Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

RNA Sequencing Characterizes Transcriptomes Differences in Cold Response Between Northern and Southern Alternanthera philoxeroides and Highlight Adaptations Associated With Northward Expansion

Alternanthera philoxeroides recently expanded its range northwards in China. It is unknown if the range expansion has a genetic and/or epigenetic basis, or merely an environmental basis due to a warming climate. To test these possibilities, we used an RNAseq approach with a common greenhouse design to examine gene expression in individuals from the northern edge and central portion of alligator weed range from China to determine if there were differences in their responses to cold temperatures. We hypothesized that if the recent range expansion was primarily environmental, we would observe few differences or only differences unrelated to low-temperature adaptations. We assembled over 75,000 genes of which over 65,000 had long open reading frames with similarity to sequences from arabidopsis. Differences in expression between northern and southern populations that were both exposed to low temperatures showed similar expression among genes in the C-REPEAT/DRE BINDING FACTOR (CBF) regulon. However, gene set and sub-network enrichment analysis indicated differences in the response of photosynthetic processes and oxidative stress responses were different between the two populations and we relate these differences to cold adaptation. The transcriptome differences in response to cold between the individuals from the two populations is consistent with adaptations potentiating or resulting from selection after expansion into colder environments and may indicate that genetic changes have accompanied the recent northward expansion of A. philoxeroides in China. However, we cannot rule out the possibility of epigenetic changes may have a role in this expansion.

Insights into the innate immunome of actiniarians using a comparative genomic approach

Background

Innate immune genes tend to be highly conserved in metazoans, even in early divergent lineages such as Cnidaria (jellyfish, corals, hydroids and sea anemones) and Porifera (sponges). However, constant and diverse selection pressures on the immune system have driven the expansion and diversification of different immune gene families in a lineage-specific manner. To investigate how the innate immune system has evolved in a subset of sea anemone species (Order: Actiniaria), we performed a comprehensive and comparative study using 10 newly sequenced transcriptomes, as well as three publically available transcriptomes, to identify the origins, expansions and contractions of candidate and novel immune gene families.

Results

We characterised five conserved genes and gene families, as well as multiple novel innate immune genes, including the newly recognised putative pattern recognition receptor CniFL. Single copies of TLR, MyD88 and NF-κB were found in most species, and several copies of IL-1R-like, NLR and CniFL were found in almost all species. Multiple novel immune genes were identified with domain architectures including the Toll/interleukin-1 receptor (TIR) homology domain, which is well documented as functioning in protein-protein interactions and signal transduction in immune pathways. We hypothesise that these genes may interact as novel proteins in immune pathways of cnidarian species. Novelty in the actiniarian immunome is not restricted to only TIR-domain-containing proteins, as we identify a subset of NLRs which have undergone neofunctionalisation and contain 3–5 N-terminal transmembrane domains, which have so far only been identified in two anthozoan species.

Conclusions

This research has significance in understanding the evolution and origin of the core eumetazoan gene set, including how novel innate immune genes evolve. For example, the evolution of transmembrane domain containing NLRs indicates that these NLRs may be membrane-bound, while all other metazoan and plant NLRs are exclusively cytosolic receptors. This is one example of how species without an adaptive immune system may evolve innovative solutions to detect pathogens or interact with native microbiota. Overall, these results provide an insight into the evolution of the innate immune system, and show that early divergent lineages, such as actiniarians, have a diverse repertoire of conserved and novel innate immune genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3204-2) contains supplementary material, which is available to authorized users.

Multiple introductions and gene flow in subtropical South American populations of the fireweed, Senecio madagascariensis(Asteraceae)

Non-indigenous plants exhibit different attributes that make them aggressive competitors with indigenous plants and serious threats to biodiversity.Senecio madagascariensis (fireweed, Asteraceae), a native from southern Africa, is a strong competitor in agricultural activities and has toxic alkaloids that may result in high cattle mortality. In Brazil, this weed was collected for the first time in 1995 and has since spread quickly throughout the Pampas region. To better understand the invasion of the fireweed in South America, we used a genetic characterization with internal transcribed spacer (ITS) and microsatellite markers. Based on the ITS data, the southern Brazil populations of S. madagascariensis shared genetic homology with samples taken from the Hawaiian Islands and South Africa. Microsatellite analysis showed the genetic diversity split in two clusters, perhaps intimating the independent introduction of each species into South America. Although fireweed was introduced recently in southern Brazil, the considerable levels of genetic diversity, gene flow, and inbreeding may indicate success in the species establishment in this environment.

