Genome-wide exploration and characterization of miR172/euAP2 genes in Brassica napus L. for likely role in flower organ development

Genome-wide analysis of glutamate receptor gene family in allopolyploid Brassica napus and its diploid progenitors

Ionotropic glutamate receptors are ligand-gated nonselective cation channels that mediate neurotransmission in the central nervous system of animals. Plants possess homologous proteins called glutamate receptor-like channels (GLRs) which are involved in vital physiological processes including seed germination, long-distance signaling, chemotaxis, Ca2+ signaling etc. Till now, a comprehensive genome-wide analysis of the GLR gene family members in different economically important species of Brassica is missing. Considering the origin of allotetraploid Brassica napus from the hybridization between the diploid Brassica oleracea and Brassica rapa, we have identified 11, 27 and 65 GLR genes in B. oleracea, B. rapa and B. napus, respectively showing an expansion of this gene family in B. napus. Chromosomal locations revealed several tandemly duplicated GLR genes in all the three species. Moreover, the gene family expanded in B. napus after allopolyploidization. The phylogenetic analysis showed that the 103 GLRs are classified into three main groups. The exon-intron structures of these genes are not very conserved and showed wide variation in intron numbers. However, protein sequences are much conserved as shown by the presence of ten short amino acid sequence motifs. Predicted cis-acting elements in 1 kb promoters of GLR genes are mainly involved in light, stress and hormone responses. RNA-seq analysis showed that in B. oleracea and B. rapa, some GLRs are more tissue specific than others. In B. napus, some GLRs are downregulated under cold stress, while others are upregulated. In summary, this bioinformatic study of the GLR gene family of the three Brassica species provides evidence for the expansion of this gene family in B. napus and also provided useful information for in-depth studies of their biological functions in Brassica.

Genome-wide identification of Apetala2 gene family in Hypericum perforatum L and expression profiles in response to different abiotic and hormonal treatments

The Apetala2 (AP2) gene family of transcription factors (TFs) play important functions in plant development, hormonal response, and abiotic stress. To reveal the biological functions and the expression profiles of AP2 genes in Hypericum perforatum, genome-wide identification of HpAP2 family members was conducted.

Methods

We identified 21 AP2 TFs in H. perforatum using bioinformatic methods; their physical and chemical properties, gene structures, conserved motifs, evolutionary relationships, cis-acting elements, and expression patterns were investigated.

Results

We found that based on the structural characteristics and evolutionary relationships, the HpAP2 gene family can be divided into three subclasses: euANT, baselANT, and euAP2. A canonical HpAP2 TF shared a conserved protein structure, while a unique motif 6 was found in HpAP2_1, HpAP2_4, and HpAP2_5 from the euANT subgroup, indicating potential biological and regulatory functions of these genes. Furthermore, a total of 59 cis-acting elements were identified, most of which were associated with growth, development, and resistance to stress in plants. Transcriptomics data showed that 57.14% of the genes in the AP2 family were differentially expressed in four organs. For example, HpAP2_18 was specifically expressed in roots and stems, whereas HpAP2_17 and HpAP2_11 were specifically expressed in leaves and flowers, respectively. HpAP2_5, HpAP2_11, and HpAP2_18 showed tissue-specific expression patterns and responded positively to hormones and abiotic stresses.

Conclusion

These results demonstrated that the HpAP2 family genes are involved in diverse developmental processes and generate responses to abiotic stress conditions in H. perforatum. This article, for the first time, reports the identification and expression profiles of the AP2 family genes in H. perforatum, laying the foundation for future functional studies with these genes.

Comparative transcriptomic analysis of male and females in the dioecious weeds Amaranthus palmeri and Amaranthus tuberculatus

BACKGROUND

Waterhemp (Amaranthus tuberculatus (Moq.) Sauer) and Palmer amaranth (Amaranthus palmeri S. Wats.) are two dioecious and important weed species in the world that can rapidly evolve herbicide-resistance traits. Understanding these two species' dioecious and sex-determination mechanisms could open opportunities for new tools to control them. This study aims to identify the differential expression patterns between males and females in A. tuberculatus and A. palmeri. Multiple analyses, including differential expression, co-expression, and promoter analyses, used RNA-seq data from multiple tissue types to identify putative essential genes for sex determination in both dioecious species.

