The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

Abstract

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.

The genomic organization and transcriptional pattern of genes encoding nitrate transporters 1 (NRT1) in cucumber

“…With completion of the Cucumis sativus genome projects in 2009 (Huang et al 2009) and 2011 (Wóycicki et al 2011), we now have another powerful model organism for studying functions, regulations, and interactions of genes in an entire genome of higher plants. Whole gene families can be rapidly identified and examined in greater detail in Cucumis sativus, allowing for a better overview on gene functions and regulations during cucumber growth, development and response to environmental changes.…”

“…The question arises, whether nitrate transporters from other species show similar regulation, expression and function as their Arabidopsis counterparts. Since the genome of cucumber has already been completely sequenced twice (Huang et al 2009;Wóycicki et al 2011) and the results of sequencing projects were made available, we searched the GenBank database for cucumber homologs of the designated A. thaliana NRT1 genes. Here we present the first inventory of cucumber NRT1 genes together with detailed analyses of their expression pattern in different organs and under constant or variable nitrate supply.…”

Advances in genomics for flatfish aquaculture

“…Although limited information about sequencing strategies and assemblies is still available, length reads and strategies to orientate adequately the scaffolds and contigs are critical. For the Senegalese sole, as in other de novo eukaryotic genomes published until now, a two-step strategy is being followed: scaffolding using matepair (Illumina Ò ) and long paired-end libraries (454) with insert sizes comprised between 2 kb and 20 kb, followed by massive whole-genome shotgun sequencing (454 and Illumina paired-ends) to be assembled into smaller contigs (Huang et al 2009;Dalloul et al 2010;Li et al 2010;Suen et al 2011;Woycicki et al 2011). However, de novo assembly of large and complex eukaryotic genomes is still challenging due to repetitive DNA and, in fish, by additional whole-genome duplication (WGD) events that occurred in the teleost lineage (3R and 4R in salmonids).…”

Molecular characterization of SCARECROW (CsSCR) gene expressed during somatic embryo development and in root of cucumber (Cucumis sativus L.)

“…The accession numbers of the sequences used in this study are listed in Table S1. Cucumber proteins similar to CsSCR were extracted using the blastp algorithm (Altschul et al 1997) from the predicted protein database of cucumber available at http://csgenome.sggw.pl (Wóycicki et al 2011). Cucumber polypeptide sequences with a minimum of 40 % similarity to CsSCR and an e-value of below 0.01 were selected.…”

“…The shorter restriction fragments of HindIII (188 bp) and XbaI (52 and 149 bp) weekly covered by molecular probes were not detected in the applied stringent washing condition. To estimate the evolutionary relationships among GRAS family members of cucumber, 36 putative Scarecrow-like proteins were selected from the translations database created using the draft version of the recently sequenced cucumber genome (Wóycicki et al 2011). The cucumber paralogues were compared with the CsSCR protein and other known SCR (Table S1) and SHR proteins from selected plant species.…”