Clearly, the search for genetic mechanisms for environmental adaptation was never on hold pending the invention of NGS. Differences in individual genes unquestionably have a big role in adaptation to stress. In some cases, they have been inferred from the primary sequences of well-characterized genes, such as the 37-amino-acid stretch in L-myo-inositol-1-phosphate synthase, which distinguishes the salt-tolerant wild rice (Porteresia coarctata) from domesticated rice (Oryza sativa) 11, or the single-amino-acid variation in AtHKT1;1 (which encodes the high-affinity K⁺ transporter 1) that distinguishes coastal from inland clines of Arabidopsis 12. In other cases, they have been implicated by the constitutively higher expression - in the absence of stress - of genes that are induced by stress in Arabidopsis, as in the resurrection plant Craterostigma plantagineum 13, the salt-tolerant poplar Populus euphratica 14, or the Arabidopsis relatives T. parvula and Thellungiella salsuginea (formerly T. halophila) 151617.

But genomes are far more than collections of protein coding sequences. To extend the search for 'genetic mechanisms' beyond this level of primary DNA or cDNA sequences, high-quality genomic resources are a paramount necessity. Especially critical are the genomes of closely related species, or even genotypes, that have adapted to different climates and habitats (that is, that have different lifestyles). Such genomes are beginning to appear, albeit few being proper extremophiles. The strawberry, apple, and peach genomes in the Rosaceae, for example, have begun to reveal how artificial selection for fruit quality has shaped these genomes 18. Differences reflecting natural selection should also be discernible, for a start, from resources such as those summarized in Table 1.

However, given the long history of Arabidopsis as a model system, the new genomes most immediately useful for comparative studies at this point are likely to be those closely related to it. One of these is the genome of Arabidopsis lyrata 19, a potential comparative model for drought tolerance 20, and T. parvula (Figure 1a,b) will be perhaps even more useful for elucidating a broad range of environmental adaptations 10. This species and the congeneric T. salsuginea are endemic to regions that experience temperature extremes, poor, degraded, and toxic soils, and especially very high salinities 621. The T. parvula genome is of particular interest because chromosomal assemblies that approach the coverage of A. thaliana are available. Moreover, because the Thellungiella species share many of the characteristics that led to the acceptance of Arabidopsis as a model (size, growth habit, seed amount, mutants, and transformation ability), they have been recognized as excellent candidates for comparative genomics studies 1522.

Given the evolutionary continuum of genome-level adaptations to abiotic stress, the signatures of the critical adaptive mechanisms must be archived in the genomes of extremophiles. These are the gems in the genome; the challenge is to find and understand them. Comparisons of known genes and transfers between species - the mainstay approach before cheap deep sequencing - can now be supplemented with more extensive genome prospecting, and thereafter with large scale data mining. In this section, we consider three issues as they apply to the problem: what has been explored so far, what has been found, and what is needed to move forward.

First, comparing gene expression at the broad level reflected in Gene Ontology (GO) profiles, stress-tolerant and -sensitive species show different patterns 10. Salt-tolerant extremophiles, on the one hand, seem to have a bias towards ion transporters in the gene function GO category that is not found in glycophytic species such as Arabidopsis. This bias is evident, for example, both in T. parvula and T. salsuginea 2324 and in the unrelated salt marsh halophyte Limonium sinense 25. Arabidopsis, on the other hand, has invested in an arsenal of pathogen-responsive and developmentally related genes. It is reasonable to suppose - although future research could prove otherwise - that transporters would be critical to salt stress tolerance, and that developmental flexibility and pathogen protection would be important for a winter annual in a high resource environment.

Whole-transcriptome analyses of two mangrove species, Heritiera littoralis (Malvaceae; Figure 1d) and Rhizophora mangle (Rhizophoraceae; Figure 1e), showed a similar high representation of transport-related genes. Interestingly, despite these species having different life histories and physiological strategies in their adaptation to tropical intertidal habitats, their transcriptomes showed strikingly similar allocations in GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories, suggesting convergent evolution as 'mangroves' 26.

Going beyond transcriptomes, at the genome level, where are the gems, that is, what are targets currently considered most promising as being part of integrative mechanisms that lead to stress adaptation? At this point, there are few genomes complete enough to allow detailed comparisons, essentially only T. parvula and A. thaliana. In these two, although the gene spaces show extensive overall colinearity, there are also major translocations of gene-rich regions and extensive changes in intergenic sequences 1015. Beyond this, there are three promising, potentially adaptive linkages to explore. These involve gene duplication, lineage-specific sequences, and epigenetic regulation. We look at these briefly below, with particular reference to their contributions as reflected in the newly released genome of T. parvula and the testable predictions that follow.

