The species Brassica rapa (2n=20, AA) is an important vegetable and oilseed crop, and serves as an excellent model for genomic and evolutionary research in Brassica species. With the availability of ...whole genome sequence of B. rapa, it is essential to further determine the activity of all functional elements of the B. rapa genome and explore the transcriptome on a genome-wide scale. Here, RNA-seq data was employed to provide a genome-wide transcriptional landscape and characterization of the annotated and novel transcripts and alternative splicing events across tissues.
RNA-seq reads were generated using the Illumina platform from six different tissues (root, stem, leaf, flower, silique and callus) of the B. rapa accession Chiifu-401-42, the same line used for whole genome sequencing. First, these data detected the widespread transcription of the B. rapa genome, leading to the identification of numerous novel transcripts and definition of 5'/3' UTRs of known genes. Second, 78.8% of the total annotated genes were detected as expressed and 45.8% were constitutively expressed across all tissues. We further defined several groups of genes: housekeeping genes, tissue-specific expressed genes and co-expressed genes across tissues, which will serve as a valuable repository for future crop functional genomics research. Third, alternative splicing (AS) is estimated to occur in more than 29.4% of intron-containing B. rapa genes, and 65% of them were commonly detected in more than two tissues. Interestingly, genes with high rate of AS were over-represented in GO categories relating to transcriptional regulation and signal transduction, suggesting potential importance of AS for playing regulatory role in these genes. Further, we observed that intron retention (IR) is predominant in the AS events and seems to preferentially occurred in genes with short introns.
The high-resolution RNA-seq analysis provides a global transcriptional landscape as a complement to the B. rapa genome sequence, which will advance our understanding of the dynamics and complexity of the B. rapa transcriptome. The atlas of gene expression in different tissues will be useful for accelerating research on functional genomics and genome evolution in Brassica species.
Crop genomics and breeding CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) proteins belong to a small peptide family in plants. During plant development,
CLE
gene family members play a pivotal role ...in regulating cell-to-cell communication and stem cell maintenance. However, the evolutionary process and functional importance of
CLE
s are unclear in Brassicaceae. In this study, a total of 70
BnCLE
s were identified in
Brassica napus
(2n = 4x = 38, A
n
C
n
): 32 from the A
n
subgenome, 36 from the C
n
subgenome, and 2 from the unanchored subgenome. Meanwhile, 29
BrCLE
and 32
BoCLE
genes were explored in
Brassica rapa
(2n = 2x = 20, A
r
) and
Brassica oleracea
(2n = 2x = 18, C
o
). Phylogenetic analysis revealed that 163
CLE
s derived from three
Brassica
species and
Arabidopsis thaliana
can be divided into seven subfamilies. Homology and synteny analyses indicated whole-genome triplication (WGT) and segmental duplication may be the major contributors to the expansion of
CLE
family. In addition, RNA-seq and qPCR analysis indicated that 19 and 16
BnCLE
s were more highly expressed in immature seeds and roots than in other tissues. Some
CLE
gene pairs exhibited different expression patterns in the same tissue, which indicated possible functional divergence. Furthermore, genetic variations and regional association mapping analysis indicated that 12
BnCLE
s were potential genes for regulating important agronomic traits. This study provided valuable information to understand the molecular evolution and biological function of
CLE
s in
B. napus
and its diploid progenitors, which will be helpful for genetic improvement of high-yield breeding in
B. napus
.
