required. We design a procedure that can be used to optimize AFLP scoring parameters to improve phylogenetic resolution and demonstrate it for two AFLP scoring programs (GeneMapper and GeneMarker). In general, we found that there was a trade-off between getting more characters of lower quality and fewer characters of high quality. Conservative settings that gave the least error did not give the best phylogenetic resolution, as too many useful characters were discarded. For example, in GeneMapper, we found that bin width was a crucial parameter, and that although reducing bin width from 1.0 to 0.5 base pairs increased the error rate, it nevertheless improved resolution due to the increased number of informative characters. For our 30-taxon data sets, moving from default to optimized parameter settings gave between 3 and 11 extra internal edges with >50% bootstrap support, in the best case increasing the number of resolved edges from 14 to 25 out of a possible 27. Nevertheless, improvements to current AFLP software packages are needed to (1) make use of replicate profiles to calibrate the data and perform error calculations and (2) perform tests to optimize scoring parameters in a rigorous and automated way. This is true not only when AFLP data are used for phylogenetics, but also for other applications, including linkage mapping and population genetics.

AFLP-based transcript profiling (cDNA-AFLP) for genome-wide expression analysis

Although DNA microarrays are currently the standard tool for genome-wide expression analysis, their application is limited to organisms for which the complete genome sequence or large collections of known transcript sequences are available. Here, we describe a protocol for cDNA-AFLP, an AFLP-based transcript profiling method that allows genome-wide expression analysis in any species without the need for prior sequence knowledge. In essence, the cDNA-AFLP method involves reverse transcription of mRNA into double-stranded cDNA, followed by restriction digestion, ligation of specific adapters and fractionation of this mixture of cDNA fragments into smaller subsets by selective PCR amplification. The resulting cDNA-AFLP fragments are separated on high-resolution gels, and visualization of cDNA-AFLP fingerprints is described using either a conventional autoradiography platform or an automated LI-COR system. Observed differences in band intensities between samples provide a good measure of the relative differences in the gene expression levels. Identification of differentially expressed genes can be accomplished by purifying cDNA-AFLP fragments from sequence gels and subsequent sequencing. This method has found widespread use as an attractive technology for gene discovery on the basis of fragment detection and for temporal quantitative gene expression analysis. The protocol can be completed in 3-4 d.

Almost forgotten or latest practice? AFLP applications, analyses and advances

Amplified fragment length polymorphism (AFLP) DNA fingerprinting is a firmly established molecular marker technique, with broad applications in population genetics, shallow phylogenetics, linkage mapping, parentage analyses, and single-locus PCR marker development. Technical advances have presented new opportunities for data analysis, and recent studies have addressed specific areas of the AFLP technique, including comparison to other genotyping methods, assessment of errors, homoplasy, phylogenetic signal and appropriate analysis techniques. Here we provide a synthesis of these areas and explore new directions for the AFLP technique in the genomic era, with the aim of providing a review that will be applicable to all AFLP-based studies.

A novel gene, screened by cDNA-AFLP approach, contributes to lowering the acidity of fruit in apple

cDNA-AFLP, coupled with bulked segregant analysis (BSA), was used to screen genes expressed differently between low- and high-acid apple fruits from hybrids of 'Toko' x 'Fuji' (Malus x domestica Borkh.). Sixty-four combinations of AFLP primers produced 2240 fragments, of which only one showed different expression between low- and high-acid fruits. The specific fragment was cloned and sequenced, and the complete cDNA was achieved by 3' and 5' rapid amplification of cDNA ends (RACE). The screened gene, designated as Mal-DDNA (GenBank accession no. DQ417661), showed no significant homology to clones in GenBank. The relatedness between fruit acidity and the transcription level of Mal-DDNA was identified by RT-PCR analysis on 30 hybrids. RT-PCR analysis indicated that Mal-DDNA transcripted in low-acid fruits at both early and ripe stages whereas in high- and mid-acid fruits, it did not transcript at the early stage. RNA gel-blot hybridization indicated that Mal-DDNA transcripted only in fruits and had clear difference between low- and high/mid-acid fruits. There was a good indication that Mal-DDNA existed as one copy in apple genome by Southern blot. Possible regulation of Mal-DDNA in apple fruit acidity is also discussed in the paper.