RESULTS

Genes were identified as potential key players for sex determination in A. palmeri. Genes PPR247, WEX, and ACD6 were differentially expressed between the sexes and located at scaffold 20 within or near the male-specific Y (MSY) region. Multiple genes involved with flower development were co-expressed with these three genes. For A. tuberculatus, no differentially expressed gene was identified within the MSY region; however, multiple autosomal class B and C genes were identified as differentially expressed and possible candidate genes.

CONCLUSIONS

This is the first study comparing the global expression profile between males and females in dioecious weedy Amaranthus species. Results narrow down putative essential genes for sex-determination in A. palmeri and A. tuberculatus and also strengthen the hypothesis of two different evolutionary events for dioecy within the genus.

Genome-wide survey of catalase genes in Brassica rapa, Brassica oleracea, and Brassica napus: identification, characterization, molecular evolution, and expression profiling of BnCATs in response to salt and cadmium stress

Catalase (CAT, EC 1.11.1.6), one of the most important antioxidant enzymes, can control excess levels of H₂O₂ produced under oxidative stress in plants. In this study, 16, 8, and 7 CAT genes in the genome of Brassica napus, B. rapa, and B. oleracea were identified, respectively. Phylogenetic studies showed that CATs could be divided into two main groups, each containing specific monocotyledon and dicotyledon subgroups. Motifs, gene structure, and intron phase of CATs in B. napus, Brassica rapa, and Brassica oleracea are highly conserved. Analysis of codon usage bias showed the mutation pressure and natural selection of the codon usage of CATs. Segmental duplication and polyploid were major factors in the expansion of this gene family in B. napus, and genes have experienced  negative selection during evolution. Existence of hormones and stress-responsive cis-elements and identifying miRNA molecules affecting CATs showed that these genes are complexly regulated at the transcriptional and posttranscriptional levels. Based on RNA-seq data, CATs are divided into two groups; the first group has moderate and specific expression in flowers, leaves, stems, and roots, while the second group shows expression in most tissues. qRT-PCR analysis showed that the expression of these genes is dynamic and has a specific expression consistent with other CAT genes in response to salinity and cadmium (Cd) stresses. These results provide information for further investigation of the function of CAT genes in response to stresses and the development of tolerant  plants.

Identification of Conserved and Novel MicroRNAs with their Targets in Garden Pea (Pisum Sativum L.) Leaves by High-Throughput Sequencing

MicroRNAs (miRNAs) are single-stranded, endogenous, non-coding RNAs of 20–24 nucleotides that play a significant role in post-transcriptional gene regulation. Various conserved and novel miRNAs have been characterized, especially from the plant species whose genomes were well-characterized; however, information on miRNA in economically important plants such as pea ( Pisum sativum L.) is limited. In this study, I have identified conserved and novel miRNA in garden pea plant leaves samples along with their targets by analyzing the next generation sequencing (NGS) data. The raw data obtained from NGS were processed and 1.38 million high-quality non-redundant reads were retained for analysis, this tremendous quantity of reads indicates a large and diverse small RNA population in pea leaves. After analyzing the deep sequencing data, 255 conserved and 11 novel miRNAs were identified in the garden pea leaves sample. Utilizing psRNATarget tool, the miRNA targets of conserved and novel miRNA were predicted. Further, the functional annotation of the miRNA targets were performed using blast2Go software and the target gene products were predicted. The miRNA target gene products along with GO_ID (Gene Ontology Identifier) were categorized into biological processes, cellular components, and molecular functions. The information obtained from this study will provide genomic resources that will help in understanding miRNA-mediated post-transcriptional gene regulation in garden peas.

