Single-molecule long-read sequencing of the full-length transcriptome of Rhododendron lapponicum L.

Rhododendron lapponicum L. is a familiar ornamental plant worldwide with important ornamental and economic value. However, a full-length R. lapponicum transcriptome is still lacking. In the present study, we used the Pacific Biosciences single-molecule real-time sequencing technology to generate the R. lapponicum transcriptome. A total of 346,270 full-length non-chimeric reads were generated, from which we obtained 75,002 high-quality full-length transcripts. We identified 55,255 complete open reading frames, 7,140 alternative splicing events and 2,011 long non-coding RNAs. In gene annotation analyses, 71,155, 33,653, 30,359 and 31,749 transcripts were assigned to the Nr, GO, COG and KEGG databases, respectively. Additionally, 3,150 transcription factors were detected. KEGG pathway analysis showed that 96 transcripts were identified coding for the enzymes associated with anthocyanin synthesis. Furthermore, we identified 64,327 simple sequence repeats from 45,319 sequences, and 150 pairs of primers were randomly selected to develop SSR markers. This study provides a large number of full-length transcripts, which will facilitate the further study of the genetics of R. lapponicum.

Identification of pre-fertilization reproductive barriers and the underlying cytological mechanism in crosses among three petal-types of Jasminum sambac and their relevance to phylogenetic relationships.

Crosses among single-, double- and multi-petal jasmine cultivars (Jasminum sambac Aiton) are unable to easily generate hybrids. To identify the reproductive barriers restricting hybrid set, dynamic changes in jasmine pollen viability and pistil receptivity were compared at different flowering stages. Pollen-pistil interactions in six reciprocal crosses were also investigated to characterize pollen-stigma compatibility. Additionally, paraffin sections of pollinated embryo sacs were prepared for subsequent analyses of developmental status. Furthermore, pistil cell ultrastructural characteristics were observed to reveal cytological mechanism regulating pistil receptivity and the pollen-pistil interactions. We observed that pollen viability and stigma receptivity varied depending on petal phenotype and flowering stage and were easily lost during flowering. Different reciprocal crosses exhibited varied pollen-stigma compatibilities according to the pollen germination rates. Although some pollen grains germinated normally on maternal stigmas, the pollen tubes were arrested in the pistils and were unable to reach the ovaries. Additionally, the embryo sacs remained unfertilized until degenerating. Therefore, jasmine crosses are affected by pre-fertilization reproductive barriers. Low pollen fertility and poor stigma receptivity are detrimental to pollen germination and pollen-pistil compatibility, indicating they are two factors affecting hybrid set. Ultrastructural observation of the pistil cells revealed that cell death occurred during flowering. Thus, the early and rapid senescence of pistils is likely responsible for the decreased pistil receptivity and inhibited pollen tube growth. These findings may be relevant for future jasmine hybridizations. They provide new insights for the development of methods to overcome reproductive barriers and may also be useful for clarifying the phylogenetic relationships among jasmine cultivars with differing petal phenotypes.

Transcriptome-based discovery of pathways and genes related to resistance against Fusarium head blight in wheat landrace Wangshuibai.

BACKGROUND: Fusarium head blight (FHB), caused mainly by Fusarium graminearum (Fg) Schwabe (teleomorph: Gibberellazeae Schwble), brings serious damage to wheat production. Chinese wheat landrace Wangshuibai is one of the most important resistance sources in the world. The knowledge of mechanism underlying its resistance to FHB is still limited. RESULTS: To get an overview of transcriptome characteristics of Wangshuibai during infection by Fg, a high-throughput RNA sequencing based on next generation sequencing (NGS) technology (Illumina) were performed. Totally, 165,499 unigenes were generated and assigned to known protein databases including NCBI non-redundant protein database (nr) (82,721, 50.0%), Gene Ontology (GO) (38,184, 23.1%), Swiss-Prot (50,702, 30.6%), Clusters of orthologous groups (COG) (51,566, 31.2%) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) (30,657, 18.5%), as determined by Blastx search. With another NGS based platform, a digital gene expression (DGE) system, gene expression in Wangshuibai and its FHB susceptible mutant NAUH117 was profiled and compared at two infection stages by inoculation of Fg at 24 and 48 hour, with the aim of identifying genes involved in FHB resistance. CONCLUSION: Pathogen-related proteins such as PR5, PR14 and ABC transporter and JA signaling pathway were crucial for FHB resistance, especially that mediated by Fhb1. ET pathway and ROS/NO pathway were not activated in Wangshuibai and may be not pivotal in defense to FHB. Consistent with the fact that in NAUH117 there presented a chromosome fragment deletion, which led to its increased FHB susceptibility, in Wangshuibai, twenty out of eighty-nine genes showed changed expression patterns upon the infection of Fg. The up-regulation of eight of them was confirmed by qRT-PCR, revealing they may be candidate genes for Fhb1 and need further functional analysis to confirm their roles in FHB resistance.

A fast-neutron induced chromosome fragment deletion of 3BS in wheat landrace Wangshuibai increased its susceptibility to Fusarium head blight.

Fusarium head blight (FHB), also called wheat scab, is an important disease in warm and humid regions worldwide, which not only reduces crop yield and grain quality, but also is a major safety concern in food and feed production due to mycotoxin contamination. Growing wheat cultivars with FHB resistance is one of the most economical and effective means to control the disease. Chinese wheat landrace Wangshuibai is an important resistant source from southern China. Several resistance QTLs in Wangshuibai were identified and mapped on chromosomes or chromosomal arms including 3BS, 4B, 6BS, 7AL, etc. In the present research, a mutant with increased FHB susceptibility, designated as NAUH117, was identified from the M(1) progenies of Wangshuibai irradiated by fast neutron. Genetic analysis of the F (1), F (2), and F (2:3) families from the reciprocal cross of Wangshuibai and NAUH117 indicated that NAUH117 was a recessive mutant. Genome-wide molecular marker analysis identified a deletion in the short arm of chromosome 3B of NAUH117, spanning the region of FL0.57 to FL1.00 that covers the locus of Fhb1 previously mapped on chromosome 3BS. Further molecular cytogenetics characterization by bi-color fluorescence in situ hybridization using three repetitive sequences, pSc119.2, pAs1 and GAA-satellite indicated that a multiple chromosome rearrangements occurred in chromosomes 3B, 6B, 3D, 4D, and 3A of the mutant. During these processes, a distal fragment of chromosome arm 3BS was eliminated, which is confirmed by molecular marker analysis. Four markers covered the deletion fragment were used for analysis of the F (2) population. The result showed that the 3BS deletion was only present in the susceptible plants, indicating that the deletion of 3BS fragment in NAUH117 increased susceptibility to FHB. The susceptible mutant will be valuable for the validation of the contribution of the resistant QTL located on 3BS, and for the characterization of the molecular mechanisms of FHB resistance in Wangshuibai.