Abstract
BackgroundIn 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.ResultsGenome-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.ConclusionsThis 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.
Highlights
In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE)
We found that the B3 domain regulatory network genes CsFUS3, CsABI3 and another B3 gene (CS_P006_E_03) exhibited increased expression during citrus SE induction and formation [41], whereas CsFUS3 was shown to promote citrus SE by regulating SE-related transcription factors (TFs) and hormone pathways, especially ABA and GA pathways [44]
Identification and genomic distribution of B3 superfamily in citrus A total of 72 (CsB3) and 69 (CgB3) B3 superfamily TFs were identified in the sweet orange (Citrus sinensis) and pummelo (C. grandis) genomes, respectively (Additional file 1)
Summary
Identification and genomic distribution of B3 superfamily in citrus A total of 72 (CsB3) and 69 (CgB3) B3 superfamily TFs were identified in the sweet orange (Citrus sinensis) and pummelo (C. grandis) genomes, respectively (Additional file 1). CgARF17 was mainly expressed in leaf (RPKM = 59.06) and ovule (RPKM = 57.40) of pummelo, whereas its orthologous gene (CsARF17) in sweet orange showed relatively low expression in all citrus tissues studied, with RPKM values ranging from 4.16 to 7.57. To explore the possible involvement of CsB3 genes during citrus SE, the expression profile of 23 CsB3 genes was investigated by qRT-PCR in the six SE stages of ‘Valencia’ orange, a citrus variety with strong SE capability These genes were selected based on their relatively high transcript abundance (RPKM values > 10) in EC, or specific accumulation in EC with lower expression level (1 < RPKM values < 10) according to the RNA-seq data. With the availability of the citrus genome sequences [46,47,48,49,50], two orthologs of CsARF19, MSYJ162170.1 (amino acids sequence identity of 99.36%) and Ciclev10030751m (amino acids sequence identity of 99.87%), were identified in Mangshan mandarin (C. reticulata, a wild mandarin) and Clementine mandarin (C. clementina, which is believed to be a chance hybrid of mandarin and sweet orange) [48, 50, 51], respectively, but
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