Differentially expressed genes related to symbiotic association in a supernodulating soybean mutant and its wild-type

SUMMARY To understand the molecular basis of symbiotic association, a cDNA-AFLP technique was used to identify differentially expressed transcripts between a supernodulating soybean mutant, SS2-2, and its wild-type, Sinpaldalkong 2. As sources of cDNA-AFLP templates, trifoliates of 2-week-old plants were collected 1 week after Bradyrhizobium japonicum inoculation. A total of 147 bands out of 4000 amplicons were recognized as differentially expressed fragments, with 40 transcript-derived fragments (TDFs) in SS2-2 and 65 TDFs in Sinpaldalkong 2. Qualitative and quantitative real-time RT-PCR assays suggested that the expression patterns of genes in both genotypes were clearly differentiated. TDFs homologous to nodulin (65S2) and a putative senescence-associated protein (9S1) were up-regulated in SS2-2, whereas Sinpaldalkong 2 showed up-regulation of a receptor-like kinase (48sin1) and a kinase-like protein (17sin1). This indicates that different genes may be involved in regulation of the symbiotic programme that distinguishes SS2-2 from its wild-type. A TDF showing a change in a single base from A (Sinpaldalkong 2) to T (SS2-2) in this study was identified as a Glycine max nodule autoregulation receptor-like protein kinase precursor, previously identified by map-based cloning. These results demonstrate that cDNA-AFLP is a powerful technique to detect interesting genes without prior assumptions about the nature of the genes. The differentially expressed genes between Sinpaldalkong 2 and SS2-2 suggest that different signal transduction pathways for symbiosis may be involved in the two soybean genotypes.

Detection of an efficient restriction enzyme combination for cDNA-AFLP analysis in Festuca mairei and evaluation of the identity of transcript-derived fragments

In cDNA-amplified fragment length polymorphism (cDNA-AFLP) analysis, it is critical to choose a suitable pair of restriction enzymes for tagging sites in cDNA for amplification. Possibility of production of chimeric fragments from cDNA-AFLP analysis remains to be researched. The objectives of this study were to detect an efficient restriction enzyme combination for cDNA-AFLP analysis when Festuca species was used as template, and to evaluate the identity of transcript-derived fragments (TDFs) from cDNA-AFLP analysis. We found that NspI coupled TaqI was a pair of highly efficient enzymes by generating a much higher number of TDFs than the commonly used EcoRI and TaqI. This was the first study to apply NspI for AFLP analysis, prompting that this enzyme may have valuable application potential for other species. The identity of TDF was evaluated by sequencing a TDF and comparing it with the sequence of the template cDNA. The result showed that the chimeric fragments derived from ligation between digested fragments was generated and could not be eliminated by increasing adapter concentration. Although the existence of chimeric fragments should be carefully considered, the unexpected sequence in the chimeric TDF may not seriously influence the sequencing and BLAST searching analyses.

Recent developments in primer design for DNA polymorphism and mRNA profiling in higher plants

Primer design is a critical step in the application of PCR-based technologies in gene expression and genetic diversity analysis. As more plant genomes have been sequenced in recent years, the emphasis of primer design strategy has shifted to genome-wide and high-throughput direction. This paper summarizes recent advances in primer design for profiling of DNA polymorphism and mRNA in higher plants, as well as new primer systems developed for animals that can be adapted for plants.

Conversion of cDNA differential display results (DDRT-PCR) into quantitative transcription profiles

BACKGROUND

Gene expression studies on non-model organisms require open-end strategies for transcription profiling. Gel-based analysis of cDNA fragments allows to detect alterations in gene expression for genes which have neither been sequenced yet nor are available in cDNA libraries. Commonly used protocols for gel-based transcript profiling are cDNA differential display (DDRT-PCR) and cDNA-AFLP. Both methods have been used merely as qualitative gene discovery tools so far.

RESULTS

We developed procedures for the conversion of cDNA Differential Display data into quantitative transcription profiles. Amplified cDNA fragments are separated on a DNA sequencer and detector signals are converted into virtual gel images suitable for semi-automatic analysis. Data processing consists of four steps: (i) cDNA bands in lanes corresponding to samples treated with the same primer combination are matched in order to identify fragments originating from the same transcript, (ii) intensity of bands is determined by densitometry, (iii) densitometric values are normalized, and (iv) intensity ratio is calculated for each pair of corresponding bands. Transcription profiles are represented by sets of intensity ratios (control vs. treatment) for cDNA fragments defined by primer combination and DNA mobility. We demonstrated the procedure by analyzing DDRT-PCR data on the effect of secondary metabolites of oilseed rape Brassica napus on the transcriptome of the pathogenic fungus Leptosphaeria maculans.

