The high level of physiological fruitlet abscission in litchi (Litchi chinensis Sonn.) causes severe yield loss. Cell separation occurs at the fruit abscission zone (FAZ) and can be triggered by ethylene. However, a deep knowledge of the molecular events occurring in the FAZ is still unknown. Here, genome-wide digital transcript abundance (DTA) analysis of putative fruit abscission related genes regulated by ethephon in litchi were studied. More than 81 million high quality reads from seven ethephon treated and untreated control libraries were obtained by high-throughput sequencing. Through DTA profile analysis in combination with Gene Ontology and KEGG pathway enrichment analyses, a total of 2,730 statistically significant candidate genes were involved in the ethephon-promoted litchi fruitlet abscission. Of these, there were 1,867 early-responsive genes whose expressions were up- or down-regulated from 0 to 1 d after treatment. The most affected genes included those related to ethylene biosynthesis and signaling, auxin transport and signaling, transcription factors, protein ubiquitination, ROS response, calcium signal transduction and cell wall modification. These genes could be clustered into 4 groups and 13 subgroups according to their similar expression patterns. qRT-PCR displayed the expression pattern of 41 selected candidate genes, which proved the accuracy of our DTA data. Ethephon treatment significantly increased fruit abscission and ethylene production of fruitlet. The possible molecular events to control the ethephon-promoted litchi fruitlet abscission were prompted out. The increased ethylene evolution in fruitlet would suppress the synthesis and polar transport of auxin and trigger abscission signaling. To the best of our knowledge, it is the first time to monitor the gene expression profile occurring in the FAZ-enriched pedicel during litchi fruit abscission induced by ethephon on the genome-wide level. This study will contribute to a better understan

Summary: MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play vital regulatory roles in plant growth and development. Little is known about these small RNAs in litchi (Litchi chinensis), an economically important fruit crop widely cultivated in Southeast Asia. We profiled the litchi small RNA population with various deep‐sequencing techniques and in‐depth bioinformatic analyses. The genome‐wide identification of miRNAs, their target genes, and phasiRNA‐generating (PHAS) genes/loci showed that the function of miR482/2118 has expanded, relative to its canonical function. We also discovered that, for 29 PHAS loci, miRNA‐mediated phasiRNA production was coupled with alternative splicing (AS) and alternative polyadenylation (APA). Most of these loci encoded long noncoding RNAs. An miR482/2118 targeted locus gave rise to four main transcript isoforms through AS/APA, and diverse phasiRNAs generated from these isoforms appeared to target long terminal repeat (LTR) retrotransposons and other unrelated genes. This coupling enables phasiRNA production from different exons of noncoding PHAS genes and yields diverse phasiRNA populations, both broadening and altering the range of downstream phasiRNA‐regulated genes. Our results reveal the diversity of miRNA and phasiRNA in litchi, and demonstrate AS/APA as a new layer of regulation in small RNA‐mediated gene silencing.

Huanglongbing (HLB) is a highly detrimental citrus disease associated with ‘Candidatus Liberibacter asiaticus’, a nonculturable alpha-proteobacterium. Characterization of the bacterial populations is important for development of disease management strategies. In this study, the ‘Ca. L. asiaticus’ populations in eight provinces in southern China where HLB is endemic were analyzed based on tandem repeat number (TRN) variations in a previously characterized genomic locus CLIBASIA_01645. Of the 224 HLB samples collected, 175 (78.3%) samples yielded single polymerase chain reaction (PCR) amplicons (the single amplicon group, SAG) and 49 (21.7%) samples produced multiple PCR amplicons (the multiple amplicon group, MAG). Variations in SAG are summarized by Nei's diversity index (H) and ratio of TRN ≤ 10/TRN > 10 genotypes (R₁₀). Variations in the MAG are described by the percentage of occurrence (P_MAG). At an orchard-level comparison, the ‘Ca. L. asiaticus’ population from a Guangdong orchard (n = 24) showed H = 0.50, R₁₀ = 23, and P_MAG = 0, significantly different from that of the non-Guangdong orchards in Yunnan (n = 23), H = 0.83, R₁₀ = 2.3, and P_MAG = 11.5, and in Hainan (n = 35), H = 0.88, R₁₀ = 1.5, and P_MAG = 16.7. In a region-level consideration, the Guangdong ‘Ca. L. asiaticus’ population (n = 78) was H = 0.77, R₁₀ = 25, and P_MAG = 1.3, whereas the non-Guangdong population (n = 84) was H = 0.91, R₁₀ = 1.6, and P_MAG = 26.9. Overall, significant differences were observed between the ‘Ca. L. asiaticus’ population from Guangdong Province and those from the other provinces. A strong aggregation of TRN = 6, 7, and 8 genotypes is characteristic to the ‘Ca. L. asiaticus’ population in Guangdong. Referenced to genome annotation, we propose that rearrangement of tandem repeats at locus CLIBASIA_01645 could be associated with bacterial environmental adaptation.

