Calotropis procera is emerging as a new, yet undomesticated, resource of fibre comparable to cotton and kapok. Screening of efficient genotypes from its wild populations would be a useful pre-domestication process. The desired genotypes can then be improved through conventional breeding programmes to develop a domesticated variety. Molecular markers play a major role in modern breeding systems. Thus, an efficient marker resource for C. procera would prove useful in germplasm selection during breeding programmes. In this study, we undertook an initial step of Simple sequence repeats (SSR) marker development for C. procera, which could be applied for germplasm selection. Furthermore, using the developed markers, we assessed the genetic diversity base within its wild populations which could be useful to identify the hotspot areas of germplasm collection. Out of 94,636 de novo assembled transcripts, 9148 sequences were found to contain 12,884 SSRs at a density of 5.5 SSRs/Mb. Twelve SSRs were found as polymorphic with a mean polymorphic information content of 0.575. We observed a moderate level of genetic diversity (Na = 3.625, Ho = 0.58) in the studied populations. Mantel's test showed significant correlation between the geographic distance and the genetic distance (r = 0.147, P = 0.010). Sirsa was found as a genetically most diverse population followed by Barnala while Gurdaspur was found with the least genetic diversity. These genetically diverse populations can serve as an important resource for effective germplasm collection for breeding programmes.

Host-specific interactions can maintain genetic and phenotypic diversity in parasites that attack multiple host species. Host diversity, in turn, may promote parasite diversity by selection for genetic divergence or plastic responses to host type. The parasitic weed purple witchweed [Striga hermonthica (Delile) Benth.] causes devastating crop losses in sub-Saharan Africa and is capable of infesting a wide range of grass hosts. Despite some evidence for host adaptation and host-by-Striga genotype interactions, little is known about intraspecific Striga genomic diversity. Here we present a study of transcriptomic diversity in populations of S. hermonthica growing on different hosts (maize [Zea mays L.] vs. grain sorghum [Sorghum bicolor (L.) Moench]). We examined gene expression variation and differences in allelic frequency in expressed genes of aboveground tissues from populations in western Nigeria parasitizing each host. Despite low levels of host-based genome-wide differentiation, we identified a set of parasite transcripts specifically associated with each host. Parasite genes in several different functional categories implicated as important in host–parasite interactions differed in expression level and allele on different hosts, including genes involved in nutrient transport, defense and pathogenesis, and plant hormone response. Overall, we provide a set of candidate transcripts that demonstrate host-specific interactions in vegetative tissues of the emerged parasite S. hermonthica. Our study shows how signals of host-specific processes can be detected aboveground, expanding the focus of host–parasite interactions beyond the haustorial connection.

Behaviour manipulation imposed by parasites is a fascinating phenomenon but our understanding is still very limited. We studied the interaction between a virus and the parasitic wasp Leptopilina boulardi that attacks Drosophila larvae. Wasps usually refrain to lay eggs into already parasitized hosts (superparasitism avoidance). On the contrary, females infected by the Leptopilina boulardi Filamentous Virus (LbFV) are much more incline to superparasitize. Interestingly, the host-sharing induced by this behaviour modification leads to the horizontal transmission of the virus, thus increasing its fitness at the expense of that of the wasp. To better understand the mechanisms underlying this behaviour manipulation, we studied by RNA sequencing the meta-transcriptome of LbFV and the parasitic wasp both in the abdomen and in the head. We found that the abundance of viral transcripts was independent of the wasp strain but strongly differed between tissues. Based on the tissue pattern of expression, we identified a set of 20 viral genes putatively involved in the manipulation process. In addition, we identified a set of wasp genes deregulated in the presence of the virus either in the abdomen or in the head, including genes with annotations suggesting involvement in behaviour (i.e. Potassium-channel protein). This dataset gives new insights into the behaviour manipulation and on the genetic basis of superparasitism in parasitoids.

Nitrogen fixation in legumes is an important agricultural trait that results from symbiosis between the root and rhizobia. To understand the molecular basis of nodulation, recent research has been focused on the identification of nodulation-related genes by functional analysis using two major model legumes, Medicago truncatula and Lotus japonicus. Thus far, three important processes have been discovered, namely Nod factor (NF) perception, NF signalling and autoregulation of nodulation. Nevertheless, application of the results of these studies is limited for non-model legume crops because a reference genome is unavailable. However, because the cost of whole-transcriptome analysis has dropped dramatically due to the Next generation sequencer (NGS) technology, minor crops for which reference sequences are yet to be constructed can still be studied at the genome level. In this study, we sequenced the leaf and root transcriptomes of Vigna angularis (accession IT213134) and de novo assembled. Our results demonstrate the feasibility of using the transcriptome assembly to effectively identify tissue-specific peptide clusters related to tissue-specific functions and species-specific nodulation-related genes.