A striking feature of all plant genomes is gene enrichment due to duplication events. Suggested by Haldane in 1932 27 and later popularized by Ohno 28, gene duplication as an evolutionary mechanism that adds new biological function is a well-established idea. Both the duplication rate and the proportion of retained duplicates seem to be greater in plants than in the other domains of life 29. With respect to individual genes, the result is termed copy number variation (CNV). From resequencing the genomes of 80 individual Arabidopsis ecotypes, it seems that natural selection has led to CNVs covering 2.2 Mb of the reference genome 30. CNVs can also arise in a short time. For example, they appeared in Arabidopsis in several generations under the selection pressure of a continuous stress in the laboratory 31. These were distributed with a 42%:58% ratio between those initiated by transposable elements (TEs) and those involving tandem duplications.

Practically all angiosperms have polyploidy somewhere in their history, either current or long past. The initially increased gene dosage following duplication is often assumed to be beneficial for survival in new habitats, at least in the short term 32. But although there are certainly polyploid species known for their extreme adaptations to abiotic stresses, an equal fraction are adapted to less harsh conditions, and there are also diploid extremophiles (including Thellungiella spp.). Thus, there is little overall evidence that polyploidy itself is a major evolutionary driving force leading to extremophiles.

In most plants, including T. parvula, genomes enriched by polyploidy have subsequently experienced extensive gene losses 33. Their modern genomes reflect this. On the other hand, the copy numbers of other genes have increased as a result of segmental or tandem duplication events and duplication-translocation events. Individual copies of duplicated genes have, in many cases, also assumed new functionality resulting from mutation (neo-functionalization), or become specialized by acquisition of new promoters or regulatory elements (sub-functionalization). One such example is found in allopolyploid cotton (Gossypium hirsutum), in which reciprocal silencing of alcohol dehydrogenase homologs led to their expression in different tissues under distinct abiotic stresses 34.

An example of changes in transcript expression and neo-functionalization is provided by homologs encoding HKT1, a plasma membrane Na⁺/K⁺ transporter considered to be a genetic determinant of salt tolerance 1235. HKT1 exists as tandem duplicated copies in both Thellungiella species 1017. One copy encodes new protein functionality and also has an expression pattern different from that of the Arabidopsis counterpart 17. This copy, called TsHKT1;2 in T. salsuginea, is induced under salt stress and leads to continued uptake of potassium ions. By contrast, TsHKT1;1 in Thellungiella behaves like the single-copy AtHKT1; because this protein transports sodium ions under salt stress 36, it exacerbates stress unless its expression is downregulated 37.

In T. parvula and in A. thaliana, a major source of CNV has been tandem duplication 10. The extant populations of unique tandem duplicates reflect the fact that both copies originated since the species diverged about 11 million years ago 38 and that selective gene loss has occurred in each taxon in response to environmental selective pressures. Either through gene duplication or expression strength differences, a large number of other seemingly stress-relevant genes that have not been recognized in Arabidopsis show the hallmarks of CNV in Thellungiella, including a variety of ion transporters and membrane-located proton ATPases 10. Such a difference might be expected, as Thellungiella shares only 40% of salt-induced regulation of transcript expression with A. thaliana 39.

Tandem duplications seem to have a more important role in shaping genomes for stress adaptations than polyploidy, segmental transposition-duplications, or ectopic duplication and translocation 40; recombination and tandem duplication events may both become accelerated by environmental challenges 29. As the result of unequal crossing-over during recombination, tandem duplications vary in their 'genetic neighborhoods', with copies receiving different regulatory motifs that can lead to drastic changes in expression 40. A comparative study on plant genomes ranging from Arabidopsis to Physcomitrella showed genes associated with defense, transport functions, or abiotic stress responses enriched in tandem duplicates, whereas duplicates due to other mechanisms included genes enriched in other intracellular regulatory roles 41.

The A. thaliana and T. parvula genomes have approximately 10% of their total genes in tandem duplicates 10, and they are clearly implicated in the species' dramatically different stress tolerance strategies. This is exemplified by the amplification of NHX8 homologs (Figure 2a), known to encode a putative Li⁺ transporter in A. thaliana 42. The duplication leads to a constitutively higher expression in T. parvula than in A. thaliana, which might be responsible for the apparently enhanced tolerance of T. parvula to high Li⁺ in its natural habitat in central Anatolia 43.

