ultivated peanut or groundnut (A. hypogaea L.) is among the most important oil and food legumes, grown on 25 million ha between latitudes 40° N and 40° S with annual production of ~46 million tons (http://www.fao.org/faostat/en/#home). It presumably was domesticated in South America ~6,000 years ago and then was widely distributed in post-Columbian times 1. Combining richness in seed oil (~46-58%) and protein (~22-32%), peanut is important in fighting malnutrition and ensuring food security.

Background B-box (BBX) proteins are important factors involving in the regulation of plant growth and development, and have been identified in many plant species. However, the characteristics and transcription patterns of BBX genes in wild peanut are limited. Results In the present study, we identified and characterized 24 BBX genes in a wild peanut Arachis duranensis. The AdBBX members distributed on 9 of the 10 chromosomes and chromosome 3 contained the most AdBBX members, with 6 AdBBXs. 16 AdBBX proteins had two distinct BBX domains, 11 members contained one CCT domain, and 7 genes had both BBX and CCT domains. Protein structure analysis revealed that AdBBX were classified into five clades: I (3 genes), II (4 genes), III (4 genes), IV (9 genes) and V (4 genes), on the basis of the diversity of conserved BBX and CCT domains. Moreover, 15 distinct motifs were found in these 24 AdBBX proteins and motif 1 and 5 existed in all the AdBBX proteins. Duplication analysis revealed that 4 interchromosomal duplicated gene pairs were obtained and all of them belonged to group IV. In addition, 95 kinds of cis-acting elements were found in the promoter regions of AdBBXs and 53 types were predicted to have putative functions. The numbers and types of cis-acting elements varied in these AdBBX promoters, as a result, AdBBX genes exhibited distinct expression levels in different tissues. The transcription investigation combined with synteny analysis suggested AdBBX8 might be the key factor involving in flowering time regulation in Arachis duranensis. Conclusion Overall, this study provides a genome-wide identification of BBX genes in a wild peanut Arachis duranensis. Characteristic and transcription pattern analysis revealed their critical roles in plant growth and development. Our study will provide essential information for further functional characteristic investigation of AdBBX genes.

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Cucurbitaceae plants are of considerable biological and economic importance, and genomes of cucumber, watermelon, and melon have been sequenced. However, a comparative genomics exploration of their genome structures and evolution has not been available. Here, we aimed at performing a hierarchical inference of genomic homology resulted from recursive paleopolyploidizations. Unexpectedly, we found that, shortly after a core-eudicot-common hexaploidy, a cucurbit-common tetraploidization (CCT) occurred, overlooked by previous reports. Moreover, we characterized gene loss (and retention) after these respective events, which were significantly unbalanced between inferred subgenomes, and between plants after their split. The inference of a dominant subgenome and a sensitive one suggested an allotetraploid nature of the CCT. Besides, we found divergent evolutionary rates among cucurbits, and after doing rate correction, we dated the CCT to be 90–102 Ma, likely common to all Cucurbitaceae plants, showing its important role in the establishment of the plant family.

The botanical family Cucurbitaceae includes a variety of fruit crops with global or local economic importance. How their genomes evolve and the genetic basis of diversity remain largely unexplored. In this study, we sequence the genome of the wax gourd (Benincasa hispida), which bears giant fruit up to 80 cm in length and weighing over 20 kg. Comparative analyses of six cucurbit genomes reveal that the wax gourd genome represents the most ancestral karyotype, with the predicted ancestral genome having 15 proto-chromosomes. We also resequence 146 lines of diverse germplasm and build a variation map consisting of 16 million variations. Combining population genetics and linkage mapping, we identify a number of regions/genes potentially selected during domestication and improvement, some of which likely contribute to the large fruit size in wax gourds. Our analyses of these data help to understand genome evolution and function in cucurbits.