scholarly journals Full-Length Transcriptome Sequencing and Comparative Transcriptome Analysis to Evaluate Drought and Salt Stress in Iris lactea var. chinensis

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 434
Author(s):  
Longjie Ni ◽  
Zhiquan Wang ◽  
Jinbo Guo ◽  
Xiaoxiao Pei ◽  
Liangqin Liu ◽  
...  

Iris lactea var. chinensis (I. lactea var. chinensis) is a perennial herb halophyte with salt and drought tolerance. In this study, full-length transcripts of I. lactea var. chinensis were sequenced using the PacBio RSII sequencing platform. Moreover, the transcriptome was investigated under NaCl or polyethylene glycol (PEG) stress. Approximately 30.89 G subreads were generated and 31,195 unigenes were obtained by clustering the same isoforms by the PacBio RSII platform. A total of 15,466 differentially expressed genes (DEGs) were obtained under the two stresses using the Illumina platform. Among them, 9266 and 8390 DEGs were obtained under high concentrations of NaCl and PEG, respectively. In total, 3897 DEGs with the same expression pattern under the two stresses were obtained. The transcriptome expression profiles of I. lactea var. chinensis under NaCl or PEG stress obtained in this study may provide a resource for the same and different response mechanisms against different types of abiotic stress. Furthermore, the stress-related genes found in this study can provide data for future molecular breeding.

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chunyan Li ◽  
Xiaoyun He ◽  
Zijun Zhang ◽  
Chunhuan Ren ◽  
Mingxing Chu

Abstract Background Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. Results Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. Conclusion All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.


2021 ◽  
Vol 12 ◽  
Author(s):  
Fenqi Chen ◽  
Xiangzhuo Ji ◽  
Mingxing Bai ◽  
Zelong Zhuang ◽  
Yunling Peng

The planting method of deep sowing can make the seeds make full use of water in deep soil, which is considered to be an effective way to respond to drought stress. However, deep sowing will affect the growth and development of maize (Zea mays L.) at seedling stage. To better understand the response of maize to deep sowing stress and the mechanism of exogenous hormones [Gibberellin (GA3), Brassinolide (BR), Strigolactone (SL)] alleviates the damaging effects of deep-sowing stress, the physiological and transcriptome expression profiles of seedlings of deep sowing sensitive inbred line Zi330 and the deep-tolerant inbred line Qi319 were compared under deep sowing stress and the conditions of exogenous hormones alleviates stress. The results showed that mesocotyl elongated significantly after both deep sowing stress and application of exogenous hormones, and its elongation was mainly through elongation and expansion of cell volume. Hormone assays revealed no significant changes in zeatin (ZT) content of the mesocotyl after deep sowing and exogenous hormone application. The endogenous GA3 and auxin (IAA) contents in the mesocotyl of the two inbred lines increased significantly after the addition of exogenous GA3, BR, and SL under deep sowing stress compared to deep sowing stress, while BR and SL decreased significantly. Transcriptome analysis showed that the deep seeding stress was alleviated by GA3, BR, and SLs, the differentially expressed genes (DEGs) mainly included cellulose synthase, expansin and glucanase, oxidase, lignin biosynthesis genes and so on. We also found that protein phosphatase 2C and GA receptor GID1 enhanced the ability of resist deep seeding stress in maize by participating in the abscisic acid (ABA) and the GA signaling pathway, respectively. In addition, we identified two gene modules that were significantly related to mesocotyl elongation, and identified some hub genes that were significantly related to mesocotyl elongation by WGCNA analysis. These genes were mainly involved in transcription regulation, hydrolase activity, protein binding and plasma membrane. Our results from this study may provide theoretical basis for determining the maize deep seeding tolerance and the mechanism by which exogenous hormones regulates deep seeding tolerance.


