scholarly journals Temporal and spatial domain-specific transcriptomic analysis of a vital reproductive meristem in Arabidopsis thaliana

2015 ◽  
Author(s):  
Gonzalo H Villarino ◽  
Miguel Flores-Vergara ◽  
Qiwen Hu ◽  
Bhupinder Sehra ◽  
Linda Robles ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Reproductive Organ ◽  
Differentially Expressed ◽  
Switching Behavior ◽  
Expression Domain ◽  
Data Set ◽  
Domain Specific ◽  
Temporal And Spatial

Background Plant meristems are analogous to animal stem cell niches as they maintain a pool of undifferentiated cells that divide and differentiate to give rise to organs. The carpel margin meristem is a vital, multi-potent structure located in the medial domain of the Arabidopsis thaliana gynoecium, the female floral reproductive organ. The carpel margin meristem generates ovules that upon fertilization become seeds. The molecular mechanisms that specify this meristematic region and regulate its organogenic potential are poorly understood. Here, we present an analysis of the transcriptional profile of the medial domain of the Arabidopsis gynoecium highlighting the developmental stages that immediately proceed ovule initiation, the earliest stages of seed development. Results Using a floral synchronization system and a SHATTERPROOF2 domain-specific reporter, paired with fluorescence-activated cell sorting and RNA sequencing, we assayed the transcriptome of the gynoecial medial domain with temporal and spatial precision. This analysis reveals a set of genes that are differentially expressed within the SHATTERPROOF2 expression domain that marks portions of the developing medial domain. Many members of this gene set have been shown previously to function during the development of medial domain-derived structures, including the ovules, thus validating our approach. Other uncharacterized members including differentially expressed cis-natural antisense transcripts, are potential novel regulators of medial domain development. Members of the REPRODUCTIVE MERISTEM (REM) family of transcriptional regulators were enriched in the SHATTERPROOF2-expressing cell population including a previously unrecognized REM family member. Finally, the analysis transcriptional isoforms in the medial domain identified genes that may exhibit 'isoform switching' behavior during gynoecial development. Conclusions This data set provides genome-wide transcriptional insight into the development of the gynoecial medial domain that contains the carpel margin meristem, a vital reproductive structure that gives rise to the ovules in Arabidopsis thaliana.

scholarly journals Revealing the developmental dynamics in male strobilus transcriptome of Gnetum luofuense using nanopore sequencing technology

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chen Hou ◽  
Yuxin Tian ◽  
Yingli Wang ◽  
Huiming Lian ◽  
Dongcheng Liang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Reproductive Organ ◽  
Differentially Expressed ◽  
Control Male ◽  
Oxford Nanopore ◽  
Developmental Dynamics ◽  
Oxford Nanopore Technologies ◽  
Male Strobilus ◽  
Male Strobili

AbstractGnetum is a pantropical distributed gymnosperm genus. As being dioecious, Gnetum species apply female and male strobili to attract and provide nutrition to insect pollinators. Due to its unique gross morphology, a Gnetum male strobilus receives much attention in previous taxonomic and evolutionary studies. However, underlying molecular mechanisms that control male strobilus development and pollination adaptation have not been well studied. In the present study, nine full-length transcriptomes were sequenced from three developmental stages of the G. luofuense male strobili using Oxford Nanopore Technologies. In addition, weighted gene co-expression network analysis (WGCNA), and RT-qPCR analysis were performed. Our results show that a total of 3138 transcription factors and 466 long non-coding RNAs (lncRNAs) were identified, and differentially expressed lncRNAs and TFs reveal a dynamic pattern during the male strobilus development. Our results show that MADS-box and Aux/IAA TFs were differentially expressed at the three developmental stages, suggesting their important roles in the regulation of male strobilus development of G. luofuense. Results of WGCNA analysis and annotation of differentially expressed transcripts corroborate that the male strobilus development of G. luofuense is closely linked to plant hormone changes, photosynthesis, pollination drop secretion and reproductive organ defense. Our results provide a valuable resource for understanding the molecular mechanisms that drive organ evolution and pollination biology in Gnetum.

scholarly journals Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

2016 ◽  
Vol 16 (1) ◽  
Author(s):  
Juan Ma ◽  
Rongyan Wang ◽  
Xiuhua Li ◽  
Bo Gao ◽  
Shulong Chen
Keyword(s):  
Sweet Potato ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Average Length ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Cylas Formicarius ◽  
Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

scholarly journals An Integrated Transcriptome and Proteome Analysis Reveals New Insights into Russeting of Bagging and Non-Bagging “Golden Delicious” Apple