Multiple Functions of MiRNAs in Brassica napus L

The worldwide climate changes every year due to global warming, waterlogging, drought, salinity, pests, and pathogens, impeding crop productivity. Brassica napus is one of the most important oil crops in the world, and rapeseed oil is considered one of the most health-beneficial edible vegetable oils. Recently, miRNAs have been found and confirmed to control the expression of targets under disruptive environmental conditions. The mechanism is through the formation of the silencing complex that mediates post-transcriptional gene silencing, which pairs the target mRNA and target cleavage and/or translation inhibition. However, the functional role of miRNAs and targets in B. napus is still not clarified. This review focuses on the current knowledge of miRNAs concerning development regulation and biotic and abiotic stress responses in B. napus. Moreover, more strategies for miRNA manipulation in plants are discussed, along with future perspectives, and the enormous amount of transcriptome data available provides cues for miRNA functions in B. napus. Finally, the construction of the miRNA regulatory network can lead to the significant development of climate change-tolerant B. napus through miRNA manipulation.

An Integrated Analysis of Transcriptome and miRNA Sequencing Provides Insights into the Dynamic Regulations during Flower Morphogenesis in Petunia

Published genome sequences can facilitate multiple genome sequencing studies of flower development, which can serve as the basis for later analysis of variation in flower phenotypes. To identify potential regulators related to flower morphology, we captured dynamic expression patterns under five different developmental stages of petunia flowers, a popular bedding plant, using transcriptome and miRNA sequencing. The significant transcription factor (TF) families, including MYB, MADS, and bHLH, were elucidated. MADS-box genes exhibited co-expression patterns with BBR-BPC, GATA, and Dof genes in different modules according to a weighted gene co-expression network analysis. Through miRNA sequencing, a total of 45 conserved and 26 novel miRNAs were identified. According to GO and KEGG enrichment analysis, the carbohydrate metabolic process, photosynthesis, and phenylalanine metabolism were significant at the transcriptomic level, while the response to hormone pathways was significantly enriched by DEmiR-targeted genes. Finally, an miRNA–RNA network was constructed, which suggested the possibility of novel miRNA-mediated regulation pathways being activated during flower development. Overall, the expression data in the present study provide novel insights into the developmental gene regulatory network facilitated by TFs, miRNA, and their target genes.

Plant RNA-mediated gene regulatory network

Not all transcribed RNAs are protein-coding RNAs. Many of them are non-protein-coding RNAs in diverse eukaryotes. However, some of them seem to be non-functional and are resulted from spurious transcription. A lot of non-protein-coding transcripts have a significant function in the translation process. Gene expressions depend on complex networks of diverse gene regulatory pathways. Several non-protein-coding RNAs regulate gene expression in a sequence-specific system either at the transcriptional level or post-transcriptional level. They include a significant part of the gene expression regulatory network. RNA-mediated gene regulation machinery is evolutionarily ancient. They well-evolved during the evolutionary time and are becoming much more complex than had been expected. In this review, we are trying to summarizing the current knowledge in the field of RNA-mediated gene silencing.

Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

CaAIL1 Acts Positively in Pepper Immunity against Ralstonia solanacearum by Repressing Negative Regulators

APETALA2 (AP2) subfamily transcription factors participate in plant growth and development, but their roles in plant immunity remain unclear. Here, we discovered that the AP2 transcription factor CaAIL1 functions in immunity against Ralstonia solanacearum infection (RSI) in pepper (Capsicum annuum). CaAIL1 expression was upregulated by RSI, and loss- and gain-of-function assays using virus-induced gene silencing and transient overexpression, respectively, revealed that CaAIL1 plays a positive role in immunity to RSI in pepper. Chromatin immunoprecipitation sequencing (ChIP-seq) uncovered a subset of transcription-factor-encoding genes, including CaRAP2-7, CaGATA17, CaGtf3a and CaTCF25, that were directly targeted by CaAIL1 via their cis-elements, such as GT or AGGCA motifs. ChIP-qPCR and electrophoretic mobility shift assays confirmed these findings. These genes, encoding transcription factors with negative roles in immunity, were repressed by CaAIL1 during pepper response to RSI, whereas genes encoding positive immune regulators such as CaEAS were derepressed by CaAIL1. Importantly, we showed that the atypical EAR motif (LXXLXXLXX) in CaAIL1 is indispensable for its function in immunity. These findings indicate that CaAIL1 enhances the immunity of pepper against RSI by repressing a subset of negative immune regulators during the RSI response through its binding to several cis-elements in their promoters.

