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

The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts

As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library construction with Juglans regia, walnut, as a model. Extracted walnuts were subjected to nano-liquid chromatography-mass spectrometry (n-LC-MS/MS), and spectra were searched against databases made from a six-frame translation of the genome (6FT), a transcriptome, and three proteomes. Searches against proteomic databases yielded a variable number of peptides (1156-1275), and only ten additional unique peptides were identified in the 6FT database. Searches against a transcriptomic database yielded results similar to those of the National Center for Biotechnology Information (NCBI) proteome (1200 and 1275 peptides, respectively). Performance of the transcriptomic database was improved via the adjustment of RNA-Seq read processing methods, which increased the number of identified peptides which align to seed allergen proteins by ~20%. Together, these findings establish a path towards the construction of robust proxy protein databases for tree nut species and other non-model organisms.

Increased chilling tolerance of the invasive species Carpobrotus edulis may explain its expansion across new territories

Invasive plants are expanding their geographical distribution across new regions. Expansion modeling is crucial for geographic prioritization in management policies. However, the assumption of niche conservatism and the lack of information of the species physiological response to the environmental factors determining species presence may hinder predictions. In this study, we aimed to understand the expansion of the widely distributed plant Carpobrotus edulis in Europe. We contrasted introduced and native C. edulis ecological niches and explored the experimental response to temperature, a major determining factor for species distribution, of native and invasive individuals in terms of different biochemical markers. Niche analysis revealed an expansion of the introduced niche to occupy colder climates. Introduced and native individuals showed differential mechanisms facing low temperatures. Individuals from the native range showed an increased sensitivity to chilling, as reflected by photosynthetic pigment degradation, increased de-epoxidation of xanthophylls and the accumulation of the lipophilic antioxidant alpha-tocopherol. The found physiological differentiation towards an increased invasive chilling tolerance of invasive C. edulis individuals together with a high propagule pressure may explain the introduced climatic niche shift to colder climates observed, allowing the extensive expansion of this species in Europe.

Deep expression analysis reveals distinct cold-response strategies in rubber tree (Hevea brasiliensis)

Background

Natural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. The rubber tree species Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg., which is native the Amazon rainforest, is the major producer of latex worldwide. Rubber tree breeding is time consuming, expensive and requires large field areas. Thus, genetic studies could optimize field evaluations, thereby reducing the time and area required for these experiments. In this work, transcriptome sequencing was used to identify a full set of transcripts and to evaluate the gene expression involved in the different cold-response strategies of the RRIM600 (cold-resistant) and GT1 (cold-tolerant) genotypes.

Results

We built a comprehensive transcriptome using multiple database sources, which resulted in 104,738 transcripts clustered in 49,304 genes. The RNA-seq data from the leaf tissues sampled at four different times for each genotype were used to perform a gene-level expression analysis. Differentially expressed genes (DEGs) were identified through pairwise comparisons between the two genotypes for each time series of cold treatments.

DEG annotation revealed that RRIM600 and GT1 exhibit different chilling tolerance strategies. To cope with cold stress, the RRIM600 clone upregulates genes promoting stomata closure, photosynthesis inhibition and a more efficient reactive oxygen species (ROS) scavenging system. The transcriptome was also searched for putative molecular markers (single nucleotide polymorphisms (SNPs) and microsatellites) in each genotype. and a total of 27,111 microsatellites and 202,949 (GT1) and 156,395 (RRIM600) SNPs were identified in GT1 and RRIM600. Furthermore, a search for alternative splicing (AS) events identified a total of 20,279 events.

Conclusions

The elucidation of genes involved in different chilling tolerance strategies associated with molecular markers and information regarding AS events provides a powerful tool for further genetic and genomic analyses of rubber tree breeding.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5852-5) contains supplementary material, which is available to authorized users.