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Most commercial banana cultivars are highly susceptible to Fusarium wilt caused by soilborne fungus Fusarium oxysporum f. sp. cubense (Foc), especially tropical race 4 (TR4). Biological control using antagonistic microorganism has been considered as an alternative method to fungicide. Our previous study showed that Streptomyces sp. SCA3-4

Lychee is an exotic tropical fruit with a distinct flavor. The genome of cultivar ‘Feizixiao’ was assembled into 15 pseudochromosomes, totaling ~470 Mb. High heterozygosity (2.27%) resulted in two complete haplotypic assemblies. A total of 13,517 allelic genes (42.4%) were differentially expressed in diverse tissues. Analyses of 72 resequenced lychee accessions revealed two independent domestication events. The extremely early maturing cultivars preferentially aligned to one haplotype were domesticated from a wild population in Yunnan, whereas the late-maturing cultivars that mapped mostly to the second haplotype were domesticated independently from a wild population in Hainan. Early maturing cultivars were probably developed in Guangdong via hybridization between extremely early maturing cultivar and late-maturing cultivar individuals. Variable deletions of a 3.7 kb region encompassed by a pair of CONSTANS-like genes probably regulate fruit maturation differences among lychee cultivars. These genomic resources provide insights into the natural history of lychee domestication and will accelerate the improvement of lychee and related crops., Two divergent haplotypes from a highly heterozygous lychee genome of the cultivar ‘Feizixiao’ and resequencing of 72 lychee accessions provide insights into the genome evolution and domestication history of lychee.

Background Litchi is a well-known subtropical fruit crop. However, irregular bearing attributed to unstable flowering is a major ongoing problem for the development of the litchi industry. In a previous study, our laboratory proved that litchi flowering was induced by low temperature and that a FLOWERING LOCUS T (FT) homologue gene named LcFT1 played a pivotal role in this process. The present study aimed to understand the natural variation in FT among litchi germplasm resources and designed markers to verify easy- and difficult-flowering litchi germplasms. A grafting experiment was also carried out to explore whether it could shorten the seedling stage of litchi seedlings. Results Two types of LcFT1 promoter existed in different litchi germplasm resources, and we named them the ‘easy-flowering type of LcFT1 promoter’ and ‘difficult-flowering type of LcFT1 promoter’, which resulted in three different LcFT1 genotypes of litchi germplasm resources, including the homozygous easy-flowering type of the LcFT1 genotype, homozygous difficult-flowering type of the LcFT1 genotype and heterozygous LcFT1 genotype of litchi germplasm resources. The homozygous easy-flowering type of the LcFT1 genotype and heterozygous LcFT1 genotype of the litchi germplasm resources completed their floral induction more easily than the homozygous difficult-flowering type of the LcFT1 genotype of litchi germplasm resources. Herein, we designed two kinds of efficient molecular markers based on the difference in LcFT1 promoter sequences and applied them to identify of the easy- and difficult-flowering litchi germplasm resources. These two kinds of molecular markers were capable of clearly distinguishing the easy- from difficult-flowering litchi germplasm resources at the seedling stage and provided the same results. Meanwhile, grafting the scion of seedlings to the annual branches of adult litchi trees could significantly shorten the seedling stage. Conclusions Understanding the flowering characteristics of litchi germplasm resources is essential for easy-flowering litchi breeding. In the present study, molecular markers provide a rapid and accurate approach for identifying the flowering characteristics. The application of these molecular markers not only significantly shortened the artificial crossbreeding cycle of easy-flowering litchi cultivars but also greatly saved manpower, material resources and land.

