Identifying similar transcripts in a related organism from de Bruijn graphs of RNA-Seq data, with applications to the study of salt and waterlogging tolerance in Melilotus.

Background: A popular strategy to study alternative splicing in non-model organisms starts from sequencing the entire transcriptome, then assembling the reads by using de novo transcriptome assembly algorithms to obtain predicted transcripts. A similarity search algorithm is then applied to a related organism to infer possible function of these predicted transcripts. While some of these predictions may be inaccurate and transcripts with low coverage are often missed, we observe that it is possible to obtain a more complete set of transcripts to facilitate possible functional assignments by starting the search from the intermediate de Bruijn graph that contains all branching possibilities.

Leaf gas films delay salt entry and enhance underwater photosynthesis and internal aeration of Melilotus siculus submerged in saline water.

A combination of flooding and salinity is detrimental to most plants. We studied tolerance of complete submergence in saline water for Melilotus siculus, an annual legume with superhydrophobic leaf surfaces that retain gas films when under water. M.

Improvement of salt and waterlogging tolerance in wheat: comparative physiology of Hordeum marinum-Triticum aestivum amphiploids with their H. marinum and wheat parents.

Hordeum marinum Huds. is a waterlogging-tolerant halophyte that has been hybridised with bread wheat (Triticum aestivum L.) to produce an amphiploid containing both genomes.

Aerenchymatous phellem in hypocotyl and roots enables O2 transport in Melilotus siculus.

• Aerenchymatous phellem (secondary aerenchyma) has rarely been studied in roots. Its formation and role in internal aeration were evaluated for Melilotus siculus, an annual legume of wet saline land. • Plants were grown for 21 d in aerated or stagnant (deoxygenated) agar solutions.

Lotus tenuis tolerates combined salinity and waterlogging: maintaining O2 transport to roots and expression of an NHX1-like gene contribute to regulation of Na+ transport.

Salinity and waterlogging interact to reduce growth for most crop and pasture species. The combination of these stresses often cause a large increase in the rate of Na(+) and Cl(-) transport to shoots; however, the mechanisms responsible for this are largely unknown. To identify mechanisms contributing to the adverse interaction between salinity and waterlogging, we compared two Lotus species with contrasting tolerances when grown under saline (200 mM NaCl) and O(2)-deficient (stagnant) treatments.

Measuring soluble ion concentrations (Na(+), K(+), Cl(-)) in salt-treated plants.

The control of Na(+) and Cl(-) uptake from soils, and the partitioning of these ions within plants, is an essential component of salinity tolerance. Genetic variation in the ability of roots to exclude Na(+) and Cl(-) from the transpiration stream flowing to the shoot has been associated with salinity tolerance in many species. The maintenance of a high uptake of K(+) is also essential, so measurements of Na(+), K(+) or Cl(-) are frequently used to screen for genetic variation in salinity tolerance.

Mechanisms of Cl(-) transport contributing to salt tolerance.

Mechanisms of Cl(-) transport in plants are poorly understood, despite the importance of minimizing Cl(-) toxicity for salt tolerance. This review summarizes Cl(-) transport processes in plants that contribute to genotypic differences in salt tolerance, identifying key traits from the cellular to whole-plant level. Key aspects of Cl(-) transport that contribute to salt tolerance in some species include reduced net xylem loading, intracellular compartmentation and greater efflux of Cl(-) from roots.

EST-derived SSR markers from defined regions of the wheat genome to identify Lophopyrum elongatum specific loci.

Lophopyrum elongatum, a close relative of wheat, provides a source of novel genes for wheat improvement. Molecular markers were developed to monitor the introgression of L. elongatum chromosome segments into hexaploid wheat.