Trans-disciplinary research in synthesis of grass pollen aerobiology and its importance for respiratory health in Australasia

Grass pollen is a major trigger for allergic rhinitis and asthma, yet little is known about the timing and levels of human exposure to airborne grass pollen across Australasian urban environments. The relationships between environmental aeroallergen exposure and allergic respiratory disease bridge the fields of ecology, aerobiology, geospatial science and public health. The Australian Aerobiology Working Group comprised of experts in botany, palynology, biogeography, climate change science, plant genetics, biostatistics, ecology, pollen allergy, public and environmental health, and medicine, was established to systematically source, collate and analyse atmospheric pollen concentration data from 11 Australian and six New Zealand sites. Following two week-long workshops, post-workshop evaluations were conducted to reflect upon the utility of this analysis and synthesis approach to address complex multidisciplinary questions. This Working Group described i) a biogeographically dependent variation in airborne pollen diversity, ii) a latitudinal gradient in the timing, duration and number of peaks of the grass pollen season, and iii) the emergence of new methodologies based on trans-disciplinary synthesis of aerobiology and remote sensing data. Challenges included resolving methodological variations between pollen monitoring sites and temporal variations in pollen datasets. Other challenges included "marrying" ecosystem and health sciences and reconciling divergent expert opinion. The Australian Aerobiology Working Group facilitated knowledge transfer between diverse scientific disciplines, mentored students and early career scientists, and provided an uninterrupted collaborative opportunity to focus on a unifying problem globally. The Working Group provided a platform to optimise the value of large existing ecological datasets that have importance for human respiratory health and ecosystems research. Compilation of current knowledge of Australasian pollen aerobiology is a critical first step towards the management of exposure to pollen in patients with allergic disease and provides a basis from which the future impacts of climate change on pollen distribution can be assessed and monitored.

Characterization of the Transcriptome of the Xerophyte Ammopiptanthus mongolicus Leaves under Drought Stress by 454 Pyrosequencing

BACKGROUND

Ammopiptanthus mongolicus (Maxim. Ex Kom.) Cheng f., an endangered ancient legume species, endemic to the Gobi desert in north-western China. As the only evergreen broadleaf shrub in this area, A. mongolicus plays an important role in the region's ecological-environmental stability. Despite the strong potential of A. mongolicus in providing new insights on drought tolerance, sequence information on the species in public databases remains scarce. To both learn about the role of gene expression in drought stress tolerance in A. mongolicus and to expand genomic resources for the species, transcriptome sequencing of stress-treated A. mongolicus plants was performed.

RESULTS

Using 454 pyrosequencing technology, 8,480 and 7,474 contigs were generated after de novo assembly of RNA sequences from leaves of untreated and drought-treated plants, respectively. After clustering using TGICL and CAP3 programs, a combined assembly of all reads produced a total of 11,357 putative unique transcripts (PUTs). Functional annotation and classification of the transcripts were conducted by aligning the 11,357 PUTs against the public protein databases and nucleotide database (Nt). Between control and drought-treated plants, 1,620 differentially expressed genes (DEGs) were identified, of which 1,106 were up-regulated and 514 were down-regulated. The differential expression of twenty candidate genes in metabolic pathways and transcription factors families related to stress-response were confirmed by quantitative real-time PCR. Representatives of several large gene families, such as WRKY and P5CS, were identified and verified in A. mongolicus for the first time.

CONCLUSIONS

The additional transcriptome resources, gene expression profiles, functional annotations, and candidate genes provide a more comprehensive understanding of the stress response pathways in xeric-adapted plant species such as A. mongolicus.