The pericarp of longan (Dimocarpus longan Lour.) is rich in secondary metabolites and typically yellow-brown or gray-yellow in appearance. Here, we obtained a specific longan type, called red pericarp (RP) longan, which has a strong red pericarp. To understand the coloring mechanism of RP longan, metabolome and transcriptome data were used to analyze its secondary metabolites and molecular mechanism. From the results of liquid chromatography tandem mass spectrometry, 597 substances were identified in RP longan and 'Shixia' (SX) longan. Among these substances, 33 (mostly including flavonoids) were found in RP longan and 23 (mostly containing phenolic acids) were identified in SX longan. We identified five types of anthocyanins in longan pericarp, including three cyanidin derivatives, one delphinidin derivative, and one pelargonidin derivative. Three cyanidin derivatives, which contained cyanidin 3-O-glucoside, cyanidin 3-O-6″-malonyl-glucoside, and cyanidin O-syringic acid, were the primary components of anthocyanidins, and they only existed in RP longan. Delphinin 3-O-glucoside existed only in SX longan, and pelargonin O-rutinoside existed in RP and SX longan. However, their contents were extremely low. The structural genes F3H, F3'H, UFGT, and GST and the controlling genes containing MYB, bHLH, NAC, and MADS in the biosynthetic pathway of anthocyanin were significantly upregulated in RP longan. In summary, the strong red hue of RP longan is due to the accumulation of cyanidin derivatives in its pericarp, and the genes F3'H and F3'5'H may play an important role in selecting which component of anthocyanins will be synthesized. These results can provide scientific guidance for understanding and developing bioactive compounds from longan fruits.

B-box zinc finger proteins contain one or two B-box domains, and sometimes, a CCT domain, which are involved in many biological processes, such as photomorphogenesis, flowering, anthocyanin synthesis and abiotic stress resistance. But the BBX gene family in pineapple has not been systematically studied. Nineteen BBX genes were detected in pineapple genome and divided into five groups according to phylogenetic analysis. The results of transcriptome analysis and RT-qPCR showed that most of AcBBX members were highly expressed during the flowering process, indicating that AcBBX gene may be involved in flower bud differentiation and morphogenesis. Transcriptional activation analysis showed that AcBBX6 and AcBBX18 had transcriptional activity and were located in the nucleus. Overexpression of AcBBX18 promoted flowering in Arabidopsis thaliana. These results provided a basis for further study functions and regulatory mechanism of BBX members in pineapple floral induction and flower development.

When exposed to pathogen infection or ultraviolet (UV) radiation, grapevine (Vitis vinifera) plants rapidly accumulate the stilbenoid resveratrol (Res) with concomitant increase of stilbene synthase (STS), the key enzyme in stilbene biosynthesis. Although a few transcription factors have been shown to regulate STSs, the molecular mechanism governing the regulation of STSs is not well elucidated. Our previous work showed that a VvMYB14–VvWRKY8 regulatory loop fine-tunes stilbene biosynthesis in grapevine through protein–protein interaction; overexpression of VvWRKY8 down-regulates VvMYB14 and VvSTS15/21; and application of exogenous Res up-regulates WRKY8 expression. Here, we identified an R2R3-MYB repressor, VvMYB30, which competes with the activator VvMYB14 for binding to the common binding sites in the VvSTS15/21 promoter. Similar to VvMYB14, VvMYB30 physically interacts with VvWRKY8 through their N-termini, forming a complex that does not bind DNA. Exposure to UV-B/C stress induces VvMYB14, VvWRKY8, and VvSTS15/21, but represses VvMYB30 in grapevine leaves. In addition, MYB30 expression is up-regulated by VvWRKY8-overexpression or exogenous Res. These findings suggest that the VvMYB14–VvWRKY8–VvMYB30 regulatory circuit allows grapevine to respond to UV stress by producing Res and prevents over-accumulation of Res to balance metabolic costs. Our work highlights the stress-mediated induction and feedback inhibition of stilbene biosynthesis through a complex regulatory network involving multiple positive and negative transcriptional regulators.

Plant height is an important and valuable agronomic trait associated with yield and resistance to abiotic and biotic stresses. Dwarfism has positive effects on plant development and field management, especially for tall monocotyledon banana (Musa spp.). However, several key genes and their regulation mechanism of controlling plant height during banana development are unclear. In the present study, the popular cultivar ‘Brazilian banana’ (‘BX’) and its dwarf mutant (‘RK’) were selected to identify plant height-related genes by comparing the phenotypic and transcriptomic data. Banana seedlings with 3–4 leaves were planted in the greenhouse and field. We found that the third and fourth weeks are the key period of plant height development of the selected cultivars. A total of 4563 and 10507 differentially expressed genes (DEGs) were identified in the third and fourth weeks, respectively. Twenty modules were produced by the weighted gene co-expression network analysis (WGCNA). Eight modules were positively correlated with the plant height, and twelve other modules were negatively correlated. Combining with the analysis of DEGs and WGCNA, 13 genes in the signaling pathway of gibberellic acid (GA) and 7 genes in the signaling pathway of indole acetic acid (IAA) were identified. Hub genes related to plant height development were obtained in light of the significantly different expression levels (|log2FC| ≥ 1) at the critical stages. Moreover, GA3 treatment significantly induced the transcription expressions of the selected candidate genes, suggesting that GA signaling could play a key role in plant height development of banana. It provides an important gene resource for the regulation mechanism of banana plant development and assisted breeding of ideal plant architecture.

