Search

Background: In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogenesis, little is known about the B3 superfamily in citrus, and which members might be involved in SE. Results: Genome-wide sequence analysis identified 72 (CsB3) and 69 (CgB3) putative B3 superfamily members in the genomes of sweet orange (Citrus sinensis, polyembryonic) and pummelo (C. grandis, monoembryonic), respectively. Genome duplication analysis indicated that segmental and tandem duplication events contributed to the expansion of the B3 superfamily in citrus, and that the B3 superfamily evolved under the effect of purifying selection. Phylogenetic relationships were well supported by conserved gene structure and motifs outside the B3 domain, which allowed possible functions to be inferred by comparison with homologous genes from Arabidopsis. Expression analysis identified 23 B3 superfamily members that were expressed during SE in citrus and 17 that may play functional roles at late SE stages. Eight B3 genes were identified that were specific to the genome of polyembryonic sweet orange compared to monoembryonic pummelo. Of these eight B3 genes, CsARF19 was found to be specifically expressed at higher levels in embryogenic callus (EC), implying its possible involvement in EC initiation. Conclusions: This study provides a genome-wide analysis of the citrus B3 superfamily, including its genome organization, evolutionary features and expression profiles, and identifies specific family members that may be associated with SE. [ABSTRACT FROM AUTHOR]

Blood orange is generally recognized to accumulate anthocyanins in its fruit pulp in a cold‐inducible manner. We observed that the fruit peel of blood orange can also accumulate anthocyanins under ample light conditions. Interestingly, purple pummelo can accumulate anthocyanins only in its fruit peel but not in its pulp. The mechanism underlying the tissue specificity of anthocyanin accumulation in citrus is unknown. Here, we show that the active promoter of Ruby1, a key activator of anthocyanin biosynthesis, is also light inducible in addition to its already known cold inducibility in blood orange. Electrophoretic mobility shift assays and transient expression assays showed that HY5 positively regulated the transcription of Ruby1 by binding to the G‐box motif (CACGTC). The tissue specificity of anthocyanin accumulation in the peel of purple pummelo may be due to the lack of a low temperature responsive element and a MYC binding site, which were shown to be involved in cold inducibility of CsRuby1 in blood orange by insertion of a long terminal repeat type retrotransposon in the promoter. These results bring new insights into the regulatory mechanism of anthocyanin biosynthesis in response to environmental stimuli and provide cis‐elements for genetic improvement of anthocyanin‐stable fruits rich in antioxidant metabolites. The accumulation of anthocyanins in fruit peel of blood orange in response to light is regulated by the G‐box (CACGTC) within the promoter of CsRuby1. On the other hand, cold‐inducible accumulation of anthocyanins in blood orange is regulated by the LTR region of the retrotransposon‐containing promoter of CsRuby1. The accumulation of anthocyanins in fruit peel of blood orange in response to light is regulated by the G‐box (CACGTC) within the promoter of CsRuby1. On the other hand, cold inducible accumulation of anthocyanins in blood orange is regulated by the LTR region of the retrotransposon‐containing promoter of CsRuby1. [ABSTRACT FROM AUTHOR]