Gene duplication may also result from single gene/segmental transposition-duplication or ectopic duplication/translocation 44 in such a way that any syntenic evidence for its ancestral origin is lost. Comparisons of T. parvula and A. thaliana genomes indicate multiple translocation-duplication events involving stress-related genes, exemplified by the duplications of orthologs of CBL10, encoding a calcium sensor 10, and AVP1, encoding a vacuolar proton transporter (Figure 2b) in T. parvula. The details of the relationship between this mechanism and stress-adaptive evolution deserve further exploration.

From these initial observations, there are a number of important questions for future studies. For example, how do duplications arise and become stabilized in targeted regions of the genome? Can stress increase the rate of their generation? How rapidly can new regulatory sequences evolve to become operational and do they evolve along with duplicated genes or independently? How rapidly can neofunctionalization occur and how is it balanced by gene loss? And how is tandem duplication called into play to adjust expression levels?

In any single genome, the suite of genes shaped by stress during adaptation should reflect, above all, the nature of the stresses. In turn, physiological and developmental changes will mirror genomic changes. Thus, both the suite of altered genes and their regulatory sequences can be expected to demonstrate lineage specificity.

Lineage-specific or taxonomically restricted genes (TRGs) are protein-coding genes that do not share sequence similarity outside the lineage. For that reason, they are also sometimes referred to as 'orphan genes' 45, or 'unknown'. Indeed, with each new EST collection or genome, the number of new unknowns (or 'unknown unknowns') proliferates. Regardless of the taxon, and in all the examples included in Table 1, 10 to 20% of the genes in eukaryote genomes or transcriptomes are TRGs 46. In the Brassicaceae, family-specific TRGs are enriched for genes responsive to abiotic stresses 47. It should be noted here that 'stress-responsive' or 'stress-related' are not labels indicating that the functions of the genes are then known. They simply mean that expression is induced by stress. In Arabidopsis, but not in T. parvula, the expansion is pronounced in pathogen-responsive genes; in T. parvula, but not in Arabidopsis, the expansion is pronounced in abiotic stress-related genes 10. Across the spectrum of plant stress tolerance, pools of rapidly evolving TRGs may function as a reservoir of adaptive potential to challenging environments.

In Arabidopsis, 3.4% of all genes share sequence similarity only within the Brassicaceae, and another 5% lack similarity with any sequences deposited in public databases 48. Because the Arabidopsis genome is the most fully annotated, it can be expected that the more evolutionarily distant from Arabidopsis a species is, the larger will be the number of TRGs, especially if the species is highly adapted to an environment in which Arabidopsis cannot survive. In the T. parvula genome, 11% of the annotated non-transposon putative protein-coding genes show no sequence similarity with A. thaliana genes. About two-thirds of those also lack similarity with any known plant sequence 10. In Lobularia maritima (sweet alyssum), a salt-tolerant coastal relative of Arabidopsis 49, 35% of the salt-induced transcriptome is 'unknown', as are half of the salt-stress-induced transcripts from a facultative halophyte, Festuca rubra ssp. litoralis 50 and nearly 55% of the contigs in two mangrove transcriptomes (R. mangle and H. littoralis) 26.

Regulatory elements in the untranslated regions and promoters also show lineage specificity. For example, a detailed comparison of the upstream regulatory region of SOS1, a gene critical for salt tolerance in both Arabidopsis and Thellungiella 51, showed conserved repeat sequences and secondary structures in Thellungiella spp. and other halophytes that are absent in Arabidopsis. These differences in regions that are not transcribed are correlated with differences in expression observed for SOS1 in Thellungiella 1516.

TEs seem to have a key role in generating TRGs 31, because novel chimeric genes originate when active retrotransposons recruit new exons from flanking sequences 52. About 10% of the Arabidopsis TRGs showed degenerate sequence conservation with transposable elements, a proportion double that among non-TRGs 47. In the T. parvula genome, TRGs are enriched in pericentromeric TE-rich regions, suggesting roles of transposons in their evolution 10.

Without sequence similarities on which to base annotation, 'orphan genes' usually lack assignable functions 1026. Clearly, this is a major obstacle to elucidating the genetic basis for any characteristic, not just for understanding stress tolerance, and overcoming this is an important target. Again, there are associated questions to be addressed. For example, why do duplications, especially those associated with TEs, seem to be clustered in centromeric regions? And how do lineage-specific, taxonomically restricted, or 'orphan' genes fit in the overall picture of functioning organisms? With regard to this last question, network analysis has already proved to be a good starting place. As has already been demonstrated in Arabidopsis transcriptional network models, the correlated expression of TRGs and genes with assigned functions in response to stresses provides, even without definitive annotations, useful linkages for visualizing co-expression patterns and identifying 'hub' genes that have core roles in regulating pathways 5354. Although still limited for extremophiles, RNA-sequencing experiments performed under both transient and chronic stress conditions should, before long, contribute the expression data needed for extending similar networks to non-model - or new model - species.