2021 ◽  
Author(s):  
Jose Manuel Latorre Estivalis ◽  
Ewald Grosse-Wilde ◽  
Gabriel R Fernandes ◽  
Bill S Hansson ◽  
Marcelo Gustavo Lorenzo

Background Triatomine bugs are the blood feeding insect vectors transmitting Chagas disease to humans, a neglected tropical disease that affects over 8 million people, mainly in Latin America. The behavioral responses to host cues and bug signals in Rhodnius prolixus are state dependent, i.e., they vary as a function of post-ecdysis age. At the molecular level, these changes in behavior are probably due to a modulation of peripheral and central processes. In the present study, we report a significant modulation of the expression of a large set of sensory-related genes. Results were generated by means of antennal transcriptomes of 5th instar larvae along the first week (days 0, 2, 4, 6 and 8) after ecdysis sequenced using the Illumina platform. Results Age induced significant changes in transcript abundance were established in more than 6,120 genes (54,7 % of 11,186 genes expressed) in the R. prolixus antenna. This was especially true between the first two days after ecdysis when more than 2,500 genes had their expression significantly altered. In contrast, expression profiles were almost identical between day 6 and 8, with only a few genes showing significant modulation of their expression. A total of 86 sensory receptors, odorant carriers and odorant degrading enzymes were significantly modulated across age points and clustered into three distinct expression profiles. Conclusions The set of sensory genes whose expression increased with age (profile 3) may include candidates underlying the increased responsiveness to host cues shown by R. prolixus during the first days after molting. For the first time, we describe the maturation process undergone at the molecular level by the peripheral sensory system is described in an hemimetabolous insect.


2006 ◽  
Vol 24 (2) ◽  
pp. 97-104 ◽  
Author(s):  
Robert Olaso ◽  
Vandana Joshi ◽  
Julien Fernandez ◽  
Natacha Roblot ◽  
Sabrina Courageot ◽  
...  

Mutations of the survival of motor neuron gene ( SMN1) are responsible for spinal muscular atrophies (SMA), a frequent recessive autosomal motor neuron disease. SMN is involved in various processes including RNA metabolism. However, the molecular pathway linking marked deficiency of SMN to SMA phenotype remains unclear. Homozygous deletion of murine Smn exon 7 directed to neurons or skeletal muscle causes severe motor axonal or myofiber degeneration, respectively. With the use of cDNA microarrays, expression profiles of 8,400 genes were analyzed in skeletal muscle and spinal cord of muscular and neuronal mutants, respectively, and compared with age-matched controls. A high proportion of genes (20 of 429, 5%) was involved in pre-mRNA splicing, ribosomal RNA processing, or RNA decay, and 18 of them were upregulated in mutant tissues. By analyzing other neuromuscular disorders, we showed that most of them (14 of 18) were specific to the SMN defect. Quantitative PCR analysis of these transcripts showed that gene activation was an early adaptive response to the lack but not reduced amount of full-length SMN in mouse mutant tissues. In human SMA tissues, activation of this program was not observed, which could be ascribed to the reduction but not the absence of full-length SMN.


2020 ◽  
Vol 21 (5) ◽  
pp. 1879 ◽  
Author(s):  
Shanshan He ◽  
Gaopeng Yuan ◽  
Shuxun Bian ◽  
Xiaolei Han ◽  
Kai Liu ◽  
...  

Major latex proteins (MLPs) play critical roles in plants defense and stress responses. However, the roles of MLPs from apple (Malus × domestica) have not been clearly identified. In this study, we focused on the biological role of MdMLP423, which had been previously characterized as a potential pathogenesis-related gene. Phylogenetic analysis and conserved domain analysis indicated that MdMLP423 is a protein with a ‘Gly-rich loop’ (GXGGXG) domain belonging to the Bet v_1 subfamily. Gene expression profiles showed that MdMLP423 is mainly expressed in flowers. In addition, the expression of MdMLP423 was significantly inhibited by Botryosphaeria berengeriana f. sp. piricola (BB) and Alternaria alternata apple pathotype (AAAP) infections. Apple calli overexpressing MdMLP423 had lower expression of resistance-related genes, and were more sensitive to infection with BB and AAAP compared with non-transgenic calli. RNA-seq analysis of MdMLP423-overexpressing calli and non-transgenic calli indicated that MdMLP423 regulated the expression of a number of differentially expressed genes (DEGs) and transcription factors, including genes involved in phytohormone signaling pathways, cell wall reinforcement, and genes encoding the defense-related proteins, AP2-EREBP, WRKY, MYB, NAC, Zinc finger protein, and ABI3. Taken together, our results demonstrate that MdMLP423 negatively regulates apple resistance to BB and AAAP infections by inhibiting the expression of defense- and stress-related genes and transcription factors.