2019 ◽  
Vol 20 (18) ◽  
pp. 4462 ◽  
Author(s):  
Gaopeng Yuan ◽  
Shuxun Bian ◽  
Xiaolei Han ◽  
Shanshan He ◽  
Kai Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Lignin Biosynthesis ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Proteomics Data ◽  
Absolute Quantitation ◽  
Physiological Disorder ◽  
Golden Delicious

Apple skin russeting naturally occurs in many varieties, particularly in “Golden Delicious” and its pedigree, and is regarded as a non-invasive physiological disorder partly caused by excessive deposition of lignin. However, the understanding of its molecular mechanism is still limited. In this study, we used iTRAQ (isobaric tags for relative and absolute quantitation) and RNA-seq to detect the changes in the expression levels of genes and proteins in three developmental stages of russeting formation, in russeted (non-bagging) and non-russeted (bagging) skin of “Golden Delicious” apple. 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups were detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptomics and proteomics data revealed that four genes (MD03G1059200, MD08G1009200, MD17G1092400, and MD17G1225100) involved in lignin biosynthesis are significant changed during apple russeting formation. Additionally, 92 transcription factors, including 4 LIM transcription factors, may be involved in apple russeting formation. Among them, one LIM transcription factor (MD15G1068200) was capable of binding to the PAL-box like (CCACTTGAGTAC) element, which indicated it was potentially involved in lignin biosynthesis. This study will provide further views on the molecular mechanisms controlling apple russeting formation.

scholarly journals Transcriptional Insights into Key Genes and Pathways Underlying Muscovy Duck Subcutaneous Fat Deposition at Different Developmental Stages

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 2099
Author(s):  
Liping Guo ◽  
Congcong Wei ◽  
Li Yi ◽  
Wanli Yang ◽  
Zhaoyu Geng ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Fatty Acid Biosynthesis ◽  
Developmental Stages ◽  
Subcutaneous Fat ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Muscovy Duck ◽  
Key Genes

Subcutaneous fat is a crucial trait for waterfowl, largely associated with meat quality and feed conversion rate. In this study, RNA-seq was used to identify differentially expressed genes of subcutaneous adipose tissue among three developmental stages (12, 35, and 66 weeks) in Muscovy duck. A total of 138 and 129 differentially expressed genes (DEGs) were identified between 35 and 12 weeks (wk), and 66 and 35 wk, respectively. Compared with 12 wk, subcutaneous fat tissue at 35 wk upregulated several genes related to cholesterol biosynthesis and fatty acid biosynthesis, including HSD17B7 and MSMO1, while it downregulated fatty acid beta-oxidation related genes, including ACOX1 and ACSL1. Notably, most of the DEGs (92.2%) were downregulated in 66 wk compared with 35 wk, consistent with the slower metabolism of aging duck. Protein network interaction and function analyses revealed GC, AHSG, FGG, and FGA were the key genes for duck subcutaneous fat from adult to old age. Additionally, the PPAR signaling pathway, commonly enriched between the two comparisons, might be the key pathway contributing to subcutaneous fat metabolism among differential developmental stages in Muscovy duck. These results provide several candidate genes and pathways potentially involved in duck subcutaneous fat deposition, expanding our understanding of the molecular mechanisms underlying subcutaneous fat deposition during development.

scholarly journals Pervasive 3′-UTR Isoform Switches During Mouse Oocyte Maturation

2021 ◽  
Vol 8 ◽  
Author(s):  
Yuanlin He ◽  
Qiuzhen Chen ◽  
Jing Zhang ◽  
Jing Yu ◽  
Meng Xia ◽  
...  
Keyword(s):  
Oocyte Maturation ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Germinal Vesicle ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Germinal Vesicle Breakdown ◽  
Oocyte Meiosis ◽  
Gene Level ◽  
Individual Mouse

Oocyte maturation is the foundation for developing healthy individuals of mammals. Upon germinal vesicle breakdown, oocyte meiosis resumes and the synthesis of new transcripts ceases. To quantitatively profile the transcriptomic dynamics after meiotic resumption throughout the oocyte maturation, we generated transcriptome sequencing data with individual mouse oocytes at three main developmental stages: germinal vesicle (GV), metaphase I (MI), and metaphase II (MII). When clustering the sequenced oocytes, results showed that isoform-level expression analysis outperformed gene-level analysis, indicating isoform expression provided extra information that was useful in distinguishing oocyte stages. Comparing transcriptomes of the oocytes at the GV stage and the MII stage, in addition to identification of differentially expressed genes (DEGs), we detected many differentially expressed transcripts (DETs), some of which came from genes that were not identified as DEGs. When breaking down the isoform-level changes into alternative RNA processing events, we found the main source of isoform composition changes was the alternative usage of polyadenylation sites. With detailed analysis focusing on the alternative usage of 3′-UTR isoforms, we identified, out of 3,810 tested genes, 512 (13.7%) exhibiting significant switches of 3′-UTR isoforms during the process of moues oocyte maturation. Altogether, our data and analyses suggest the importance of examining isoform abundance changes during oocyte maturation, and further investigation of the pervasive 3′-UTR isoform switches in the transition may deepen our understanding on the molecular mechanisms underlying mammalian early development.