Identification of miRNAs and their target genes in genic male sterility lines in Brassica napus by small RNA sequencing

BACKGROUND

Brassica napus is the third leading source of edible oil in the world. Genic male sterility (GMS) lines provide crucial material for harnessing heterosis for rapeseed. GMS lines have been used successfully for rapeseed hybrid production in China. MicroRNAs (miRNAs) play crucial regulatory roles in various plant growth, development, and stress response processes. However, reports on miRNAs that regulate the pollen development of GMS lines in B. napus are few.

RESULTS

In this study, 12 small RNA and transcriptome libraries were constructed and sequenced for the flower buds from the fertile and sterile lines of two recessive GMS (RGMS) lines, namely, "6251AB" and "6284AB". At the same time, 12 small RNA and transcriptome libraries were also constructed and sequenced for the flower buds from the fertile and sterile lines of two dominant GMS (DGMS) lines, namely, "4001AB" and "4006AB". Based on the results, 46 known miRNAs, 27 novel miRNAs on the other arm of known pre-miRNAs, and 44 new conserved miRNAs were identified. Thirty-five pairs of novel miRNA-3p/miRNA-5p were found. Among all the identified miRNAs, fifteen differentially expressed miRNAs with over 1.5-fold change between flower buds of sterile and fertile lines were identified, including six differentially expressed miRNAs between "4001A" and "4001B", two differentially expressed miRNAs between "4006A" and "4006B", four differentially expressed miRNAs between "6251A" and "6251B", and ten differentially expressed miRNAs between "6284A" and "6284B". The correlation analysis of small RNA and transcriptome sequencing was conducted. And 257 candidate target genes were predicted for the 15 differentially expressed miRNAs. The results of 5' modified RACE indicated that BnaA09g48720D, BnaA09g11120D, and BnaCnng51960D were cleaved by bna-miR398a-3p, bna-miR158-3p and bna-miR159a, respectively. Among the differentially expressed miRNAs, miR159 was chosen to analyze its function. Overexpression of bna-miR159 in Arabidopsis resulted in decreased seed setting rate, and shortened siliques, illustrating that miR159 may regulate the fertility and silique development in rapeseed.

CONCLUSIONS

Our findings provide an overview of miRNAs that are potentially involved in GMS and pollen development. New information on miRNAs and their related target genes are provided to exploit the GMS mechanism and reveal the miRNA networks in B. napus.

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development

Circular RNAs (circRNAs) are covalently closed RNA molecules generated by the back-splicing of exons from linear precursor mRNAs. Though various linear RNAs have been shown to play important regulatory roles in many biological and developmental processes, little is known about the role of their circular counterparts. In this study, we performed high-throughput RNA sequencing to delineate the expression profile and potential function of circRNAs during the five stages of pollen development in Brassica rapa. A total of 1180 circRNAs were detected in pollen development, of which 367 showed stage-specific expression patterns. Functional enrichment and metabolic pathway analysis showed that the parent genes of circRNAs were mainly involved in pollen-related molecular and biological processes such as mitotic and meiotic cell division, DNA processes, protein synthesis, protein modification, and polysaccharide biosynthesis. Moreover, by predicting the circRNA–miRNA network from our differentially expressed circRNAs, we found 88 circRNAs with potential miRNA binding sites, suggesting their role in post-transcriptional regulation of the genes. Finally, we confirmed the back-splicing sites of nine selected circRNAs using divergent primers and Sanger sequencing. Our study presents the systematic analysis of circular RNAs during pollen development and forms the basis of future studies for unlocking complex gene regulatory networks underpinning reproduction in flowering plants.