Beyond adaptations embedded in the basic nucleotide sequence of a genome, epigenetic controls have key roles in ensuring plant survival and reproduction under suboptimal growth conditions 5556. Selective hypermethylation on salt stress adaptation in the extremophile Crassulacean acid metabolism (CAM) plant Mesembryanthemum crystallinum, for example, indicates both specific and global epigenetic restructuring in plant abiotic stress response regulation 57.

Methylation, alone or in combination with small interfering RNA degradation pathways, can also regulate transposon activity 58. Although most TEs are inactive at any time, the proportion that is active is highly dynamic and stress responsive 5960. TE copies can vary significantly within single species (for example, maize haplotypes 58), or between closely related species; in T. parvula and T. salsuginea, TEs make up about 7.4% 10 and up to 50% (Q Xie, personal communication) of the genome, respectively.

The potential influence of retrotransposon-rich gene neighborhoods undoubtedly varies in ways yet to be fully appreciated. It may, for example, be represented in the HKT1 locus in T. parvula 10, as it is for Arabidopsis TIP1;2, the aquaporin whose high basal expression has been caused by TEs in the promoter region 61.

Plant microRNAs (miRNAs) also act epigenetically, through target mRNA cleavage or translational inhibition, and their effects are further compounded by feedback regulation. The majority are lineage specific or species specific. Even conserved miRNAs, however, have species-specific functions, as demonstrated by comparisons of Arabidopsis and poplar 62. Only 80% of known miRNAs identified in the T. parvula genome share sequence similarity with A. thaliana miRNAs. Another 10% are found in Brassicaceae species, but not in A. thaliana 10.

An in silico comparison of the target sequences of miRNAs in the mRNAs of mangroves and Arabidopsis showed that both the conservation of miRNA targets in stress-responsive genes and their placements within those genes are lineage specific. They may also be similarly represented in unrelated species showing similar ecological affinities 23.

Both methylation and miRNA-based epigenetic regulation are fields of intense activity at present and, from the standpoint of stress adaptation, how miRNA targeting comes about and varies between species is an important question. Another is how the functions of miRNAs and protein-coding genes are regulated and coordinated. Can epigenetic signatures due to stress adaptation be trans-generational, and if so, for how many generations? The concept of trans-generational epigenetic stress signatures has support from some studies. For example, when Arabidopsis parent populations were exposed to abiotic stresses that increased global methylation, their progeny were more stress tolerant 63. Similarly, in rice, parents with hypermethylation of particular loci in response to low-nutrient stress produced progeny with increased tolerance 64. In dandelion (Taraxacum officinale), exposure to stress resulted in heritable markers, again implying epigenetic heritability for stress adaptation 65. In Arabidopsis mutants impaired for small interfering RNA biogenesis, increased copy numbers of the ONSEN retrotransposon element were induced by heat stress. ONSEN insertion, in turn, rendered adjacent genes heat inducible. Unlike in wild-type plants, these numbers failed to decay over a period of 20 to 30 days. Because transposition was particularly active during flower development and before gametogenesis, the effect was trans-generational 60.

To know that the phenomena we have presented here operate is not sufficient. By themselves, sequences provide only the raw materials for addressing more important questions. On the one hand, they set the stage for exploring how genomes have evolved in plants with different adaptations to environmental conditions. On the other, and more fundamentally, expanding genomic resources bring the opportunity to explore mechanisms of genome evolution themselves.

The recently completed genome sequences of T. parvula 10 and the soon to be available genome of T. salsuginea 66 are critical resources, enabling high-resolution genome-wide comparisons between extremophiles and their non-extremophile crucifer relatives. Along with a dozen other transcriptomes of extremophile plants and numerous genomes from non-extremophiles, they have supported the ideas, first, that there is a basal set of genes shared between all plants, and second, that a subset of these has experienced selective modification and amplification of a sort required for adaptation to and success in changing or stressful environments. With sequencing technologies evolving rapidly, a 'third generation' of instruments will undoubtedly have an even greater transforming effect.

As output increases in amount and quality and cost comes down, it seems clear that the genome sequence of any plant species deemed important, and eventually multiple ecotypes of each, can, as needed, become available. The value and importance of this cannot be overstated in a world where the population is rising much faster than total agricultural production and land degradation is rapidly reducing the area useable for crops. Extremophiles provide not only a model for what is possible, but for the traits that may be necessary for crops in the future.

The authors declare that they have no competing interests.

D-HO and MD were responsible for assembling the literature, the figures and all comparisons between Thellungiella spp. and Arabidopsis. All authors contributed equally to the final writing.