MicroRNAs (miRNAs) are small non-coding RNA molecules that are processed from large 'hairpin' precursors and function as post-transcriptional regulators of target genes. Although many individual ...miRNAs have recently been extensively studied, there has been very little research on miRNA transcriptomes in teleost fishes. By using high throughput sequencing technology, we have identified 167 and 166 conserved miRNAs (belonging to 108 families) in bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), respectively. We compared the expression patterns of conserved miRNAs by means of hierarchical clustering analysis and log2 ratio. Results indicated that there is not a strong correlation between sequence conservation and expression conservation, most of these miRNAs have similar expression patterns. However, high expression differences were also identified for several individual miRNAs. Several miRNA* sequences were also found in our dataset and some of them may have regulatory functions. Two computational strategies were used to identify novel miRNAs from un-annotated data in the two carps. A first strategy based on zebrafish genome, identified 8 and 22 novel miRNAs in bighead carp and silver carp, respectively. We postulate that these miRNAs should also exist in the zebrafish, but the methodologies used have not allowed for their detection. In the second strategy we obtained several carp-specific miRNAs, 31 in bighead carp and 32 in silver carp, which showed low expression. Gain and loss of family members were observed in several miRNA families, which suggests that duplication of animal miRNA genes may occur through evolutionary processes which are similar to the protein-coding genes.
Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica ...oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana.
Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species.
This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome triplication analysis in B. oleracea, B. rapa and A. thaliana genomes, our study provides insight into the evolutionary history of NBS-encoding genes after divergence of A. thaliana and the Brassica lineage. These results together with expression pattern analysis of NBS-encoding orthologous genes provide useful resource for functional characterization of these genes and genetic improvement of relevant crops.
Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, ...kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives.
We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea, Brassica rapa and Arabidopsis thaliana, synonymous (Ks) and non-synonymous (Ka) substitution rates between orthologous gene pairs, gene families or clusters, and differences in quantity, category, and distribution of transposable elements on chromosomes. Bolbase provides useful search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can be used to extract annotations of genome components, identify similar sequences and visualize syntenic regions among species. Users can download all genomic data and explore comparative genomics in a highly visual setting.
Bolbase is the first resource platform for the B. oleracea genome and for genomic comparisons with its relatives, and thus it will help the research community to better study the function and evolution of Brassica genomes as well as enhance molecular breeding research. This database will be updated regularly with new features, improvements to genome annotation, and new genomic sequences as they become available. Bolbase is freely available at http://ocri-genomics.org/bolbase.
Trehalose and trehalose-6 phosphate played important roles in floral organ development, embryonic development, cell morphogenesis, and signal transduction under abiotic stress. However, little is ...known about the trehalose-6-phosphate synthase (
) gene family in
. In this study, in total, 26
genes in
(
genes) were identified and classified into two groups. In each group, the
genes showed relatively conserved gene structures. The protein-protein interaction (PPI) network and enrichment analysis indicated that
genes were involved in the glycolysis/gluconeogenesis, fructose and mannose metabolism, galactose metabolism, pentose phosphate pathway, carbohydrate transmembrane transport, trehalose-phosphatase activity, etc. The expression of
genes varied greatly across different tissues, while most of the
genes showed a considerable improvement in expression under different abiotic stresses, indicating that
genes were significantly responsive to the abiotic treatments. In addition, the association mapping analysis revealed that eight
genes were potential regulators of particular agronomic traits. Among them, the gene
was significantly associated with the primary flowering time (PFT), full flowering time (FFT1), and final flowering time (FFT2), suggesting that
genes may play an important role in regulating key agronomic traits in
. In summary, our research provides a better understanding of
genes, facilitates the breeding of superior
varieties, and paves the way for future functional studies.
E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been ...discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies show their role in plant adaptations processes against the external environment. Presently, the functions of ARI proteins are largely unknown in plants. Therefore, in this study, we performed genome-wide analysis to identify the
gene family and explore their potential importance in
. A total of 39
genes were identified in the
genome and were classified into three subfamilies (A, B and C) based on phylogenetic analysis. The protein-protein interaction networks and enrichment analysis indicated that
genes could be involved in endoreduplication, DNA repair, proteasome assembly, ubiquitination, protein kinase activity and stress adaptation. The transcriptome data analysis in various tissues provided us an indication of some
genes' functional importance in tissue development. We also identified potential
genes that were significantly responsive towards the abiotic stresses. Furthermore, eight
genes were identified as candidate genes for multiple agronomic traits through association mapping analysis in
; among them,
, which is the ortholog of
, was significantly associated with ten agronomic traits. This study provided useful information on
genes, which could aid targeted functional research and genetic improvement for breeding in
.
Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although
genes have ...been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in
. In the present study, 200 putative
were identified in
, which were clustered into 18 subgroups based on phylogenetic analysis.
s within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of
-acting regulatory elements in
promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three
s were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the
family in
and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of
.
The potential infection biology of
Plasmodiophora brassicae
in resistant hosts and non-hosts is still not completely understood. Clubroot resistance assay on European clubroot differentials (ECD) set ...revealed that ECD10 (
Brassica napus
) and ECD4 (
Brassica rapa
) show a complete resistance to the tested
P. brassicae
isolate in contrast to highly susceptible hosts Westar (
B. napus
) and ECD5 (
B. rapa
). Previously, we used fluorescent probe-based confocal microscopy (FCM) to refine the life cycle of
P. brassicae
and indicate the important time points during its infection in
Arabidopsis
. Here, we used FCM to systematically investigate the infection of
P. brassicae
in two resistant host species ECD10 and ECD4 and two non-host crops wheat and barley at each indicated time points, compared with two susceptible hosts Westar and ECD5. We found that
P. brassicae
can initiate the primary infection phase and produce uninucleate primary plasmodia in both resistant hosts and non-hosts just like susceptible hosts at 2 days post-inoculation (dpi). Importantly,
P. brassicae
can develop into zoosporangia and secondary zoospores and release the secondary zoospores from the zoosporangia in resistant hosts at 7 dpi, comparable to susceptible hosts. However, during the secondary infection phase, no secondary plasmodium was detected in the cortical cells of both resistant hosts in contrast to massive secondary plasmodia present in the cortex tissue of two susceptible hosts leading to root swelling at 15 dpi. In both non-host crops, only uninucleate primary plasmodia were observed throughout roots at 7 and 15 dpi. Quantitative PCR based on DNA revealed that the biomass of
P. brassicae
has no significant increase from 2 dpi in non-host plants and from 7 dpi in resistant host plants, compared to the huge biomass increase in susceptible host plants from 2 to 25 dpi. Our study reveals that the primary infection phase in the root epidermis and the secondary infection phase in the cortex tissue are, respectively, blocked in non-hosts and resistant hosts, contributing to understanding of cellular and molecular mechanisms underlying clubroot non-host and host resistance.
Rapeseed (
Brassica napus
) is an allotetraploid crop that is the main source of edible oils and feed proteins in the world. The ideal plant architecture breeding is a major objective of rapeseed ...breeding and determining the appropriate plant height is a key element of the ideal plant architecture. Therefore, this study aims to improve the understanding of the genetic controls underlying plant height. The plant heights of 230 rapeseed accessions collected worldwide were investigated in field experiments over two consecutive years in Wuhan, China. Whole-genome resequencing of these accessions yielded a total of 1,707,194 informative single nucleotide polymorphisms (SNPs) that were used for genome-wide association analysis (GWAS). GWAS and haplotype analysis showed that
BnaA01g09530D
, which encodes BRASSINOSTEROID-INSENSITIVE 2 and belongs to the
GLYCOGEN SYNTHASE KINASE 3
(
GSK3
) family, was significantly associated with plant height in
B. napus
. Moreover, a total of 31
BnGSK3s
with complete domains were identified from
B. napus
genome and clustered into four groups according to phylogenetic analysis, gene structure, and motif distribution. The expression patterns showed that
BnGSK3s
exhibited significant differences in 13 developmental tissues in
B. napus
, suggesting that
BnGSK3s
may be involved in tissue-specific development. Sixteen
BnGSK3
genes were highly expressed the in shoot apical meristem, which may be related to plant height or architecture development. These results are important for providing new haplotypes of plant height in
B. napus
and for extending valuable genetic information for rapeseed genetic improvement of plant architecture.
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