Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar – Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration- and ethylene-responsive cis-regulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.
SummarySensory characteristics, carotenoids content and antioxidant activity of sprouted seeds of eight plant species were investigated. Seeds of lentil, broccoli, clover, amaranth, wheat, radish, pea, and alfalfa were germinated for 3 days in the dark, at the temperature of 25ºC and then sprouted seeds were stored for the next 2 days in a refrigerator, in the dark, at the temperature of 4-5ºC. Sensory quality was evaluated in the expert panel, with the quantitative descriptive analysis method (QDA), using 15 sensory attributes, concerning odour, texture and flavour. Radish, alfalfa and lentil sprouts showed the highest overall sensory quality. Sensory attributes of sprouts were strongly differentiated among the species and the biggest differences were found for spicy flavour and sweet taste attributes. 2-day storage of sprouts affected some taste/flavour descriptors. Total carotenoids and ȕ-carotene content were the highest in broccoli and radish sprouts. During the storage of sprouts carotenoids content decreased. Antioxidant activity was differentiated between species, and both radish and broccoli sprouts showed the highest antioxidant activity.
New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length and N50 2’324 Kbp. In the Celera/Arachne method contigs after prior pyrosequencing reads assembly (in the form of ~ 800 nt reads) were used together with the STCs as the input to Arachne assembler. Number of contigs were 15’764 of the length 193 Mbp with N50 23’280 bp. Number of supercontigs were 12’438 with the coverage of 323 Mbp and N50 323’092 bp. Correctness of the assemblies were proven after mapping 95,56% of 63’035 cucumber unigenes with the average identity 97,81%. Additionally 6 BAC/Fosmid cucumber sequences (totally 372’277 bp) had identity of 97,61% to the assembled genome. Average reads coverage of the genome were 14,20x and 98% of the assembled genome had reads coverage higher than 3x.Taking into consideration coverage used in already reported cucumber assemblies (32x by Miller J. et al., 2009 and 72x by Huang S. et al., 2009), as well as no differences in the quality and the best overall quantity statistics of contigs/scaffold lengths, the Celera approach used in this project should be considered the most optimal one to get omics-ready quality draft sequence of highly repeated eukaryotic genome.
Przeprowadzono ocenę fenotypową populacji dyni olbrzymiej pod względem cech ilościowych takich jak: średnia masa owocu, liczba owoców na roślinę oraz plon handlowy. W eksperymencie wykorzystano populację mapującą składającą się ze 112 rekombinacyjnych linii wsobnych (RIL) pokolenia F6 dyni olbrzymiej uzyskanych z mieszańca dwóch linii wsobnych 802 × 801 o odmien¬nym pochodzeniu i skrajnie zróżnicowanych pod względem badanych cech. Doświadczenie polowe założono w układzie losowym w trzech powtórzeniach w 2013 i 2014 roku. Linie rodzicielskie wykazywały istotne statystycznie różnice w odniesieniu do wartości cech. Zakres zmienności cech w populacji mapującej przekraczał wartości cech dla linii rodzicielskich. Zakres zmienności dla średniej masy owocu wynosił od 0,6 kg do 9,0 kg, dla średniej liczby owoców na roślinie od 1,0 do 7,5 (2013) i od 1,0 do 11,5 (2014), dla plonu handlowego (kg/roślinę) 1,7–11,8 (2013) i 1,26–30,0 (2014). Odziedziczalność cech wynosiła 71% dla plon handlowego, 70% dla średniej masy owoców i 82% dla średniej liczby owoców na roślinę.
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