Banana is an important fruit crop. Fusarium wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) seriously threatens the global banana industry. It is difficult to control the disease spread using chemical measures. In addition, commercial resistant cultivars are also lacking. Biological control is considered as a promising strategy using antagonistic microbes. Actinomycetes, especially Streptomyces, are potential sources of producing novel bioactive secondary metabolites. Here, strain SCA2-4T with strong antifungal activity against Foc TR4 was isolated from the rhizospheric soil of Opuntia stricta in a dry hot valley. The morphological, physiological and chemotaxonomic characteristics of the strain were consistent with the genus Streptomyces. Based on the homology alignment and phylogenetic trees of 16S rRNA gene, the taxonomic status of strain SCA2-4T exhibited a paradoxical result and low bootstrap value using different algorithms in the MEGA software. It prompted us to further discriminate this strain from the closely related species by the multilocus sequence analysis (MLSA) using five house-keeping gene alleles (atpD, gyrB, recA, rpoB, and trpB). The MLSA trees calculated by three algorithms demonstrated that strain SCA2-4T formed a distinct clade with Streptomyces mobaraensis NBRC 13819T. The MLSA distance was above 0.007 of the species cut-off. Average nucleotide identity (ANI) values between strain SCA2-4T genome and two standard strain genomes were below 95-96% of the novel species threshold. Strain SCA2-4T was assigned to a novel species of the genus Streptomyces and named as Streptomyces huiliensis sp. nov. The sequenced complete genome of SCA2-4T encoded 51 putative biosynthetic gene clusters of secondary metabolites. Genome alignment revealed that ten gene clusters were involved in the biosynthesis of antimicrobial metabolites. It was supported that strain SCA2-4T showed strong antifungal activities against the pathogens of banana fungal diseases. Extracts abstracted from the culture filtrate of strain SCA2-4T seriously destroyed cell structure of Foc TR4 and inhibited mycelial growth and spore germination. These results implied that strain SCA2-4T could be a promising candidate for biological control of banana Fusarium wilt.

Mango (2n = 2x = 40) is an important tropical/subtropical evergreen fruit tree grown worldwide and yields nutritionally rich and high-value fruits. Here, a high-quality mango genome (396 Mb, contig N50 = 1.03 Mb) was assembled using the cultivar “Irwin” from Florida, USA. A total of 97.19% of the sequences were anchored to 20 chromosomes, including 36,756 protein-coding genes. We compared the β-carotene content, in two different cultivars (“Irwin” and “Baixiangya”) and growth periods. The variation in β-carotene content mainly affected fruit flesh color. Additionally, transcriptome analysis identified genes related to β-carotene biosynthesis. MiPSY1 was proved to be a key gene regulating β-carotene biosynthesis. Weighted gene co-expression network analysis, dual luciferase, and yeast one-hybrid assays confirmed that transcription factors (TFs) MibZIP66 and MibHLH45 activate MiPSY1 transcription by directly binding to the CACGTG motif of the MiPSY1 promoter. However, the two TFs showed no significant synergistic effect on promoter activity. The results of the current study provide a genomic platform for studying the molecular basis of the flesh color of mango fruit.

