BackgroundEragrostis tef is an allotetraploid (2n = 4 × = 40) annual, C4 grass with an estimated nuclear genome size of 730 Mbp. It is widely grown in Ethiopia, where it provides basic nutrition for more than half of the population.Although a draft assembly of the E. tef genome was made available in 2014, characterization of the repetitive portion of the E. tef genome has not been a subject of a detailed analysis.Repetitive sequences constitute most of the DNA in eukaryotic genomes. Transposable elements are usually the most abundant repetitive component in plant genomes. They contribute to genome size variation, cause mutations, can result in chromosomal rearrangements, and influence gene regulation. An extensive and in depth characterization of the repetitive component is essential in understanding the evolution and function of the genome.ResultsUsing new paired-end sequence data and a de novo repeat identification strategy, we identified the most repetitive elements in the E. tef genome. Putative repeat sequences were annotated based on similarity to known repeat groups in other grasses.Altogether we identified 1,389 medium/highly repetitive sequences that collectively represent about 27 % of the teff genome. Phylogenetic analyses of the most important classes of TEs were carried out in a comparative framework including paralog elements from rice and maize. Finally, an abundant tandem repeat accounting for more than 4 % of the whole genome was identified and partially characterized.ConclusionsAnalyzing a large sample of randomly sheared reads we obtained a library of the repetitive sequences of E. tef. The approach we used was designed to avoid underestimation of repeat contribution; such underestimation is characteristic of whole genome assembly projects. The data collected represent a valuable resource for further analysis of the genome of this important orphan crop.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0725-4) contains supplementary material, which is available to authorized users.
Salinity adversely affects 20-30% of the irrigated area in the world. Tomato is sensitive to salinity. It is one of the most severe abiotic factors of many agricultural crops and it becoming the main problem in Ethiopia. This study was conducted to evaluate the effects of different salinity levels on the seed germination parameters of tomato varieties. It was laid out in a completely randomized design with three replicates. The treatment included four tomato varieties (Sirinka, Weyno, ARP D2, and Roma VF) and five salinity levels (1 dS m-1, 2 dS m-1, 3 dS m-1, 4 dS m-1, and control). Fifty seeds were placed in a Petri dish over a moistened germination paper for germination and seedlings and allowed to grow for 14 days. The germination rate, speed and energy of tomato seeds were significantly (p < 0.001) affected by the combined effect of variety and salinity. The shortest mean germination time, the highest mean germination rate, and the highest speed of germination were recorded in the ARP D2 variety in the control treatment. The lowest first and last days of germination, and the uncertainty of germination were recorded from ARP D2. However, an increase in the days of germination and in the uncertainty of germination, and a decrease in the germination index and total germination percentage trends were observed with increasing salinity levels. The highest level of salinity (4 dS m-1) affected the germination of tomato varieties. Among the four tested tomato varieties, ARP D2 and Roma VF were tolerant to salinity.
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