Relationship between Secondary Metabolism and miRNA for Important Flavor Compounds in Different Tissues of Tea Plant (Camellia sinensis) As Revealed by Genome-Wide miRNA Analysis

This study investigated the regulatory relationship between important flavor compounds and microRNA (miRNA) in nine different tissues of tea plant by analyzing the related metabolites, small RNAs (sRNAs), degradome, and coexpression network. A total of 272 differential expressed miRNAs (DEmiRNAs) were obtained, including 198 conserved miRNAs and 74 novel miRNAs. Meanwhile, the expression patterns of miR159-GAMYB, miR167-ARF, and miR396-GRF pairs were investigated by quantitative real-time polymerase chain reaction (qRT-PCR) and the target sites were verified by 5'RNA ligase-mediated RACE (5' RLM-RACE). Further coexpression analysis showed that the content of gallated catechins was significantly and negatively correlated with the expression of miR156, but positively correlated with the expression of miR166 and miR172. Additionally, the expression of miR169a, miR169l, and miR319h was shown to be positively correlated with the content of nongallated catechins and the experssion levels of ANRa, ANRb, and LARb. Moreover, important volatile compounds, such as linalool, geraniol, and 2-phenylethanol, were found to be highly positively correlated with the expression of miR171o, miRN71a, miRN71b, miRN71c, and miRN71d. Our data indicate that these miRNAs may play important roles in regulating the biosynthesis of flavor compounds in different tissues of tea plant.

Turnip mosaic virus in oilseed rape activates networks of sRNA-mediated interactions between viral and host genomes

Virus-induced plant diseases in cultivated plants cause important damages in yield. Although the mechanisms of virus infection are intensely studied at the cell biology level, only little is known about the molecular dialog between the invading virus and the host genome. Here we describe a combinatorial genome-wide approach to identify networks of sRNAs-guided post-transcriptional regulation within local Turnip mosaic virus (TuMV) infection sites in Brassica napus leaves. We show that the induction of host-encoded, virus-activated small interfering RNAs (vasiRNAs) observed in virus-infected tissues is accompanied by site-specific cleavage events on both viral and host RNAs that recalls the activity of small RNA-induced silencing complexes (RISC). Cleavage events also involve virus-derived siRNA (vsiRNA)–directed cleavage of target host transcripts as well as cleavage of viral RNA by both host vasiRNAs and vsiRNAs. Furthermore, certain coding genes act as virus-activated regulatory hubs to produce vasiRNAs for the targeting of other host genes. The observations draw an advanced model of plant-virus interactions and provide insights into the complex regulatory networking at the plant-virus interface within cells undergoing early stages of infection.

Pitzalis et al. use replicative RNAseq, small RNA (sRNA)seq, and parallel analysis of RNA ends (PARE)seq analysis to identify networks of sRNAs-guided post-transcriptional regulation within local Turnip mosaic virus infection sites. This study provides insights into the complex regulatory networking at the plantvirus interface within cells undergoing early stages of infection.

Molecular and Hormonal Regulation of Leaf Morphogenesis in Arabidopsis

Shoot apical meristems (SAM) are tissues that function as a site of continuous organogenesis, which indicates that a small pool of pluripotent stem cells replenishes into lateral organs. The coordination of intercellular and intracellular networks is essential for maintaining SAM structure and size and also leads to patterning and formation of lateral organs. Leaves initiate from the flanks of SAM and then develop into a flattened structure with variable sizes and forms. This process is mainly regulated by the transcriptional regulators and mechanical properties that modulate leaf development. Leaf initiation along with proper orientation is necessary for photosynthesis and thus vital for plant survival. Leaf development is controlled by different components such as hormones, transcription factors, miRNAs, small peptides, and epigenetic marks. Moreover, the adaxial/abaxial cell fate, lamina growth, and shape of margins are determined by certain regulatory mechanisms. The over-expression and repression of various factors responsible for leaf initiation, development, and shape have been previously studied in several mutants. However, in this review, we collectively discuss how these factors modulate leaf development in the context of leaf initiation, polarity establishment, leaf flattening and shape.