Summary: Long intergenic non‐coding RNAs (lincRNAs) play important roles in various biological processes in plants. However, little information is known about the evolutionary characteristics of lincRNAs among closely related plant species. Here, we present a large‐scale comparative study of lincRNA transcription patterns in nine citrus species. By strand‐specific RNA‐sequencing, we identified 18 075 lincRNAs (14 575 lincRNA loci) from 34 tissue samples. The results indicated that the evolution of lincRNA transcription is more rapid than that of mRNAs. In total, 82.8–97.6% of sweet orange (Citrus sinensis) lincRNA genes were shown to have homologous sequences in other citrus genomes. However, only 15.5–28.8% of these genes had transcribed homologous lincRNAs in these citrus species, presenting a strong contrast to the high conservation of mRNA transcription (81.6–84.7%). Moreover, primitive and modern citrus lincRNAs were preferentially expressed in reproductive and vegetative organs, respectively. Evolutionarily conserved lincRNAs showed higher expression levels and lower tissue specificity than species‐specific lincRNAs. Notably, we observed a similar tissue expression pattern of homologous lincRNAs in sweet orange and pummelo (Citrus grandis), suggesting that these lincRNAs may be functionally conserved and selectively maintained. We also identified and validated a lincRNA with the highest expression in fruit that acts as an endogenous target mimic (eTM) of csi‐miR166c, and two lincRNAs that act as a precursor and target of csi‐miR166c, respectively. These lincRNAs together with csi‐miR166c could form an eTM166‐miR166c‐targeted lincRNA regulatory network that possibly affects citrus fruit development. Significance Statement: Here, 18 075 lincRNAs have been identified from 34 tissue samples from nine citrus species. The data uncover the rapid turnover of lincRNA transcription among different citrus species and highlights the potential contribution of the eTM166‐miR166‐targeted lincRNA regulatory network to fruit development. [ABSTRACT FROM AUTHOR]

Fruit shape is an important trait for fruit appearance and commercial value. Diversity of fruit-shape has been utilized in the breeding of pummelo (Citrus maxima), a basic species in Citrus. However, little is known about genetic basis of fruit shape in citrus. In this study, we identified 16 OVATE family protein (OFP) genes in the pummelo genome. Phylogenetically, they were classified into three subfamilies, which was consistent with the classification of their Arabidopsis orthologs. Synteny analysis suggested that segment and tandem duplications were responsible for their expansion in pummelo. Expression pattern analysis of Citrus OFPs (CitOFP s) showed that CitOFP19 had significantly higher expression level in the ovaries of round pummelo than in those of pear-shaped pummelo. Heterologous overexpression of CitOFP19 in tomato resulted in pear-shaped ovary and fruit shape. Taken together, this study characterized OVATE gene family in Citrus genome and assessed the function of CitOFP19. • We summarized the distribution pattern of the fruit shape index in the natural pummelo populations. • We identified the OVATE gene family in Citrus and segment and tandem duplications responsible for their expansion. • Heterologous overexpression of CitOFP19 in tomato resulted in pear-shaped ovary and fruit shape, which provided the basis for investigating its function in Citrus. [ABSTRACT FROM AUTHOR]

• 'Huarongdao Zhoupigan' is a cultivated landrace with a history of more than a hundred years. • Parentage and origination was predicted by morphological, SSR marker and genomic analyses. • 'Huarongdao Zhoupigan' may be a natural hybrid with sour orange (a sexual hybrid of pummelo and mandarin) as the seed parent and mandarin as the pollen parent. The cultivated landrace 'Huarongdao Zhoupigan' originated in China, and it has a history of more than a hundred years. It is widely cultivated for its distinctive pericarp, soft juicy pulp, slight bitter taste, and rich flavonoids and vitamin C (17.2 ± 0.08 mg•mL−1). Morphological observation shows that 'Huarongdao Zhoupigan' is mandarin-like in leaf shape, fruit flesh, easy peeling and crumpled pericarp, implying this variety may be a hybrid of orange and mandarin. To reveal the genetic background of 'Huarongdao Zhoupigan', 21 citrus accessions were evaluated using nuclear and chloroplast SSR markers and whole-genome SNP information. 'Huarongdao Zhoupigan' was grouped with mandarins and closely clustered with 'Yuanjiang Nanju' in the nuclear SSR analysis and sub-grouped with 'Goutou' sour orange, 'Dahong' sweet orange and 'Newhall' navel orange in the chloroplast SSR analysis. The genomic sequence similarity rate of 'Huarongdao Zhoupigan' with mandarin was 36.09%, with mandarin heterozygosity of 46.50%; the rough ratio of the two main parts was nearly 1:1, except for the unknown (19.11%) and pummelo (1.46%) parts. Thus, 'Huarongdao Zhoupigan' may be a natural hybrid with sour orange (a sexual hybrid of pummelo and mandarin) as the seed parent and mandarin as the pollen parent. [ABSTRACT FROM AUTHOR]