CONCLUSION

We developed a data processing procedure for the quantitative analysis of amplified cDNA fragments separated by electrophoresis. The system utilizes common software and provides an open-end alternative to DNA microarray analysis of the transcriptome. It is expected to work equally well with DDRT-PCR and cDNA-AFLP data and be useful particularly in research on organisms for which microarray analysis is not available or economical.

Optimization of cDNA-AFLP experiments using genomic sequence data

MOTIVATION

cDNA amplified fragment length polymorphism (cDNA-AFLP) is one of the few genome-wide level expression profiling methods capable of finding genes that have not yet been cloned or even predicted from sequence but have interesting expression patterns under the studied conditions. In cDNA-AFLP, a complex cDNA mixture is divided into small subsets using restriction enzymes and selective PCR. A large cDNA-AFLP experiment can require a substantial amount of resources, such as hundreds of PCR amplifications and gel electrophoresis runs, followed by manual cutting of a large number of bands from the gels. Our aim was to test whether this workload can be reduced by rational design of the experiment.

RESULTS

We used the available genomic sequence information to optimize cDNA-AFLP experiments beforehand so that as many transcripts as possible could be profiled with a given amount of resources. Optimization of the selection of both restriction enzymes and selective primers for cDNA-AFLP experiments has not been performed previously. The in silico tests performed suggest that substantial amounts of resources can be saved by the optimization of cDNA-AFLP experiments.

Downstream targets of the Phytophthora infestans Galpha subunit PiGPA1 revealed by cDNA-AFLP

SUMMARY In many plant pathogens heterotrimeric G-proteins are essential signalling components involved in development and pathogenicity. In the late blight oomycete pathogen Phytophthora infestans the G-protein alpha subunit PiGPA1 controls zoospore motility and is required for virulence. To identify G-protein targets and signalling pathways downstream of PiGPA1, we used an optimized cDNA-AFLP protocol for analysing gene expression profiles in hypovirulent P. infestans strains that were previously generated by silencing the Pigpa1 gene. First, expression profiles in sporangia and mycelium of the wild-type strain were compared, and this revealed a substantial number of mycelium- or sporangia-specific transcript derived fragments (TDFs). Subsequently, profiles in sporangia of wild-type, Pigpa1-silenced mutants and of a strain expressing a constitutively active form of PiGPA1 were compared. From a total of 2860 TDFs, 92 were down- and 19 up-regulated in the Pigpa1-silenced mutants. A subset of the differential TDFs was cloned and sequenced, and homology searches were carried out against Phytophthora EST and genomic databases and the NCBI database. cDNA-AFLP expression profiles were verified by Northern blot analysis or RT-PCR. The power of cDNA-AFLP for the identification of target genes in knock-down or gain-of-function mutants is discussed.

Molecular markers from the transcribed/expressed region of the genome in higher plants

In recent years, molecular marker technology in higher plants has witnessed a shift from the so-called random DNA markers (RDMs), developed in the past arbitrarily from genomic DNA and cDNA, to the molecular markers representing the transcriptome and the other coding sequences. These markers have been described as gene targeted markers (GTMs). Another specific class of markers includes the so-called functional markers (FMs), which are supposed to have a cause and effect relationship with the traits of interest. In this review, we first describe the development of these markers representing the transcriptome or genes per se; we then discuss the uses of these markers in some detail and finally add a note on the future directions of research and the implications of the wider application of these markers in crop improvement programmes. Using suitable examples, we describe markers of different classes derived from cDNA clones, expressed sequence tags (ESTs), gene sequences and the unique (coding) sequences obtained through methyl filtration or genome normalization (high C(0) t fraction) from gDNA libraries. While we briefly describe RFLPs, SSRs, AFLPs and SNPs developed from the transcriptome (cDNA clones and EST databases), we have discussed in more detail some of the novel markers developed from the transcriptome and specific genes. These novel markers include expressed sequence tag polymorphisms (ESTPs), conserved orthologue set (COS) markers, amplified consensus genetic markers (ACGMs), gene specific tags (GSTs), resistance gene analogues (RGAs) and exon-retrotransposon amplification polymorphism (ERAP). Uses of these markers have been discussed in some detail under the following headings: development of transcript and functional maps, estimations of genetic diversity, marker-assisted selection (MAS), candidate-gene (CG) approach and map-based cloning, genetical genomics and identification of eQTLs, study of genome organization and taxonomic and phylogenetic studies. At the end, we also append a list of websites relevant to further studies on the transcriptome. For want of space, considerable information including voluminous data in the form of 12 tables, and a long list of references cited in these tables, has been placed on the Internet as electronic supplementary material (ESM), which the readers may find useful.