Banana is a key staple food and fruit in countries all over the world. However, the development of the global banana industry is seriously threatened by Fusarium wilt disease, which is caused by Fusarium oxysporum f. sp. cubense (Foc). In particular, Foc tropical race 4 (Foc TR4) could infect more than 80% of global banana and plantain crops. Until now, there were no commercial chemicals or resistant cultivars available to control the disease. Biological control using actinomycetes is considered a promising strategy. In this study, 88 actinomycetes were isolated from a banana orchard without symptoms of Fusarium wilt disease for more than 10 years. An actinobacterial strain labeled as JBS5-6 has exhibited strong antifungal activities against Foc TR4 and other selected 10 phytopathogenic fungi. Based on phenotypic and biochemical traits as well as complete genome analysis, strain JBS5-6 was assigned to Streptomyces violaceusniger. Extracts of the strain inhibited the mycelial growth and spore germination of Foc TR4 by destroying membrane integrity and the ultrastructure of cells. The complete genome of strain JBS5-6 was sequenced and revealed a number of key function gene clusters that contribute to the biosynthesis of active secondary metabolites. Sixteen chemical compounds were further identified by gas chromatography-mass spectrometry (GC-MS). 5-hydroxymethyl-2-furancarboxaldehyde was one of the dominant components in strain JBS5-6 extracts. Moreover, fermentation broth of strain JBS5-6 significantly reduced the disease index of banana seedlings by inhibiting the infection of Foc TR4 in a pot experiment. Hence, strain JBS5-6 is a potential biocontrol agent for the management of disease and the exploitation of biofertilizer.

Avocado is an important tropical fruit whose after-ripening process is still poorly understood. The fatty acid, phenolics, flavonoids, and tannins were analyzed in ‘Lisa’ avocado (Persea americana Mill. ‘Lisa’) fruit pulp during after-ripening. The transcriptome was analyzed to screen for transcripts associated with the aforementioned after-ripening parameters. The results showed that there were no significant differences in the total fatty acid content among the preclimacteric, climacteric, and postclimacteric stages. Nevertheless, the concentrations of C18:3 (α-linolenic acid) were significantly higher in the climacteric and postclimacteric stages than the preclimacteric stage. RNAseq generated 235,082 transcripts and 151,545 unigenes. In addition, 4,324 DEGs were produced among the three stages. KEGG analysis of the DEGs suggested the pathways about “α-linolenic acid metabolism, unsaturated fatty acid biosynthesis”, “fatty acid degradation”, “linoleic acid metabolism and fatty acid biosynthesis”, “linoleic acid metabolism and fatty acid elongation”, and “fatty acid elongation” may all contribute to the C18:3 variations in ‘Lisa’ avocado fruit pulp. Several transcription factors, including the ethylene-related transcription factors, such as NAC, MYB, bHLH, and WRKY, were also identified in the DEGs database. This study generated transcript data and screened the transcription factors involved in the avocado after-ripening process. This information could be used to control after-ripening in avocado and maintain fruit quality during storage.

DELLA proteins are members of the plant-specific GRAS family, acting as negative regulators of plant growth. In this study, we identified two DELLA protein-coding genes in litchi, denoted as LcGAI and LcRGL1. Motif analysis showed that LcGAI and LcRGL1 proteins both contain a conserved DELLA and TVHYNP motif at the N-terminus as well as LHR1, VHIID, LHR2, PFYRE, and SAW motifs at the C terminus. The fused proteins of LcGAI-GFP and LcRGL1-GFP were both localized in the nucleus. Overexpression of LcGAI and LcRGL1 in Arabidopsis substantially inhibits leaf growth. Expression analysis showed that HLH factors, PRE1 and PRE5, were restrained, whereas gibberellin (GA) receptors GID1a and LcGID1b were enhanced in LcGAI and LcRGL1 overexpression lines. Results of the yeast two-hybrid assay showed that LcGAI and LcRGL1 interact with LcGID1b/LcGID1c in a GA dose-dependent manner, whereas LcGAI and LcRGL1 had a greater binding capacity to LcGID1b than LcGID1c. These observations suggested that LcGAI and LcRGL1 proteins are nuclear growth repressors.