2019 ◽  
Vol 20 (24) ◽  
pp. 6230
Author(s):  
Fengying Qiu ◽  
Xindong Wang ◽  
Yongjie Zheng ◽  
Hongming Wang ◽  
Xinliang Liu ◽  
...  

Leaves of C. porrectum are rich in essential oils containing monoterpenes, sesquiterpenes and aromatic compounds, but the molecular mechanism of terpenoid biosynthesis in C. porrectum is still unclear. In this paper, the differences in the contents and compositions of terpenoids among three chemotypes were analyzed using gas chromatography mass spectrometry (GC/MS). Furthermore, the differential expression of gene transcripts in the leaf tissues of the three C. porrectum chemotypes were analyzed through a comparison of full-length transcriptomes and expression profiles. The essential oil of the three C. porrectum chemotypes leaves was mainly composed of monoterpenes. In the full-length transcriptome of C. porrectum, 104,062 transcripts with 306,337,921 total bp, an average length of 2944 bp, and an N50 length of 5449 bp, were obtained and 94025 transcripts were annotated. In the eucalyptol and linalool chemotype, the camphor and eucalyptol chemotype, and the camphor and linalool chemotype comparison groups, 21, 22 and 18 terpene synthase (TPS) unigenes were identified respectively. Three monoterpene synthase genes, CpTPS3, CpTPS5 and CpTPS9, were upregulated in the eucalyptol chemotype compared to the linalool chemotype and camphor chemotype. CpTPS1 was upregulated in the camphor chemotype compared to the linalool chemotype and the eucalyptol chemotype. CpTPS4 was upregulated in the linalool chemotype compared to the camphor chemotype and the eucalyptol chemotype. Different unigenes had different expression levels among the three chemotypes, but the unigene expression levels of the 2-C-methyl-D-erythritol 4phosphate (MEP) pathway were generally higher than those of the mevalonate acid (MVA) pathway. Quantitative reverse transcription PCR(qRT-PCR) further validated these expression levels. The present study provides new clues for the functional exploration of the terpenoid synthesis mechanism and key genes in different chemotypes of C. porrectum.


BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shenghui Zhou ◽  
Jinpeng Zhang ◽  
Haiming Han ◽  
Jing Zhang ◽  
Huihui Ma ◽  
...  

Abstract Background Agropyron cristatum (L.) Gaertn. (2n = 4x = 28; genomes PPPP) is a wild relative of common wheat (Triticum aestivum L.) and provides many desirable genetic resources for wheat improvement. However, there is still a lack of reference genome and transcriptome information for A. cristatum, which severely impedes functional and molecular breeding studies. Results Single-molecule long-read sequencing technology from Pacific Biosciences (PacBio) was used to sequence full-length cDNA from a mixture of leaves, roots, stems and caryopses and constructed the first full-length transcriptome dataset of A. cristatum, which comprised 44,372 transcripts. As expected, the PacBio transcripts were generally longer and more complete than the transcripts assembled via the Illumina sequencing platform in previous studies. By analyzing RNA-Seq data, we identified tissue-enriched transcripts and assessed their GO term enrichment; the results indicated that tissue-enriched transcripts were enriched for particular molecular functions that varied by tissue. We identified 3398 novel and 1352 A. cristatum-specific transcripts compared with the wheat gene model set. To better apply this A. cristatum transcriptome, the A. cristatum transcripts were integrated with the wheat genome as a reference sequence to try to identify candidate A. cristatum transcripts associated with thousand-grain weight in a wheat-A. cristatum translocation line, Pubing 3035. Conclusions Full-length transcriptome sequences were used in our study. The present study not only provides comprehensive transcriptomic insights and information for A. cristatum but also proposes a new method for exploring the functional genes of wheat relatives under a wheat genetic background. The sequence data have been deposited in the NCBI under BioProject accession number PRJNA534411.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 28-28
Author(s):  
Jamie O' Sullivan ◽  
Orla Rawley ◽  
Vince Jenkins ◽  
Alain Chion ◽  
Teresa M Brophy ◽  
...  