Ectopic expression of miRNA172 in tomato (Solanum lycopersicum) reveals novel function in fruit development through regulation of an AP2 transcription factor

BACKGROUND

MicroRNAs (miRNAs) are short non-coding RNAs that can influence gene expression via diverse mechanisms. Tomato is a fruit widely consumed for its flavor, culinary attributes, and high nutritional quality. Tomato fruit are climacteric and fleshy, and their ripening is regulated by endogenous and exogenous signals operating through a coordinated genetic network. Much research has been conducted on mechanisms of tomato fruit ripening, but the roles of miRNA-regulated repression/expression of specific regulatory genes are not well documented.

RESULTS

In this study, we demonstrate that miR172 specifically targets four SlAP2 transcription factor genes in tomato. Among them, SlAP2a was repressed by the overexpression of SlmiR172, manifesting in altered flower morphology, development and accelerated ripening. miR172 over-expression lines specifically repressed SlAP2a, enhancing ethylene biosynthesis, fruit color and additional ripening characteristics. Most previously described ripening-regulatory genes, including RIN-MADS, NR, TAGL1 and LeHB-1 were not influenced by miR172 while CNR showed altered expression.

CONCLUSIONS

Tomato fruit ripening is directly influenced by miR172 targeting of the APETALA2 transcription factor, SlAP2a, with minimal influence over additional known ripening-regulatory genes. miR172a-guided SlAP2a expression provides insight into another layer of genetic control of ripening and a target for modifying the quality and nutritional value of tomato and possibly other fleshy fruit crops.

De novo assembly and characterization of transcriptome towards understanding molecular mechanism associated with MYMIV-resistance in Vigna mungo - A computational study.. [DOI: 10.1101/844639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The fast climate change affects yield in Vigna mungo via enhancing both biotic and abiotic stresses. Out of all factors, the yellow mosaic disease has the most damaging effect. However, due to lack of reference genome of Vigna mungo, the complete mechanism associated with MYMIV (Mungbean Yellow Mosaic Indian Virus) resistance in Vigna mungo remain elusive to date. Considering this, the authors made an attempt to release new transcriptome and its annotation by employing computational approaches. Quality assessment of the generated transcriptomes reveals that it successfully aligned with 99.03% of the raw reads and hence can be employed for future research. Functional annotation of the transcriptome reveals that 31% and ∼14% of the total transcripts encode lncRNAs and protein-coding sequences, respectively. Further, analysis reveals that, out of total transcripts, only 4536 and 78808 are significantly down and up-regulated during MYMIV infection in Vigna mungo, respectively. These significant transcripts are mainly associated with ribosome, spliceosome, glycolysis /gluconeogenesis, RNA transport, oxidative phosphorylation, protein processing in the endoplasmic reticulum, MAPK signaling pathway - plant, methionine and cysteine metabolism, purine metabolism and RNA degradation. Unlike the previous study, this is for the first time, the present study identified these pathways may play key role in MYMIV resistance in Vigna mungo. Thus, information and transcriptomes data available in the present study make a significant contribution to understanding the genomic structure of Vigna mungo, enabling future analyses as well as downstream applications of gene expression, sequence evolution, and genome annotation.

De novo assembly and characterization of transcriptome towards understanding molecular mechanism associated with MYMIV-resistance in Vigna mungo - A computational study.. [DOI: 10.1101/844639]