Litchi ( Litchi chinenis Sonn.) is a woody mycorrhizal fruit tree. Hypha and root hairs are the most important structures for nutrition and water absorption in litchi. Girdling is an important technique in litchi cultivation. However, the effects of girdling on arbuscular mycorrhiza (AM) colonization and root hair development remain unknown. To understand the effects of girdling on AM and root hairs in litchi, the carbohydrate content, enzyme activities related to sucrose metabolism, AM colonization, and length and density of root hairs were measured under girdling, wounding and control conditions in the roots of one-year-old seedlings. Results showed that sufficient carbohydrates were available for AM and root hairs in the mycorrhizal roots of litchi in the wounding and control groups. Girdling significantly decreased the concentrations of glucose at 3 days (3D), 1 week (1W), 2 weeks (2W), 1 month (1M) and 2 months (2M) after treatment, of fructose at 3D, 1W, 2W, 1M and 2 M after treatment, of sucrose at 1W, 2W, 1M and 2M after treatment, and of starch at 2W, 1M and 2M after treatment. Consistent with its effects on carbohydrates, girdling significantly reduced arbuscular colonization (1M and 2M) and root hair length (1M). The correlations of arbuscular colonization and root hair length with concentrations of carbohydrates (fructose, sucrose and starch) were significant only under girdling treatment. Under conditions of hexose starvation caused by girdling, litchi seedlings exhibited significantly upregulated neutral invertase activity in sucrose-cleaving parts and downregulated sucrose phosphate synthase and sucrose synthase (synthesis direction) in sucrose synthesis parts. The correlations of arbuscular colonization with levels of sucrose-cleaving enzymes (neutral invertase and acid invertase) and root hair length with levels of sucrose-cleaving enzymes (neutral invertase and acid invertase) were also significant only under girdling treatment. Our findings indicated that AM colonization was more sensitive to carbohydrates than root hair length in litchi seedlings. Furthermore, girdling likely affected AM colonization and root hair length by decreasing the carbohydrate contents and regulating the activities of sucrose-metabolising enzymes.

As a non-climacteric fruit, longan does not continue to ripen until harvest due to pericarp browning and aril breakdown. The patterns of fruit growth and changes in physico-chemical properties of longan fruits (‘cv. Shixia’) after post-anthesis (DPA) were investigated over two different year seasons, with the aim to identify a reliable maturity index for harvest. Fruit growth, based on fruit weight, volume and diameter, followed a smooth sigmoidal type of curve for eleven selected periods. Vc contents showed an ascending trend in aril. A similar variation was also demonstrated in the ratio of TSS/TA and activities of PPO and POD. However, MDA in aril showed less accumulation than that in pericarp, though the change trends of MDA were similar in both of tissues. By contrast, sucrose was the primary accumulated form in the later growth stage of longan fruit. Increases in the proportion of sucrose were associated with a decline of AI, NI, and SS-C activities and an increase of SPS activity approximately 70 DPA. Information on fruit morphology and physico-chemical properties is benefit for better understanding of the physiological maturity status of longan. Based on charateristics of different indexes, TSS/TA and sucrose contents revealed increasing trend with advancing maturity and reached the steady status during 100–110 DPA. So their indexes was applied to determine the physiological mature stage of fruits, that would present the optimum values of harvesting properties desirable in the investigated cultivar. It could contribute to assist growers in assessing fruit readiness for harvest.

International audience; Resveratrol (Res) is a stilbenoid, a group of plant phenolic metabolites derived from stilbene that possess activities against pests, pathogens, and abiotic stresses. Only a few species, including grapevine (Vitis), synthesize and accumulate Res. Although stilbene synthases (STSs) have been isolated and characterized in several species, the gene regulatory mechanisms underlying stilbene biosynthesis are still largely unknown. Here, we characterize a grapevine WRKY transcription factor, VvWRKY8, that regulates the Res biosynthetic pathway. Transient and stable overexpression of VvWRKY8 in grapevine results in decreased expression of VvSTS15/21 and VvMYB14, as well as in a reduction of Res accumulation. VvWRKY8 does not bind to or activate the promoters of VvMYB14 and VvSTS15/21; however, it physically interacts with VvMYB14 proteins through their N-terminal domains to prevent them from binding to the VvSTS15/21 promoter. Application of exogenous Res results in the stimulation of VvWRKY8 expression and in a decrease of VvMYB14 and VvSTS15/21 expression in grapevine suspension cells, and in the activation of the VvWRKY8 promoter in tobacco leaves. These results demonstrate that VvWRKY8 represses VvSTS15/21 expression and Res biosynthesis through interaction with VvMYB14. In this context, the VvMYB14-VvSTS15/21-Res-VvWRKY8 regulatory loop may be an important mechanism for the fine-tuning of Res biosynthesis in grapevine.