Technical advances: genome-wide cDNA-AFLP analysis of the Arabidopsis transcriptome

cDNA-AFLP, a technology historically used to identify small numbers of differentially expressed genes, was adapted as a genome-wide transcript profiling method. mRNA levels were assayed in a diverse range of tissues from Arabidopsis thaliana plants grown under a variety of environmental conditions. The resulting cDNA-AFLP fragments were sequenced. By linking cDNA-AFLP fragments to their corresponding mRNAs via these sequences, a database was generated that contained quantitative expression information for up to two-thirds of gene loci in A. thaliana, ecotype Ws. Using this resource, the expression levels of genes, including those with high nucleotide sequence similarity, could be determined in a high-throughput manner merely by comparing cDNA-AFLP profiles with the database. The lengths of cDNA-AFLP fragments inferred from their electrophoretic mobilities correlated well with actual fragment lengths determined by sequencing. In addition, the concentrations of AFLP fragments from single cDNAs were highly correlated, illustrating the validity of cDNA-AFLP as a quantitative, genome-wide, transcript profiling method. cDNA-AFLP profiles were also qualitatively consistent with mRNA profiles obtained from parallel microarray analysis, and with data from previous studies.

Promoter analysis and transcription profiling: Integration of genetic data enhances understanding of gene expression

It is increasingly evident that transcription control might be conserved among organisms. For this reason, genome sequencing and gene expression profiling methods, which have yielded a plethora of data in different organisms, may be applied in species where genomic sequence is limited to mostly expression array and EST data. The identification of transcription factors and promoters associated with gene expression profiles and ESTs could therefore contribute to elucidate and predict complex regulatory events in plants.

Genomic signature tags (GSTs): a system for profiling genomic DNA

Genomic signature tags (GSTs) are the products of a method we have developed for identifying and quantitatively analyzing genomic DNAs. The DNA is initially fragmented with a type II restriction enzyme. An oligonucleotide adaptor containing a recognition site for MmeI, a type IIS restriction enzyme, is then used to release 21-bp tags from fixed positions in the DNA relative to the sites recognized by the fragmenting enzyme. These tags are PCR-amplified, purified, concatenated, and then cloned and sequenced. The tag sequences and abundances are used to create a high-resolution GST sequence profile of the genomic DNA. GSTs are shown to be long enough for use as oligonucleotide primers to amplify adjacent segments of the DNA, which can then be sequenced to provide additional nucleotide information or used as probes to identify specific clones in metagenomic libraries. GST analysis of the 4.7-Mb Yersinia pestis EV766 genome using BamHI as the fragmenting enzyme and NlaIII as the tagging enzyme validated the precision of our approach. The GST profile predicts that this strain has several changes relative to the archetype CO92 strain, including deletion of a 57-kb region of the chromosome known to be an unstable pathogenicity island.

AFLP-based transcript profiling

This unit presents an alternative to differential display that allows the quantification of transcripts, based on AFLP-fingerprinting of double-stranded cDNA. The protocol described includes the following steps: the isolation of poly(A)+ RNA from total RNA, the synthesis of double-stranded cDNA, the preparation of template fragments by digestion of the cDNA library with a combination of two restriction enzymes and the ligation of adaptors to the fragment ends, the selective amplification of specific subsets of fragments, and the electrophoretic analysis of these amplification products on standard denaturing polyacrylamide gels. The transcript profiles obtained by this technique are a reliable and efficient tool to identify differentially expressed mRNAs. This unit presents an alternative to differential display that allows the quantification of transcripts, based on AFLP-finger his unit presents an alternative to differential display that allows the quantification of transcripts, based on AFLP-finger.

Comprehensive gene expression analysis by transcript profiling

After the completion of the genomic sequence of Arabidopsis thaliana, it is now a priority to identify all the genes, their patterns of expression and functions. Transcript profiling is playing a substantial role in annotating and determining gene functions, having advanced from one-gene-at-a-time methods to technologies that provide a holistic view of the genome. In this review, comprehensive transcript profiling methodologies are described, including two that are used extensively by the authors, cDNA-AFLP and cDNA microarraying. Both these technologies illustrate the requirement to integrate molecular biology, automation, LIMS and data analysis. With so much uncharted territory in the Arabidopsis genome, and the desire to tackle complex biological traits, such integrated systems will provide a rich source of data for the correlative, functional annotation of genes.