Malay Das

The Parasitic Plant Genome Project: New Tools for Understanding the Biology of Orobanche and Striga

Abstract The Parasitic Plant Genome Project has sequenced transcripts from three parasitic species and a nonparasitic relative in the Orobanchaceae with the goal of understanding genetic changes associated with parasitism. The species studied span the trophic spectrum from free-living nonparasite to obligate holoparasite. Parasitic species used were Triphysaria versicolor, a photosynthetically competent species that opportunistically parasitizes roots of neighboring plants; Striga hermonthica, a hemiparasite that has an obligate need for a host; and Orobanche aegyptiaca, a holoparasite with absolute nutritional dependence on a host. Lindenbergia philippensis represents the closest nonparasite sister group to the parasitic Orobanchaceae and was included for comparative purposes. Tissues for transcriptome sequencing from each plant were gathered to identify expressed genes for key life stages from seed conditioning through anthesis. Two of the species studied, S. hermonthica and O. aegyptiaca, are economically important weeds and the data generated by this project are expected to aid in research and control of these species and their relatives. The sequences generated through this project will provide an abundant resource of molecular markers for understanding population dynamics, as well as provide insight into the biology of parasitism and advance progress toward understanding parasite virulence and host resistance mechanisms. In addition, the sequences provide important information on target sites for herbicide action or other novel control strategies such as trans-specific gene silencing. Nomenclature: Egyptian broomrape, Orobanche aegyptiaca (Pers.) (Syn. Phelipanche aegyptiaca) ORAAE; Lindenbergia philippensis (Cham. & Schltdl.) Benth. LINPH; yellowbeak owls-clover, Triphysaria versicolor (Fisch. & C.A. Mey) TRVEV; purple witchweed, Striga hermonthica, (Del.) Benth. STRHE.

A composite transcriptional signature differentiates responses towards closely related herbicides in Arabidopsis thaliana and Brassica napus

In this study, genome-wide expression profiling based on Affymetrix ATH1 arrays was used to identify discriminating responses of Arabidopsis thaliana to five herbicides, which contain active ingredients targeting two different branches of amino acid biosynthesis. One herbicide contained glyphosate, which targets 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), while the other four herbicides contain different acetolactate synthase (ALS) inhibiting compounds. In contrast to the herbicide containing glyphosate, which affected only a few transcripts, many effects of the ALS inhibiting herbicides were revealed based on transcriptional changes related to ribosome biogenesis and translation, secondary metabolism, cell wall modification and growth. The expression pattern of a set of 101 genes provided a specific, composite signature that was distinct from other major stress responses and differentiated among herbicides targeting the same enzyme (ALS) or containing the same chemical class of active ingredient (sulfonylurea). A set of homologous genes could be identified in Brassica napus that exhibited a similar expression pattern and correctly distinguished exposure to the five herbicides. Our results show the ability of a limited number of genes to classify and differentiate responses to closely related herbicides in A. thaliana and B. napus and the transferability of a complex transcriptional signature across species.

Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty

The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative “parasitism genes.” Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus, a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria.

Clonal Propagation and Production of Genetically Uniform Regenerants from Axillary Meristems of Adult Bamboo

The axillary bud-break and multiple bud induction were obtained from the nodal explants of field-grown culms of Bambusa tulda in liquid Murashige and Skoog’s (MS) basal medium supplemented with 2.0 mg l−1 6-benzylaminopurine (BAP), 1.0 mg l−1 kinetin (Kn) and 8% coconut water. Multiple shoots regenerated and proliferated in the liquid MS medium fortified with 3.0 mg l−1 indolebutyric acid (IBA). While, in B. balcooa, MS medium supplemented with 2.5 mg l−1 BAP and 1.0 mg l−1 Kn induced axillary bud-break, bud multiplication and subsequently shoot elongation was obtained after three passages in the same medium. A clump with at least three shoots of both these bamboo species was used as propagule for successful root induction in half-strength MS liquid basal medium supplemented with 0.2 mg l−1 IBA. Sympodial type of microrhizomes developed in B. tulda and the regenerants acclimatized in the soil easily. Explants collected in the month of October produced best in vitro regeneration response in these two bamboo species. Endogenous phenol content proved detrimental for efficient shoot regeneration. The clonal fidelity of the regenerants was established by RAPD analysis advocating clonal propagation through axillary meristem culture of B. balcooa and B. tulda is reliable for commercial exploitation.

Bamboo Taxonomy and Diversity in the Era of Molecular Markers

Abstract A total of ∼1400 species of bamboos are grouped under the sub‐family Bambusoideae within the family Poaceae. The plant group harbours both herbaceous and woody members while the taxonomy has traditionally been dependent on morphological characters. Classification systems proposed to date need further support, and taxonomic delineation at lower levels often lack sufficient resolution. Infrequent flowering events and extensive genome polyploidization are an additional challenge for the woody group. The tremendous advancement of molecular marker technologies holds the promise to address different needs of bamboo taxonomy (systematics and identification) and diversity studies. One of the most important prerequisites is to apply the appropriate molecular tool at the proper taxonomic level. More studies are required to better understand the population level genetic diversity in bamboo.