‘Sijihua’ longan (Dimocarpus longan Lour.) blossoms throughout the year, and hence it is a useful material for studies on the mechanism of flowering. However, few genomic resources such as DNA sequences or markers are currently available for ‘Sijihua’ longan. To increase our understanding of the genetic control of important flowering characteristics in ‘Sijihua’ longan, we constructed a mixed cDNA library of ‘Sijihua’ longan using Illumina paired-end sequencing technology and obtained a total of 90,069,246 high-quality reads. Among the unigenes, 43.16% (59,588) had at least one BLASTX hit against the Arabidopsis thaliana sequence database and 42.83% (59,130) had significant similarity with proteins in the NCBI non-redundant protein database. Of these annotated unigenes, a total of 15,956 (11.56%) were mapped onto 271 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database. Furthermore, 11,402 unigenes were converted into 13,236 potential simple sequence repeats (SSRs). Dinucleo...

Extended Biologische Bundesantalt, Bundessortenamt and Chemische Industrie scale was applied to achieve precise and normative description of each growth stage of longan. The entire growth cycle of longan was divided into seven primary stages, namely, development of shoots, leaves and branches, formation of inflorescence, flowering, fruit development and maturity. These primary stages were further subdivided into 47 secondary stages. This study focused on the entire fruit development process of longan. The correlation between phenology, temperature and humidity was also discussed. Knowledge of these rules will provide guidance for the implementation of production management measures, including fertilisation, disease and pest control, branch control, flower induction, flower and fruit retention and application of growth regulator. The present findings will also help longan planters to adopt the most appropriate cultivation and management measures according to the climate conditions and growth status of the trees.

Fruit cracking has long been a topic of great concern for growers and researchers of litchi (Litchi chinensis Sonn.). To understand the molecular mechanisms underlying fruit cracking, high-throughput RNA sequencing (RNA-Seq) was first used for de novo assembly and characterization of the transcriptome of cracking pericarp of litchi. Comparative transcriptomic analyses were performed on non-cracking and cracking fruits. A total of approximately 26 million and 29 million high quality reads were obtained from the two groups of samples, and were assembled into 46,641 unigenes with an average length of 993 bp. These unigenes can be useful resources for future molecular studies of the pericarp in litchi. Furthermore, four genes (LcAQP, 1, LcPIP, 1, LcNIP, 1, LcSIP, 1) involved in water transport, five genes (LcKS, 2, LcGA2ox, 2, LcGID1, 1) involved in GA metabolism, 21 genes (LcCYP707A, 2, LcGT, 9, Lcβ-Glu, 6, LcPP2C, 2, LcABI1, 1, LcABI5, 1) involved in ABA metabolism, 13 genes (LcTPC, 1, Ca2+/H+ exchanger, 3, Ca2+-ATPase, 4, LcCDPK, 2, LcCBL, 3) involved in Ca transport and 24 genes (LcPG, 5, LcEG, 1, LcPE, 3, LcEXP, 5, Lcβ-Gal, 9, LcXET, 1) involved in cell wall metabolism were identified as genes that are differentially expressed in cracked fruits compared to non-cracked fruits. Our results open new doors to further understand the molecular mechanisms behind fruit cracking in litchi and other fruits, especially Sapindaceae plants.

Comparative transcriptome analysis of litchi ( Litchi chinensis Sonn.) buds at two developmental stages revealed multiple processes involving various phytohormones regulating floral initiation, and expression of numerous flowering-related genes. Floral initiation is a critical and complicated plant developmental process involving interactions of numerous endogenous and environmental factors, but little is known about the complex network regulating floral initiation in litchi (Litchi chinensis Sonn.). Illumina second-generation sequencing is an efficient method for obtaining massive transcriptional information resulting from phase changes in plant development. In this study, comparative transcriptomic analysis was performed with resting and emerging panicle stage buds, to gain further understanding of the molecular mechanisms involved in floral initiation in litchi. Abundance analysis identified 5,928 unigenes exhibiting at least twofold differences in expression between the two bud stages. Of these, 4,622 unigenes were up-regulated and 1,306 were down-regulated in panicle-emerging buds compared with resting buds. KEGG pathway enrichment analysis revealed that unigenes exhibiting differential expression were involved in the metabolism and signal transduction of various phytohormones. The expression levels of unigenes annotated as auxin, cytokinin, jasmonic acid, and salicylic acid biosynthesis were up-regulated, whereas those unigenes annotated as abscisic acid biosynthesis were down-regulated during floral initiation. In addition, 188 unigenes exhibiting sequence similarities to known flowering-related genes from other plants were differentially expressed during floral initiation. Thirteen genes were selected for confirmation of expression levels using quantitative-PCR. Our results provide abundant sequence resources for studying mechanisms underlying floral initiation in litchi and establish a platform for further studies of litchi and other evergreen fruit trees.