Comparative Analysis and Distribution of Omega-3 lcPUFA Biosynthesis Genes in Marine Molluscs

Recent research has identified marine molluscs as an excellent source of omega-3 long-chain polyunsaturated fatty acids (lcPUFAs), based on their potential for endogenous synthesis of lcPUFAs. In this study we generated a representative list of fatty acyl desaturase (Fad) and elongation of very long-chain fatty acid (Elovl) genes from major orders of Phylum Mollusca, through the interrogation of transcriptome and genome sequences, and various publicly available databases. We have identified novel and uncharacterised Fad and Elovl sequences in the following species: Anadara trapezia, Nerita albicilla, Nerita melanotragus, Crassostrea gigas, Lottia gigantea, Aplysia californica, Loligo pealeii and Chlamys farreri. Based on alignments of translated protein sequences of Fad and Elovl genes, the haeme binding motif and histidine boxes of Fad proteins, and the histidine box and seventeen important amino acids in Elovl proteins, were highly conserved. Phylogenetic analysis of aligned reference sequences was used to reconstruct the evolutionary relationships for Fad and Elovl genes separately. Multiple, well resolved clades for both the Fad and Elovl sequences were observed, suggesting that repeated rounds of gene duplication best explain the distribution of Fad and Elovl proteins across the major orders of molluscs. For Elovl sequences, one clade contained the functionally characterised Elovl5 proteins, while another clade contained proteins hypothesised to have Elovl4 function. Additional well resolved clades consisted only of uncharacterised Elovl sequences. One clade from the Fad phylogeny contained only uncharacterised proteins, while the other clade contained functionally characterised delta-5 desaturase proteins. The discovery of an uncharacterised Fad clade is particularly interesting as these divergent proteins may have novel functions. Overall, this paper presents a number of novel Fad and Elovl genes suggesting that many mollusc groups possess most of the required enzymes for the synthesis of lcPUFAs.

Genetic bottlenecks in time and space: reconstructing invasions from contemporary and historical collections

Herbarium accession data offer a useful historical botanical perspective and have been used to track the spread of plant invasions through time and space. Nevertheless, few studies have utilised this resource for genetic analysis to reconstruct a more complete picture of historical invasion dynamics, including the occurrence of separate introduction events. In this study, we combined nuclear and chloroplast microsatellite analyses of contemporary and historical collections of Senecio madagascariensis, a globally invasive weed first introduced to Australia c. 1918 from its native South Africa. Analysis of nuclear microsatellites, together with temporal spread data and simulations of herbarium voucher sampling, revealed distinct introductions to south-eastern Australia and mid-eastern Australia. Genetic diversity of the south-eastern invasive population was lower than in the native range, but higher than in the mid-eastern invasion. In the invasive range, despite its low resolution, our chloroplast microsatellite data revealed the occurrence of new haplotypes over time, probably as the result of subsequent introduction(s) to Australia from the native range during the latter half of the 20^th century. Our work demonstrates how molecular studies of contemporary and historical field collections can be combined to reconstruct a more complete picture of the invasion history of introduced taxa. Further, our study indicates that a survey of contemporary samples only (as undertaken for the majority of invasive species studies) would be insufficient to identify potential source populations and occurrence of multiple introductions.

Understanding the genetic basis of invasiveness

Invasive species provide excellent study systems to evaluate the ecological and evolutionary processes that contribute to the colonization of novel environments. While the ecological processes that contribute to the successful establishment of invasive plants have been studied in detail, investigation of the evolutionary processes involved in successful invasions has only recently received attention. In particular, studies investigating the genomic and gene expression differences between native and introduced populations of invasive species are just beginning and are required if we are to understand how plants become invasive. In the current issue of Molecular Ecology, Hodgins et al. (2013) tackle this unresolved question, by examining gene expression differences between native and introduced populations of annual ragweed, Ambrosia artemisiifolia. The study identifies a number of potential candidate genes based on gene expression differences that may be responsible for the success of annual ragweed in its introduced range. Furthermore, genes involved in stress response are over-represented in the differentially expressed gene set. Future experiments could use functional studies to test whether changes in gene expression at these candidate genes do in fact underlie changes in growth characteristics and reproductive output observed in this and other invasive species.

Does time since introduction influence enemy release of an invasive weed?

