Abstract
BackgroundChenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. The basic leucine zipper (bZIP) transcription factor represents exclusively in eukaryotes and can be related to many biological processes. So far, the genomes of quinoa and 3 other Amaranthaceae crops (Spinacia oleracea, Beta vulgaris, and Amaranthus hypochondriacus) have been fully sequenced. However, information about the bZIPs in these Amaranthaceae species is limited, and genome-wide analysis of the bZIP family is lacking in quinoa.ResultsWe identified 94 bZIPs in quinoa (named as CqbZIP1-CqbZIP94). All the CqbZIPs were phylogenetically splitted into 12 distinct subfamilies. The proportion of CqbZIPs was different in each subfamily, and members within the same subgroup shared conserved exon-intron structures and protein motifs. Besides, 32 duplicated CqbZIP gene pairs were investigated, and the duplicated CqbZIPs had mainly undergone purifying selection pressure, which suggested that the functions of the duplicated CqbZIPs might not diverge much. Moreover, we identified the bZIP members in 3 other Amaranthaceae species, and 41, 32, and 16 orthologous gene pairs were identified between quinoa and S. oleracea, B. vulgaris, and A. hypochondriacus, respectively. Among them, most were a single copy being present in S. oleracea, B. vulgaris, and A. hypochondriacus, and two copies being present in allotetraploid quinoa. The function divergence within the bZIP orthologous genes might be limited. Additionally, 11 selected CqbZIPs had specific spatial expression patterns, and 6 of 11 CqbZIPs were up-regulated in response to salt stress. Among the selected CqbZIPs, 3 of 4 duplicated gene pairs shared similar expression patterns, suggesting that these duplicated genes might retain some essential functions during subsequent evolution.ConclusionsThe present study provided the first systematic analysis for the phylogenetic classification, motif and gene structure, expansion pattern, and expression profile of the bZIP family in quinoa. Our results would lay an important foundation for functional and evolutionary analysis of CqbZIPs, and provide promising candidate genes for further investigation in tissue specificity and their functional involvement in quinoa’s resistance to salt stress.
Highlights
Chenopodium quinoa Willd. is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity
Phylogenetic analysis To determine the evolutionary relationships of basic leucine zipper (bZIP) in quinoa, phylogenetic trees were constructed with the 94 CqbZIP proteins and the known bZIPs from Arabidopsis (Figs. 1 and 2a, Additional file 3)
A complete set of 94 bZIP genes were identified in quinoa, and the size of the genes is similar with that of Arabidopsis (78) [14] and rice (89) [23], but significantly lower that of soybean (160) [39] in which recent whole genome duplication (WGD) events have occurred due to palaeopolyploid, suggesting that besides the genome fusion event that happened around 4.3 million years ago, no other lineage-specific recent WGD were involved in quinoa genome evolution [40]
Summary
Chenopodium quinoa Willd. (quinoa) is a pseudocereal crop of the Amaranthaceae family and represents a promising species with the nutritional content and high tolerance to stressful environments, such as soils affected by high salinity. Quinoa (Chenopodium quinoa Willd.) is a halophytic pseudocereal crop that originated from the Andean region of South America [1] It is an allotetraploid (2n = 4x = 36) with an estimated genome size of approximately 1.5 Gbp. Quinoa belongs to the Amaranthaceae family, which includes other economically important crops such as Spinacia oleracea (spinach, 2n = 2x = 12), Beta vulgaris (sugar beet, 2n = 2x = 18), and Amaranthus hypochondriacus (amaranth, 2n = 2x = 32) [2]. To expand quinoa production worldwide and accelerate the improvement of quinoa, increasing researchers have devoted into the study of quinoa, and a draft of the C. quinoa genome sequence was reported recently [7], which provided the foundation for accelerating the genetic improvement of the crop and enhanced global food security for a growing world population
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