Ovule Transcriptome Analysis Discloses Deregulation of Genes and Pathways in Sexual and Apomictic Limonium Species (Plumbaginaceae).

The genus Limonium Mill. (sea lavenders) includes species with sexual and apomixis reproductive strategies, although the genes involved in these processes are unknown. To explore the mechanisms beyond these reproduction modes, transcriptome profiling of sexual, male sterile, and facultative apomictic species was carried out using ovules from different developmental stages. In total, 15,166 unigenes were found to be differentially expressed with apomictic vs. sexual reproduction, of which 4275 were uniquely annotated using an Arabidopsis thaliana database, with different regulations according to each stage and/or species compared. Gene ontology (GO) enrichment analysis indicated that genes related to tubulin, actin, the ubiquitin degradation process, reactive oxygen species scavenging, hormone signaling such as the ethylene signaling pathway and gibberellic acid-dependent signal, and transcription factors were found among differentially expressed genes (DEGs) between apomictic and sexual plants. We found that 24% of uniquely annotated DEGs were likely to be implicated in flower development, male sterility, pollen formation, pollen-stigma interactions, and pollen tube formation. The present study identifies candidate genes that are highly associated with distinct reproductive modes and sheds light on the molecular mechanisms of apomixis expression in Limonium sp.

A first look at sea-lavenders genomics - can genome wide SNP information tip the scales of controversy in the Limonium vulgare species complex?

BACKGROUND: Sea-lavenders (Limonium Mill., Plumbaginaceae) are a cosmopolitan group of diploid and polyploid plants often adapted to extreme saline environments, with a mostly Tethyan distribution, occurring in the Mediterranean, Irano-Turanian, Euro-Siberian and in the New World. The halophylic Limonium vulgare polyploid complex in particular, presents a large distribution throughout extreme salt-marsh habitats and shows little morphological but high taximetric variation, frequently blurring species delimitation. In this work we pursue three main goals: assert whether SNP data from polyploid individuals has the resolution to distinguish the seven sampled species, to better understand how genetically structured Limonium vulgare is, and attempt to identify specific molecular mechanisms for the differentiation between L. maritimum and L. vulgare. For this purpose, 95 individuals were genotyped using Genotyping by Sequencing (GBS), which were assembled as two independent datasets using IPYRAD. All analyses performed downstream of assembly were fully automated. Phylogenetic inference, PCA, and admixture plots were used to infer answers to the study's main goals. RESULTS: Close to 10,000 SNPs were obtained for each dataset. Phylogenetic analyses reveal that polyploid data can be used to infer species relationships. Population structure analyses suggest a genetically structured L. vulgare. A set of 34 SNPs were found to be fully segregated between L. vulgare and L. maritimum, two of which are potentially linked to proteins that might be involved in the speciation process. CONCLUSION: Despite polyploid data analyses shortcomings, GBS generated SNPs have the resolution to discern all seven included species. Limonium vulgare revealed pronounced genetic structure along a geographical north-south cline. L. maritimum always appears as a distinct genetic entity. Segregated SNPs between L. vulgare and L. maritimum indicate salinity response and morphological trait control genes as potentially interesting to follow up for studying these species' divergence process.

Text Mining for Building Biomedical Networks Using Cancer as a Case Study.

In the assembly of biological networks it is important to provide reliable interactions in an effort to have the most possible accurate representation of real-life systems. Commonly, the data used to build a network comes from diverse high-throughput essays, however most of the interaction data is available through scientific literature. This has become a challenge with the notable increase in scientific literature being published, as it is hard for human curators to track all recent discoveries without using efficient tools to help them identify these interactions in an automatic way. This can be surpassed by using text mining approaches which are capable of extracting knowledge from scientific documents. One of the most important tasks in text mining for biological network building is relation extraction, which identifies relations between the entities of interest. Many interaction databases already use text mining systems, and the development of these tools will lead to more reliable networks, as well as the possibility to personalize the networks by selecting the desired relations. This review will focus on different approaches of automatic information extraction from biomedical text that can be used to enhance existing networks or create new ones, such as deep learning state-of-the-art approaches, focusing on cancer disease as a case-study.

Reproductive Output and Insect Behavior in Hybrids and Apomicts from Limonium ovalifolium and L. binervosum Complexes (Plumbaginaceae) in an Open Cross-Pollination Experiment.

Ex situ plant collections established from seeds of natural populations are key tools for understanding mating systems of intricate taxonomic complexes, as in the Limonium Mill. genus (sea lavenders, Plumbaginaceae). Plants show a polymorphic sexual system associated to flower polymorphisms such as ancillary pollen and stigma and/or heterostyly that prevents self and intramorph mating. The main objectives of this study were to investigate the significance of pollen-stigma dimorphisms and the role of flower visitors in the reproductive output of hybrids arising from sexual diploids of Limonium ovalifolium complex and apomicts tetraploids of L. binervosum complex in an open cross-pollination experiment. Results showed that, similarly to parental plants, hybrids present inflorescence types, self-incompatible flowers, and produced regular pollen grains with the typical exine patterns, with medium to high viability. By contrast, apomicts show floral polymorphisms, inflorescences, and pollen grains of maternal phenotype but with low stainability. Several insects' species visited the inflorescences of parental plants and both hybrids and apomicts and some of these insects carried A and/or B pollen grains on their bodies, especially Clepsis coriacana (Rebel) and Tapinoma sp. Insects' floral visits to hybrids and apomicts seem to be independent of pollen fertility and plants' reproductive modes. Both hybrids and apomicts were able to produce fertile seeds, although the latter showed more seedlings with developmental anomalies than the first plants. The findings demonstrate that there is a weak reproductive barrier between the diploid species of L. ovalifolium complex as they can hybridize and produce fertile hybrids, provided there is pollen transport by pollinator insects. This study supports that apomixis is a strong reproductive barrier between both L. ovalifolium and L. binervosum complexes but did not allow us to exclude reproductive interferences of apomict pollen into sexuals.