Release from natural enemies is considered to potentially play an important role in the initial establishment and success of introduced plants. With time, the species richness of herbivores using non-native plants may increase [species-time relationship (STR)]. We investigated whether enemy release may be limited to the early stages of invasion. Substituting space for time, we sampled invertebrates and measured leaf damage on the invasive species Senecio madagascariensis Poir. at multiple sites, north and south of the introduction site. Invertebrate communities were collected from plants in the field, and reared from collected plant tissue. We also sampled invertebrates and damage on the native congener Senecio pinnatifolius var. pinnatifolius A. Rich. This species served as a control to account for environmental factors that may vary along the latitudinal gradient and as a comparison for evaluating the enemy release hypothesis (ERH). In contrast to predictions of the ERH, greater damage and herbivore abundances and richness were found on the introduced species S. madagascariensis than on the native S. pinnatifolius. Supporting the STR, total invertebrates (including herbivores) decreased in abundance, richness and Shannon diversity from the point of introduction to the invasion fronts of S. madagascariensis. Leaf damage showed the opposite trend, with highest damage levels at the invasion fronts. Reared herbivore loads (as opposed to external collections) were greater on the invader at the point of introduction than on sites further from this region. These results suggest there is a complex relationship between the invader and invertebrate community response over time. S. madagascariensis may be undergoing rapid changes at its invasion fronts in response to environmental and herbivore pressure.

Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit

Soybean has a wide range of applications in the industry and, due to its crop potential, its improvement is widely desirable. During drought conditions, soybean crops suffer significant losses in productivity. Therefore, understanding the responses of the soybean under this stress is an effective way of targeting crop improvement techniques. In this study, we employed the Suppressive Subtractive Hybridization (SSH) technique to investigate differentially expressed genes under water deficit conditions. Embrapa 48 and BR 16 soybean lines, known as drought-tolerant and -sensitive, respectively, were grown hydroponically and subjected to different short-term periods of stress by withholding the nutrient solution. Using this approach, we have identified genes expressed during the early response to water deficit in roots and leaves. These genes were compared among the lines to assess probable differences in the plant transcriptomes. In general, similar biochemical processes were predominant in both cultivars; however, there were more considerable differences between roots and leaves of Embrapa 48. Moreover, we present here a fast, clean and straightforward method to obtain drought-stressed root tissues and a large enriched collection of transcripts expressed by soybean plants under water deficit that can be useful for further studies towards the understanding of plant responses to stress.

AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha

Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.

Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression

PREMISE OF STUDY

Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization.

METHODS

We generated 22 expressed sequence tag (EST) libraries for the 11 targeted weeds using Sanger, 454, and Illumina sequencing, compared the coverage and quality of sequence assemblies, and developed NimbleGen microarrays for expression analyses in five taxa. When possible, we also compared the distributions of Ks values between orthologs of congeneric taxa to detect and quantify hybridization and introgression.

RESULTS

Gene discovery was enhanced by sequencing from multiple tissues, normalization of cDNA libraries, and especially greater sequencing depth. However, assemblies from short sequence reads sometimes failed to resolve close paralogs. Substantial introgression was detected in Centaurea and Helianthus, but not in Ambrosia and Lactuca.

CONCLUSIONS

Transcriptome sequencing using next-generation platforms has greatly reduced the cost of genomic studies of nonmodel organisms, and the ESTs and microarrays reported here will accelerate evolutionary and molecular investigations of Compositae weeds. Our study also shows how ortholog comparisons can be used to approximately estimate the genome-wide extent of introgression and to identify genes that have been exchanged between hybridizing taxa.

AFLP genome scan to detect genetic structure and candidate loci under selection for local adaptation of the invasive weed Mikania micrantha

Why some species become successful invaders is an important issue in invasive biology. However, limited genomic resources make it very difficult for identifying candidate genes involved in invasiveness. Mikania micrantha H.B.K. (Asteraceae), one of the world's most invasive weeds, has adapted rapidly in response to novel environments since its introduction to southern China. In its genome, we expect to find outlier loci under selection for local adaptation, critical to dissecting the molecular mechanisms of invasiveness. An explorative amplified fragment length polymorphism (AFLP) genome scan was used to detect candidate loci under selection in 28 M. micrantha populations across its entire introduced range in southern China. We also estimated population genetic parameters, bottleneck signatures, and linkage disequilibrium. In binary characters, such as presence or absence of AFLP bands, if all four character combinations are present, it is referred to as a character incompatibility. Since character incompatibility is deemed to be rare in populations with extensive asexual reproduction, a character incompatibility analysis was also performed in order to infer the predominant mating system in the introduced M. micrantha populations. Out of 483 AFLP loci examined using stringent significance criteria, 14 highly credible outlier loci were identified by Dfdist and Bayescan. Moreover, remarkable genetic variation, multiple introductions, substantial bottlenecks and character compatibility were found to occur in M. micrantha. Thus local adaptation at the genome level indeed exists in M. micrantha, and may represent a major evolutionary mechanism of successful invasion. Interactions between genetic diversity, multiple introductions, and reproductive modes contribute to increase the capacity of adaptive evolution.