The fast climate change affects yield in Vigna mungo via enhancing both biotic and abiotic stresses. Out of all factors, the yellow mosaic disease has the most damaging effect. However, due to lack of reference genome of Vigna mungo, the complete mechanism associated with MYMIV (Mungbean Yellow Mosaic Indian Virus) resistance in Vigna mungo remain elusive to date. Considering this, the authors made an attempt to release new transcriptome and its annotation by employing computational approaches. Quality assessment of the generated transcriptomes reveals that it successfully aligned with 99.03% of the raw reads and hence can be employed for future research. Functional annotation of the transcriptome reveals that 31% and ∼14% of the total transcripts encode lncRNAs and protein-coding sequences, respectively. Further, analysis reveals that, out of total transcripts, only 4536 and 78808 are significantly down and up-regulated during MYMIV infection in Vigna mungo, respectively. These significant transcripts are mainly associated with ribosome, spliceosome, glycolysis /gluconeogenesis, RNA transport, oxidative phosphorylation, protein processing in the endoplasmic reticulum, MAPK signaling pathway - plant, methionine and cysteine metabolism, purine metabolism and RNA degradation. Unlike the previous study, this is for the first time, the present study identified these pathways may play key role in MYMIV resistance in Vigna mungo. Thus, information and transcriptomes data available in the present study make a significant contribution to understanding the genomic structure of Vigna mungo, enabling future analyses as well as downstream applications of gene expression, sequence evolution, and genome annotation.

De novo assembly and characterization of transcriptome towards understanding molecular mechanism associated with MYMIV-resistance in Vigna mungo - A computational study.. [DOI: 10.1101/844639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The fast climate change affects yield in Vigna mungo via enhancing both biotic and abiotic stresses. Out of all factors, the yellow mosaic disease has the most damaging effect. However, due to lack of reference genome of Vigna mungo, the complete mechanism associated with MYMIV (Mungbean Yellow Mosaic Indian Virus) resistance in Vigna mungo remain elusive to date. Considering this, the authors made an attempt to release new transcriptome and its annotation by employing computational approaches. Quality assessment of the generated transcriptomes reveals that it successfully aligned with 99.03% of the raw reads and hence can be employed for future research. Functional annotation of the transcriptome reveals that 31% and ∼14% of the total transcripts encode lncRNAs and protein-coding sequences, respectively. Further, analysis reveals that, out of total transcripts, only 4536 and 78808 are significantly down and up-regulated during MYMIV infection in Vigna mungo, respectively. These significant transcripts are mainly associated with ribosome, spliceosome, glycolysis /gluconeogenesis, RNA transport, oxidative phosphorylation, protein processing in the endoplasmic reticulum, MAPK signaling pathway - plant, methionine and cysteine metabolism, purine metabolism and RNA degradation. Unlike the previous study, this is for the first time, the present study identified these pathways may play key role in MYMIV resistance in Vigna mungo. Thus, information and transcriptomes data available in the present study make a significant contribution to understanding the genomic structure of Vigna mungo, enabling future analyses as well as downstream applications of gene expression, sequence evolution, and genome annotation.

Genome-Wide Identification and Analysis of the AP2 Transcription Factor Gene Family in Wheat (Triticum aestivum L.)

The AP2 transcription factors play important roles in regulating plant growth and development. However, limited data are available on the contributions of AP2 transcription factors in wheat (Triticum aestivum L.). In the present study, a total of 62 AP2 genes were identified in wheat from a genome-wide search against the latest wheat genome data. Phylogenetic and sequence alignment analyses divided the wheat AP2 genes into 3 clusters, euAP2, euANT, and basalANT. Chromosomal distribution, gene structure and duplication, and motif composition were subsequently investigated. The 62 TaAP2 genes were unevenly distributed on 21 chromosomes. Twenty-four homologous gene sets among A, B, and D sub-genomes were detected, which contributed to the expansion of the wheat AP2 gene family. The expression levels of TaAP2 genes were examined using the WheatExp database; most detected genes exhibited tissue-specific expression patterns. The transcript levels of 9 randomly selected TaAP2 genes were validated through qPCR analyses. Overexpression of TaAP2-10-5D, the most likely homolog of Arabidopsis ANT gene, increased organ sizes in Arabidopsis. Our results extend our knowledge of the AP2 gene family in wheat, and contribute to further functional characterization of AP2s during wheat development with the ultimate goal of improving crop production.