Evolution of a horizontally acquired legume gene, albumin 1, in the parasitic plant Phelipanche aegyptiaca and related species

BackgroundParasitic plants, represented by several thousand species of angiosperms, use modified structures known as haustoria to tap into photosynthetic host plants and extract nutrients and water. As a result of their direct plant-plant connections with their host plant, parasitic plants have special opportunities for horizontal gene transfer, the nonsexual transmission of genetic material across species boundaries. There is increasing evidence that parasitic plants have served as recipients and donors of horizontal gene transfer (HGT), but the long-term impacts of eukaryotic HGT in parasitic plants are largely unknown.ResultsHere we show that a gene encoding albumin 1 KNOTTIN-like protein, closely related to the albumin 1 genes only known from papilionoid legumes, where they serve dual roles as food storage and insect toxin, was found in Phelipanche aegyptiaca and related parasitic species of family Orobanchaceae, and was likely acquired by a Phelipanche ancestor via HGT from a legume host based on phylogenetic analyses. The KNOTTINs are well known for their unique “disulfide through disulfide knot” structure and have been extensively studied in various contexts, including drug design. Genomic sequences from nine related parasite species were obtained, and 3D protein structure simulation tests and evolutionary constraint analyses were performed. The parasite gene we identified here retains the intron structure, six highly conserved cysteine residues necessary to form a KNOTTIN protein, and displays levels of purifying selection like those seen in legumes. The albumin 1 xenogene has evolved through >150 speciation events over ca. 16 million years, forming a small family of differentially expressed genes that may confer novel functions in the parasites. Moreover, further data show that a distantly related parasitic plant, Cuscuta, obtained two copies of albumin 1 KNOTTIN-like genes from legumes through a separate HGT event, suggesting that legume KNOTTIN structures have been repeatedly co-opted by parasitic plants.ConclusionsThe HGT-derived albumins in Phelipanche represent a novel example of how plants can acquire genes from other plants via HGT that then go on to duplicate, evolve, and retain the specialized features required to perform a unique host-derived function.

Expression pattern similarities support the prediction of orthologs retaining common functions after gene duplication events

Expressologs identify functional orthologs and will be a powerful tool in future orthology assignment. The identification of functionally equivalent, orthologous genes (functional orthologs) across genomes is necessary for accurate transfer of experimental knowledge from well-characterized organisms to others. This frequently relies on automated, coding sequence-based approaches such as OrthoMCL, Inparanoid, and KOG, which usually work well for one-to-one homologous states. However, this strategy does not reliably work for plants due to the occurrence of extensive gene/genome duplication. Frequently, for one query gene, multiple orthologous genes are predicted in the other genome, and it is not clear a priori from sequence comparison and similarity which one preserves the ancestral function. We have studied 11 organ-dependent and stress-induced gene expression patterns of 286 Arabidopsis lyrata duplicated gene groups and compared them with the respective Arabidopsis (Arabidopsis thaliana) genes to predict putative expressologs and nonexpressologs based on gene expression similarity. Promoter sequence divergence as an additional tool to substantiate functional orthology only partially overlapped with expressolog classification. By cloning eight A. lyrata homologs and complementing them in the respective four Arabidopsis loss-of-function mutants, we experimentally proved that predicted expressologs are indeed functional orthologs, while nonexpressologs or nonfunctionalized orthologs are not. Our study demonstrates that even a small set of gene expression data in addition to sequence homologies are instrumental in the assignment of functional orthologs in the presence of multiple orthologs.

Morphological and molecular characterization of Thamnocalamus spathiflorus subsp. spathiflorus at population level

Comprehensive morphological characterization and an incidence of gregarious flowering in Thamnocalamus spathiflorus (Trin.) Munro subsp. spathiflorus are described. Twenty-eight key vegetative characters as well as reproductive morphology were studied. They are in gross agreement with prior taxonomic descriptions, yet more elaborate. Statistical analyses of the quantitative vegetative characters revealed significant high variability existing between populations, but not within populations. However, DNA fingerprinting analyses by applying highly polymorphic random primers could not detect any polymorphism either between populations or within populations. Insignificant within-population variability indicates possibility of clonal propagation from the donor(s) possessing similar genetic background and thus reducing genetic variability.

Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics

Bamboos are an important member of the subfamily Bambusoideae, family Poaceae. The plant group exhibits wide variation with respect to the timing (1–120 years) and nature (sporadic vs. gregarious) of flowering among species. Usually flowering in woody bamboos is synchronous across culms growing over a large area, known as gregarious flowering. In many monocarpic bamboos this is followed by mass death and seed setting. While in sporadic flowering an isolated wild clump may flower, set little or no seed and remain alive. Such wide variation in flowering time and extent means that the plant group serves as repositories for genes and expression patterns that are unique to bamboo. Due to the dearth of available genomic and transcriptomic resources, limited studies have been undertaken to identify the potential molecular players in bamboo flowering. The public release of the first bamboo genome sequence Phyllostachys heterocycla, availability of related genomes Brachypodium distachyon and Oryza sativa provide us the opportunity to study this long-standing biological problem in a comparative and functional genomics framework. We identified bamboo genes homologous to those of Oryza and Brachypodium that are involved in established pathways such as vernalization, photoperiod, autonomous, and hormonal regulation of flowering. Additionally, we investigated triggers like stress (drought), physiological maturity and micro RNAs that may play crucial roles in flowering. We also analyzed available transcriptome datasets of different bamboo species to identify genes and their involvement in bamboo flowering. Finally, we summarize potential research hurdles that need to be addressed in future research.