Abstract During biosynthesis, Factor VIII (FVIII) undergoes complex post-translational modification including significant glycosylation. Consequently each FVIII molecule can contains 25 N- and 6 O-linked glycans. These carbohydrate structures are of physiological significance. For example, FVIII glycan expression modulates intracellular trafficking and also regulates FVIII clearance by dendritic cells. Nevertheless, the molecular mechanisms through which glycan structures influence FVIII biology remains poorly defined. Interestingly, carbohydrate-binding galectins (Gal) -1 and -3 have recently been reported to bind human VWF. Moreover, these galectin interactions significantly influence VWF function. In this study, based upon similar glycans expression profiles, we hypothesised that galectins might also constitute novel binding partners for human FVIII. In brief, His-tagged Gal-1 and Gal-3 were expressed in E-coli and purified using nickel chromatography. Recombinant FVIII (rFVIII) was purified from different commercial concentrates. Subsequently, FVIII glycosylation was modified using specific exoglycosidases and quantified by lectin-binding ELISA. Galectin-FVIII interaction was characterised using modified immunosorbant assays and surface plasmon resonance (SPR). In plate–binding assays using purified proteins and SPR studies, both Gal-1 and Gal-3 bound to full length rFVIII in a time- and dose-dependent manner. Interestingly the apparent affinities of the galectin-FVIII interactions (Kd of 0.11 ± 0.02nM for Gal-1 and 0.21 ± 0.1nM for Gal-3 respectively) were unusually high for these lectins. Digestion with PNGase F to remove N-linked glycans ablated FVIII binding to Gal-1 (8.6 ± 1%; p<0.0001). In contrast, PNG-FVIII retained significant ability to bind Gal-3 (30.3 ± 3%; p<0.0001). However, combined FVIII digestion with both PNGase F and O glycosidase further attenuated Gal-3 binding (16.5 ± 2%; p<0.05). Cumulatively these findings suggest that whilst Gal-1 binding is mediated predominantly through the N-linked glycans of FVIII, both N- and O-linked glycans modulate its interaction with Gal-3. The majority of FVIII glycans are contained within the B domain. Unsurprisingly, Gal-1 and Gal-3 binding were both markedly attenuated for B domain deleted rFVIII compared to full length rFVIII (42 ± 1% and 26 ± 0.8%; p<0.0001). Previous studies have described different glycosylation profiles for specific full length commercial rFVIII products. To investigate the relevance of this differential glycosylation, we compared the galectin-binding properties of Advate® (CHO cell line) and Helixate® (BHK cell line). Interestingly, Gal-1 and Gal-3 both displayed significantly enhanced affinity for Helixate (107 ± 2% and 124 ± 1%; p<0.05). These findings are consistent with the fact that the N-linked glycans of BHK-derived FVIII express galactose α1-3 galactose epitopes which constitute preferential galectin-binding ligands. To determine whether FVIII interacts with galectins in vivo, immunoprecipitation studies were performed using plasma from VWF-/- mice. We observed that that both Gal-1 and Gal-3 were co-precipitated with FVIII even in the absence of VWF. Consequently, both the VWF-FVIII complex and free FVIII in plasma are likely to circulate in a complex with galectins. Importantly, recent studies have reported a prothrombotic phenotype in Gal-1/Gal-3 double deficient mice compared to wild type controls following ferric chloride injury. To investigate whether galectin-binding influences FVIII function, FVIII activity was assessed using a one-stage clotting assay in the presence of increasing galectin concentrations. Interestingly, preincubation of FVIII with Gal-1 (0.5-17µM) resulted in a significant dose-dependent prolongation of the APTT (58 ± 0.2 sec compared to 26 ± 3 secs, p<0.001) In contrast, no such effect was observed for galectin-3 up to 20µM, suggesting these galectins may have differential effects on FVIII biology. In conclusion, we identify Gal-1 and Gal-3 as novel direct ligands for human FVIII. Both the N- and O-linked carbohydrates of FVIII contribute to galectin binding. Importantly, different commercial FVIII concentrates do not interact with galectins in the same manner. Finally, we also demonstrate that plasma FVIII can circulate in complex with both Gal-1 and Gal-3, and that Gal-1 binding can inhibit the procoagulant function of FVIII. Disclosures: No relevant conflicts of interest to declare.


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