Background: Carotenoid cleavage oxygenases (CCOs) include the carotenoid cleavage dioxygenase (CCD) and 9-cis-epoxycarotenoid (NCED), which can catalize carotenoid to form various apocarotenoids and their derivatives, has been found that play important role in the plant world. But little information of CCO gene family has been reported in litchi (Litchi chinensis Sonn.) till date. Results: In this study, a total of 15 LcCCO genes in litchi were identified based on genome wide lever. Phylogeny analysis showed that LcCCO genes could be classified into six subfamilies (CCD1, CCD4, CCD7, CCD8, CCD-like, and NCED), which gene structure, domain and motifs exhibited similar distribution patterns in the same subfamilies. MiRNA target site prediction found that there were 32 miRNA target sites in 13 (86.7%) LcCCO genes. Cis-elements analysis showed that the largest groups of elements were light response related, following was plant hormones, stress and plant development related. Expression pattern analysis revealed that LcCCD4, LcNCED1, and LcNCED2 might be involving with peel coloration, LcCCDlike-b might be an important factor deciding fruit flavor, LcNCED2 and LcNCED3 might be related to flower control, LcNCED1 and LcNCED2 might function in fruitlet abscission, LcCCD4a1, LcCCD4a2, LcCCD1, LcCCD4, LcNCED1, and LcNCED2 might participate in postharvest storage of litchi. Conclusion: Herein, Genome-wide analysis of the LcCCO genes was conducted in litchi to investigate their structure features and potential functions. These valuable and expectable information of LcCCO genes supplying in this study will offer further more possibility to promote quality improvement and breeding of litchi and further function investigation of this gene family in plant.

N6-methyladenosine (m6A) RNA modification is the most prevalent type of RNA methylation and plays a pivotal role in the development of plants. However, knowledge of the m6A modification in litchi remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in litchi was performed and 31 litchi m6A regulatory genes were identified in total, including 7 m6A writers, 12 m6A erases, and 12 readers. Phylogeny analysis showed that all three of the kinds of litchi m6A regulatory proteins could be divided into three groups; domains and motifs exhibited similar patterns in the same group. MiRNA target site prediction showed that 77 miRNA target sites were located in 25 (80.6%) litchi m6A regulatory genes. Cis-elements analysis exhibited that litchi m6A regulatory genes were mainly responsive to light and plant hormones, followed by environmental stress and plant development. Expression analysis revealed litchi m6A regulatory genes might play an important role during the peel coloration and fruit abscission of litchi. This study provided valuable and expectable information of litchi m6A regulatory genes and their potential epigenetic regulation mechanism in litchi.

The problem of Feizixiao lychee fruit cracking is typically solved by the application of calcium to the leaves. However, lychee trees are sensitive to excessive amounts of calcium, and in practice, it is easy to spray excessive amounts that result in fertilizer burns. This paper intends to explore the effects of excessive calcium fertilizer application on lychee fruit pulp quality and the underlying molecular physiological mechanism. Adult Feizixiao lychee trees were used as test materials; concerning treatment, a 54 μM anhydrous CaCl₂ aqueous solution was sprayed onto the leaves, and water was used as a control (CK). The levels of pulp sugar and the activities of key enzymes involved in glucose metabolism were observed, and transcriptome analysis and genetic screening were performed on the pulp. Spraying excessive amounts of calcium onto the leaf surfaces caused the downregulation of trehalase-encoding genes and SUS-encoding genes, thus inhibiting the activities of trehalase, SS-I and SS-II, and further inhibiting the accumulation of glucose, fructose, and sucrose. Moreover, upregulation of VIN gene expression enhanced AI activity and inhibited sucrose accumulation, thus inhibiting upregulation of NI gene expression during fruit growth and expansion; in turn, this inhibited the increase in NI activity in the fruit pulp, which then decreased the glucose and fructose accumulation in the pulp in the high-calcium treatment group compared with the CK group. The downregulation and expression of CHS family genes may lead to a decrease in chalcone accumulation, which may lead to damage caused by active oxygen production in the fruit pulp, thus inhibiting the accumulation of soluble sugars in that tissue.