Transposable elements cause the loss of self-incompatibility in citrus

Self-incompatibility (SI) is a widespread prezygotic mechanism for flowering plants to avoid inbreeding depression and promote genetic diversity. Citrus has an S-RNase-based SI system, which was frequently lost during evolution. We previously identified a single nucleotide mutation in Sm-RNase, which is responsible for the loss of SI in mandarin and its hybrids. However, little is known about other mechanisms responsible for conversion of SI to self-compatibility (SC) and we identify a completely different mechanism widely utilized by citrus. Here, we found a 786-bp miniature inverted-repeat transposable element (MITE) insertion in the promoter region of the FhiS2-RNase in Fortunella hindsii Swingle (a model plant for citrus gene function), which does not contain the Sm-RNase allele but are still SC. We demonstrate that this MITE plays a pivotal role in the loss of SI in citrus, providing evidence that this MITE insertion prevents expression of the S-RNase; moreover, transgenic experiments show that deletion of this 786-bp MITE insertion recovers the expression of FhiS2-RNase and restores SI. This study identifies the first evidence for a role for MITEs at the S-locus affecting the SI phenotype. A family-wide survey of the S-locus revealed that MITE insertions occur frequently adjacent to S-RNase alleles in different citrus genera, but only certain MITEs appear to be responsible for the loss of SI. Our study provides evidence that insertion of MITEs into a promoter region can alter a breeding strategy and suggests that this phenomenon may be broadly responsible for SC in species with the S-RNase system

Complete chloroplast genome and phylogenetic analysis of Lonicera caerulea var. edulis (Caprifoliaceae)

Lonicera caerulea var. edulis, known as “blue honeysuckle” or “Haskap,” is a deciduous shrub that belongs to the Caprifoliaceae family. Characterized by the high cold hardiness and high quality of fruit, it has become a novel cash crop in cold regions worldwide. The lack of available chloroplast (cp) genome information limits studies of its molecular breeding and phylogeny. Here, the complete cp genome of Lonicera caerulea var. edulis was assembled and characterized for the first time. It was 155,142 bp in length with 38.43% of GC content, including 23,841 bp inverted repeat regions (IRs), an 88,737 bp large single-copy region (LSC), and an 18,723 bp small single-copy region (SSC). A total of 132 genes, including 85 protein-coding genes, 8 rRNA genes, and 39 tRNA genes were annotated. Phylogenetic analysis indicated that L. caerulea var. edulis was closely related to L. tangutica. These data and results provide a valuable resource for the development of breeding tools and genetic diversity studies for L. caerulea

Plant Regeneration via Somatic Embryogenesis and Indirect Organogenesis in Blue Honeysuckle (<i>Lonicera caerulea</i> L.)

Blue honeysuckle (Lonicera caerulea L.), which belongs to the Caprifoliaceae family, is an emerging fruit crop worldwide. For the development of a transgenic system and multipurpose tissue culture, this study for the first time established an in vitro regeneration system via somatic embryogenesis, as well as improving the previously established indirect organogenesis-based regeneration system. For embryogenesis, Murashige and Skoog (MS) medium supplemented with 1.0 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) showed the highest induction rate of the embryogenic callus (97.6%), and MS supplemented with 0.1 mg/L 6-benzyladenine (6-BA), 0.1 mg/L α-naphthaleneacetic acid (NAA), and 0.5 g/L activated carbon (AC) achieved the highest somatic embryo rate (28.3%). For indirect organogenesis, MS medium supplemented with 1.0 mg/L 6-BA and 0.1 mg/L NAA resulted in the highest non-embryogenic callus induction rate (98.9%) and adventitious shoot induction rate (51.6%). For adventitious root induction, MS supplemented with 1.0 mg/L indole-3-butyric acid (IBA) achieved the highest root induction rate (96.0%) and average root length (4.6 cm), whereas MS supplemented with 0.5 mg/L indole-3-acetic acid (IAA) resulted in the highest average regenerated root number (8.8). The total time for the regeneration from explants to soil-planted seedlings (10 euphylla) was 105 and 150 days with an efficiency of 44.1% and 23.9% through organogenesis and somatic embryogenesis, respectively. This study provides a powerful tool for rapid propagation, proliferation, and transformation, as well as laying a technological foundation for gene function research and genetic improvement of blue honeysuckle

Complete chloroplast genome assembly and phylogenetic analysis of blackcurrant (Ribes nigrum), red and white currant (Ribes rubrum), and gooseberry (Ribes uva-crispa) provide new insights into the phylogeny of Grossulariaceae

Background Blackcurrant (Ribes nigrum), red currant (R. rubrum), white currant (R. rubrum), and gooseberry (R. uva-crispa) belong to Grossulariaceae and are popular small-berry crops worldwide. The lack of genomic data has severely limited their systematic classification and molecular breeding. Methods The complete chloroplast (cp) genomes of these four taxa were assembled for the first time using MGI-DNBSEQ reads, and their genome structures, repeat elements and protein-coding genes were annotated. By genomic comparison of the present four and previous released five Ribes cp genomes, the genomic variations were identified. By phylogenetic analysis based on maximum-likelihood and Bayesian methods, the phylogeny of Grossulariaceae and the infrageneric relationships of the Ribes were revealed. Results The four cp genomes have lengths ranging from 157,450 to 157,802 bp and 131 shared genes. A total of 3,322 SNPs and 485 Indels were identified from the nine released Ribes cp genomes. Red currant and white currant have 100% identical cp genomes partially supporting the hypothesis that white currant (R. rubrum) is a fruit color variant of red currant (R. rubrum). The most polymorphic genic and intergenic region is ycf1 and trnT-psbD, respectively. The phylogenetic analysis demonstrated the monophyly of Grossulariaceae in Saxifragales and the paraphyletic relationship between Saxifragaceae and Grossulariaceae. Notably, the Grossularia subgenus is well nested within the Ribes subgenus and shows a paraphyletic relationship with the co-ancestor of Calobotrya and Coreosma sections, which challenges the dichotomous subclassification of the Ribes genus based on morphology (subgenus Ribes and subgenus Grossularia). These data, results, and insights lay a foundation for the phylogenetic research and breeding of Ribes species