scholarly journals Comparative RNA-Seq Analysis of High- and Low-Oil Yellow Horn During Embryonic Development

2018 ◽  
Vol 19 (10) ◽  
pp. 3071 ◽  
Author(s):  
Li Wang ◽  
Chengjiang Ruan ◽  
Lingyue Liu ◽  
Wei Du ◽  
Aomin Bao
Keyword(s):  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Acyl Carrier Protein ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Oil Accumulation ◽  
Carboxylase Activity

Yellow horn (Xanthoceras sorbifolium Bunge) is an endemic oil-rich shrub that has been widely cultivated in northern China for bioactive oil production. However, little is known regarding the molecular mechanisms that contribute to oil content in yellow horn. Herein, we measured the oil contents of high- and low-oil yellow horn embryo tissues at four developmental stages and investigated the global gene expression profiles through RNA-seq. The results found that at 40, 54, 68, and 81 days after anthesis, a total of 762, 664, 599, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil lines. Gene ontology (GO) enrichment analysis revealed some critical GO terms related to oil accumulation, including acyl-[acyl-carrier-protein] desaturase activity, pyruvate kinase activity, acetyl-CoA carboxylase activity, and seed oil body biogenesis. The identified differentially expressed genes also included several transcription factors, such as, AP2-EREBP family members, B3 domain proteins and C2C2-Dof proteins. Several genes involved in fatty acid (FA) biosynthesis, glycolysis/gluconeogenesis, and pyruvate metabolism were also up-regulated in the high-oil line at different developmental stages. Our findings indicate that the higher oil accumulation in high-oil yellow horn could be mostly driven by increased FA biosynthesis and carbon supply, i.e. a source effect.

Pattern formation and growth during floral organogenesis: HUELLENLOS and AINTEGUMENTA are required for the formation of the proximal region of the ovule primordium in Arabidopsis thaliana

Development ◽  
1998 ◽  
Vol 125 (14) ◽  
pp. 2555-2563 ◽  
Author(s):  
K. Schneitz ◽  
S.C. Baker ◽  
C.S. Gasser ◽  
A. Redweik
Keyword(s):  
Arabidopsis Thaliana ◽  
Pattern Formation ◽  
Molecular Mechanisms ◽  
Embryo Sac ◽  
Typical Feature ◽  
Proximal Region ◽  
Ovule Development ◽  
Linear Arrangement ◽  
Floral Organogenesis ◽  
Temporal And Spatial

Our understanding of the molecular mechanisms that regulate and integrate the temporal and spatial control of cell proliferation during organ ontogenesis, particularly of floral organs, continues to be primitive. The ovule, the progenitor of the seed, of Arabidopsis thaliana has been used to develop an effective model system for the analysis of plant organogenesis. A typical feature of a generalized ovule is the linear arrangement of at least three distinct elements, the funiculus, chalaza and nucellus, along a proximal-distal axis. This pattern is supposed to be established during the early proliferative phase of ovule development. We provide genetic evidence that the young ovule primordium indeed is a composite structure. Two genes, HUELLENLOS and AINTEGUMENTA have overlapping functions in the ovule and differentially control the formation of the central and proximal elements of the primordium. The results indicate that proximal-distal pattern formation in the Arabidopsis ovule takes place in a sequential fashion, starting from the distal end. Furthermore, we show that HUELLENLOS also regulates the initiation and/or maintenance of integument and embryo sac ontogenesis and interestingly prevents inappropriate cell death in the young ovule.

scholarly journals Comprehensive Analysis of MicroRNA–Messenger RNA from White Yak Testis Reveals the Differentially Expressed Molecules Involved in Development and Reproduction

2018 ◽  
Vol 19 (10) ◽  
pp. 3083 ◽  
Author(s):  
Quanwei Zhang ◽  
Qi Wang ◽  
Yong Zhang ◽  
Shuru Cheng ◽  
Junjie Hu ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Age Groups ◽  
Comprehensive Analysis ◽  
Differentially Expressed ◽  
Messenger Rnas ◽  
Dynamic Regulation ◽  
Testis Development ◽  
Rna Interaction