With the development of molecular quantitative genetics, particularly, genetic linkage map construction, quantitative trait loci mapping or genes fine mapping and association analysis etc., more and more PCR products separated in polyacrylamide gels need to be silver-stained. However, conventional silver-staining procedures are complicated and time-consuming as they require a lot of preparation and handling of several solutions prior to use. In this study, a simple and rapid protocol for silver staining of PCR products was developed. The number of steps was reduced compared to conventional protocols, thus achieving detection of PCR products in 7 min, saving time and resources. Fixation and staining solution and developing solution in present staining procedure allowed a reutilization for 12 and 8 times, respectively, reducing the cost greatly. Meanwhile, the sensitivity was significantly improved with the improved method and the minimum of 0.097 ng/μL of DNA amount can be detected in denaturing polyacrylamide gel. The protocol developed in this study will facilitate the development of molecular quantitative genetics.

This study presents codes and detailed crop-specific descriptions for the growth stages of the lychee tree in southern China. Our codes are based on the extended Biologische Bundesantalt, Bundessortenamt, and Chemische Industrie (BBCH)-scale and describe the growth stages of the lychee plant using a three-digit numerical system. A total of 7 principal growth stages are described for bud, leaf, and shoot development, inflorescence emergence, flowering, fruit development, and fruit maturity. In addition, 41 secondary growth stages are described. The extended BBCH-scale for lychee presented in this study is broadly applicable because it describes all the phenophases pertaining to bud, shoot, leaf, panicle, and fruit development, as well as the growth pattern of the shoots and their seasonal variation. These data should facilitate more effective management of lychee orchards and contribute to the standardization of international testing systems for fruit growing.

The diurnal change of LcFT1 expression. The relative RT-qPCR expression level of LcFT1 was shown on the y-axis, and the sampled time was indicated on the x-axis. Actin was used as the internal control. The color white represented day, gray stood for night. Bars represent the standard error (nâ =â 3). (PDF 30 kb)

Schematics of the transcriptome sequencing analysis in litchi. (A) Experiment pipeline of transcriptome. Beads with Oligo(dT) are used to isolate poly(A) mRNA after total RNA is collected from eukaryote. Fragmentation buffer is added for interrupting mRNA to short fragments. Taking these short fragments as templates, random hexamer-primer is used to synthesize the first-strand cDNA. The second-strand cDNA is synthesized using buffer, dNTPs, RNaseH and DNA polymerase I, respectively. Short fragments are purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly (A). After that, the short fragments are connected with sequencing adapters. And, after the agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. At last, the library could be sequenced using Illumina HiSeqâ ˘ 2500. (B) Workflow of the data assembly. Transcriptome de novo assembly is carried out with short reads assembling program-Trinity. Trinity firstly combines reads with certain length of overlap to form longer fragments without N, which are called contigs. Then, these contigs will be taken into further process of sequence cluster with sequence clustering software to form longer sequences without N, Such sequences are defined as Unigenes. When multiple samples from a same species are sequenced, Unigenes from each sampleâ s assembly can be taken into further process of sequence splicing and redundancy removing with sequence clustering software to acquire non-redundant Unigenes as long as possible. (PDF 120 kb)

Primers of candidate and reference genes used for RT-qPCR. (PDF 90 kb)

Histogram of GO classifications for litchi leaf transcriptome. The unigenes were assigned to three main categories: biological process, cellular component, and molecular function. The left and right-hand y-axes indicate the percentage and number of annotated unigenes respectively. (PDF 224 kb)

COG functional classifications of the litchi leaf transcriptome. COG is a database where orthologous gene products are classified. Every protein in COG is assumed to evolve from an ancestor protein, and the whole database is built on coding proteins with complete genome as well as system evolution relationships of bacteria, algae and eukaryotic creatures. Unigenes are aligned to COG database to predict and classify possible functions of Unigenes. A total of 18,497 unigenes were classified into 25 COG categories. (PDF 54 kb)

Length distribution and number of Contigs (A) and Unigenes (B) assembly. The horizontal coordinates are lengths and the vertical coordinates are numbers of Contigs and Unigenes. (PDF 19 kb)