Unraveling plant-microbe interactions: can multi-species transcriptomics help?

Plants in their natural habitats are surrounded by a large number of microorganisms. Some microbes directly interact with plants in a mutually beneficial manner whereas others colonize the plant only for their own benefit. In addition, microbes can indirectly affect plants by drastically altering their environments. Understanding the complex nature of plant-microbe interactions can potentially offer new strategies to enhance plant productivity in an environmentally friendly manner. As briefly reviewed here, the emerging area of multi-species transcriptomics holds the promise to provide knowledge on how this can be achieved. We discuss key aspects of how transcriptome analysis can be used to provide a more comprehensive picture of the complex interactions of plants with their biotic and abiotic environments.

Transcriptome analysis and comparison reveal divergence between two invasive whitefly cryptic species

BACKGROUND

Invasive species are valuable model systems for examining the evolutionary processes and molecular mechanisms associated with their specific characteristics by comparison with closely related species. Over the past 20 years, two species of the whitefly Bemisia tabaci species complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), have both spread from their origin Middle East/Mediterranean to many countries despite their apparent differences in many life history parameters. Previously, we have sequenced the transcriptome of MED. In this study, we sequenced the transcriptome of MEAM1 and took a comparative genomic approach to investigate the transcriptome evolution and the genetic factors underlying the differences between MEAM1 and MED.

RESULTS

Using Illumina sequencing technology, we generated 17 million sequencing reads for MEAM1. These reads were assembled into 57,741 unique sequences and 15,922 sequences were annotated with an E-value above 10-5. Compared with the MED transcriptome, we identified 3,585 pairs of high quality orthologous genes and inferred their sequence divergences. The average differences in coding, 5' untranslated and 3' untranslated region were 0.83%, 1.66% and 1.43%, respectively. The level of sequence divergence provides additional support to the proposition that MEAM1 and MED are two species. Based on the ratio of nonsynonymous and synonymous substitutions, we identified 24 sequences that have evolved in response to positive selection. Many of those genes are predicted to be involved in metabolism and insecticide resistance which might contribute to the divergence of the two whitefly species.

CONCLUSIONS

Our data present a comprehensive sequence comparison between the two invasive whitefly species. This study will provide a road map for future investigations on the molecular mechanisms underlying their biological differences.

Reverse transcription-PCR methods significantly impact richness and composition measures of expressed fungal cellobiohydrolase I genes in soil and litter

The importance of soil fungi in complex carbon degradation and the recent identification of genes involved in this process have sparked considerable interest in examining fungal gene expression in situ. Expression of target eukaryotic genes is commonly examined using reverse transcription (RT)-PCR, during which single-stranded (ss) complementary DNA (cDNA) is synthesized from an oligo (dT) primer and the gene of interest is subsequently amplified by PCR using gene specific primers. Another method that is being increasingly employed in environmental gene expression studies is SMART PCR, which generates and amplifies double-stranded (ds) complementary DNA (cDNA) from sscDNA using PCR, prior to gene-specific PCR. We performed a replicated comparison of these two methods using RNA extracted from forest soil and litter to determine if the two approaches yielded comparable results. Richness, composition and reproducibility of gene expression profiles of the fungal glycosyl hydrolase family 7 (GH7) cellobiohydrolase I gene (cbhI) were examined when amplified from sscDNA or dscDNA synthesized using SMART PCR. In the dscDNA libraries from soil or litter samples, richness was significantly reduced and the composition was altered relative to sscDNA libraries. Library composition was significantly more reproducible among replicate sscDNA libraries than among parallel dscDNA libraries from litter. In sum, the reduced richness and altered composition produced in the dscDNA libraries could substantially influence ecological interpretations of the data. Defining the factors underpinning the methodological biases will potentially aid in optimizing the design of gene expression studies in soils and other complex environmental samples.