Testis development is a vital and tightly regulated process in mammals. Understanding the biological mechanisms underlying testis development will benefit the animal reproduction industry. Expression changes in microRNA and messenger RNA in response to dynamic regulation effects have been associated with this process. However, very little is known about the roles of these molecules in yak development. Using whole-genome small RNA and messenger RNA sequencing, we performed a comprehensive analysis of the microRNA–messenger RNA interaction network expression in the testicles of Tianzhu white yaks during three developmental stages. Using Short Time-series Expression Miner analysis we identified 589 differentially expressed microRNAs (DERs) and 3383 differentially expressed messenger RNAs (DEGs) in the three age groups. A total of 93 unique DEGs are primarily involved in reproduction and testis development. Subsequently, four integration networks were constructed according to the DEGs and DERs in three biological processes. Nineteen DEGs were potentially regulated by 60 DERs, of which miR-574 and target gene AURKA played a crucial role in yak testis development and reproduction. The results of this study provide a basis for further exploration of the microRNA–messenger RNA interactions in testis development and reproduction and aid in uncovering the molecular mechanisms of spermatogenesis in male mammals.

scholarly journals Comparative Transcriptome Sequencing of Taro Corm Development With a Focus on the Starch and Sucrose Metabolism Pathway

2021 ◽  
Vol 12 ◽  
Author(s):  
Weiqing Dong ◽  
Fanglian He ◽  
Huiping Jiang ◽  
Lili Liu ◽  
Zuyang Qiu
Keyword(s):  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Developmental Stages ◽  
Sucrose Metabolism ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Growth Stages ◽  
Metabolism Pathway ◽  
Root Tuber

Taro (Colocasia esculenta) is an important tuber crop and staple food. Taro corms have higher nutritional value and starch contents as compared to most of the other root/tuber crops. However, the growth and development of the taro rhizome have not been critically examined in terms of transcriptomic signatures in general or specific to carbohydrates (starch and sucrose) accumulation. In current study, we have conducted a comprehensive survey of transcripts in taro corms aged 1, 2, 3, 4, 5, and 8 months. In this context, we have employed a whole transcriptome sequencing approach for identification of mRNAs, CircRNAs, and miRNAs in corms and performed functional enrichment analysis of the screened differentially expressed RNAs. A total of 11,203 mRNAs, 245 CircRNAs, and 299 miRNAs were obtained from six developmental stages. The mRNAs included 139 DEGs associated with 24 important enzymes of starch and sucrose metabolism. The expression of genes encoding key enzymes of starch and sucrose metabolism pathway (GBSS, AGPase, UGPase, SP, SSS, βFRUCT and SuSy) demonstrated significant variations at the stage of 4 months (S4). A total of 191 CircRNAs were differentially expressed between the studied comparisons of growth stages and 99 of these were associated with those miRNA (or target genes) that were enriched in starch and sucrose metabolism pathway. We also identified 205 miRNAs including 46 miRNAs targeting DEGs enriched in starch and sucrose biosynthesis pathway. The results of current study provide valuable resources for future exploration of the molecular mechanisms involved in the starch properties of Taro.

scholarly journals Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hye-In Kang ◽  
Chae-Bin Lee ◽  
Soon-Ho Kwon ◽  
Ji-Min Park ◽  
Kyu-Suk Kang ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Signal Transduction Pathway ◽  
Woody Species ◽  
Differentially Expressed ◽  
Transcriptional Analysis ◽  
Direct Somatic Embryogenesis ◽  
Rna Seq ◽  
Tilia Amurensis

AbstractTilia species are valuable woody species due to their beautiful shape and role as honey trees. Somatic embryogenesis can be an alternative method for mass propagation of T. amurensis. However, the molecular mechanisms of T. amurensis somatic embryogenesis are yet to be known. Here, we conducted comparative transcriptional analysis during somatic embryogenesis of T. amurensis. RNA-Seq identified 1505 differentially expressed genes, including developmental regulatory genes. Auxin related genes such as YUC, AUX/IAA and ARF and signal transduction pathway related genes including LEA and SERK were differentially regulated during somatic embryogenesis. Also, B3 domain family (LEC2, FUS3), VAL and PKL, the regulatory transcription factors, were differentially expressed by somatic embryo developmental stages. Our results could provide plausible pathway of signaling somatic embryogenesis of T. amurensis, and serve an important resource for further studies in direct somatic embryogenesis in woody plants.

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