Whole Transcriptome Analysis: Implication to Estrous Cycle Regulation

2021 ◽  
Author(s):  
Xiaopeng An ◽  
Yue Zhang ◽  
Fu Li ◽  
Zhanhang Wang ◽  
Shaohua Yang ◽  
...  
Keyword(s):  
Estrous Cycle ◽  
Transcriptome Analysis ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
Whole Transcriptome Analysis ◽  
Cycle Regulation ◽  
Whole Transcriptome ◽  
Goat Ovary

Abstract BackgroundEstrous cycle is one of female characteristics after sexual maturity, including estrus (ES) and diestrus (DS) stages. Estrous cycle is important in female physiology and its disorder may lead to diseases. In the latest years, effects of non-coding RNAs and mRNA on estrous cycle start to arouse much concern, however, a whole transcriptome analysis among non-coding RNAs and mRNA has not been reported.ResultsHere we report a whole transcriptome analysis of goat ovary in estrus and diestrus periods. Estrus synchronization was conducted to induce the estrus phase and on day 32, the goats naturally shifted into diestrus stage. The ovary RNA of estrus and diestrus stages was respectively collected to perform RNA-sequencing. Then the circular RNA; microRNA; long non-coding RNA; mRNA databases of goat ovary were acquired, and the differentially expressions between estrus and diestrus stages were screened to construct circRNA-miRNA-mRNA/lncRNA and lncRNA-miRNA/mRNA networks, thus providing potential pathways that involved in the regulation of estrous cycle. Differentially expressed mRNAs, such as MMP9, TIMP1, 3BHSD and PTGIS, and differentially expressed microRNAs, such as miR-21-3p，miR-202-3p and miR-223-3p, which play key roles in estrous cycle regulation were extracted from the network.ConclusionsOur data provided the miRNA, circRNA, lncRNA and mRNA databases of goat ovary and each differentially expressed profile between ES and DS. Networks among differentially expressed miRNAs, circRNAs, lncRNAs and mRNAs were constructed to provide valuable resources for the study of estrous cycle and related diseases.

scholarly journals Whole Transcriptome Analysis: Implication to Estrous Cycle Regulation

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 464
Author(s):  
Xiaopeng An ◽  
Yue Zhang ◽  
Fu Li ◽  
Zhanhang Wang ◽  
Shaohua Yang ◽  
...  
Keyword(s):  
Estrous Cycle ◽  
Transcriptome Analysis ◽  
Messenger Rna ◽  
Polycystic Ovary ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Non Coding Rnas ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
Goat Ovary

Estrous cycle is one of the placental mammal characteristics after sexual maturity, including estrus stage (ES) and diestrus stage (DS). Estrous cycle is important in female physiology and its disorder may lead to diseases, such as polycystic ovary syndrome, ovarian carcinoma, anxiety, and epilepsy. In the latest years, effects of non-coding RNAs and messenger RNA (mRNA) on estrous cycle have started to arouse much concern, however, a whole transcriptome analysis among non-coding RNAs and mRNA has not been reported. Here, we report a whole transcriptome analysis of goat ovary in estrus and diestrus periods. Estrus synchronization was conducted to induce the estrus phase and on day 32, the goats shifted into the diestrus stage. The ovary RNA of estrus and diestrus stages was respectively collected to perform RNA-sequencing. Then, the circular RNA (circRNA), microRNA (miRNA), long non-coding RNA (lncRNA), and mRNA databases of goat ovary were acquired, and the differential expressions between estrus and diestrus stages were screened to construct circRNA-miRNA-mRNA/lncRNA and lncRNA-miRNA/mRNA networks, thus providing potential pathways that are involved in the regulation of estrous cycle. Differentially expressed mRNAs, such as MMP9, TIMP1, 3BHSD, and PTGIS, and differentially expressed miRNAs that play key roles in the regulation of estrous cycle, such as miR-21-3p, miR-202-3p, and miR-223-3p, were extracted from the network. Our data provided the miRNA, circRNA, lncRNA, and mRNA databases of goat ovary and each differentially expressed profile between ES and DS. Networks among differentially expressed miRNAs, circRNAs, lncRNAs, and mRNAs were constructed to provide valuable resources for the study of estrous cycle and related diseases.

scholarly journals Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium

2020 ◽  
Author(s):  
Hua Liu ◽  
Chang Luo ◽  
Dongliang Chen ◽  
Yaqin Wang ◽  
Shuang Guo ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Anthocyanin Biosynthesis ◽  
Floral Organ ◽  
Chrysanthemum Morifolium ◽  
Differentially Expressed ◽  
Vegetative Buds ◽  
Ray Florets ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Background: Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils.Results: We conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds. Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding.Conclusions: The whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.

scholarly journals Whole transcriptome analysis resulted in the identification of Chinese sprangletop (Leptochloa chinensis) genes involved in cyhalofop-butyl tolerance

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ke Chen ◽  
Yajun Peng ◽  
Liang Zhang ◽  
Long Wang ◽  
Donghai Mao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cytochrome P450 ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Herbicide Tolerance ◽  
Differentially Expressed ◽  
Metabolic Resistance ◽  
Cytochrome P450 Genes ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Background Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual malignant weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. However, in many areas, L. chinensis has become tolerant to this key herbicide due to its continuous long-term use. Results In this study, we utilized a tolerant (LC18002) and a sensitive (LC17041) L. chinensis populations previously identified in our laboratory, which were divided into four different groups. We then employed whole transcriptome analysis to identify candidate genes which may be involved in cyhalofop-butyl tolerance. This analysis resulted in the identification of six possible candidate genes, including three cytochrome P450 genes and three ATP-binding cassette transporter genes. We then carried out a phylogenetic analysis to identify homologs of the differentially expressed cytochrome P450 genes. This phylogenetic analysis indicated that all genes have close homologs in other species, some of which have been implicated in non-target site resistance (NTSR). Conclusions This study is the first to use whole transcriptome analysis to identify herbicide non-target resistance genes in L. chinensis. The differentially expressed genes represent promising targets for better understanding herbicide tolerance in L. chinensis. The six genes belonging to classes already associated in herbicide tolerance may play important roles in the metabolic resistance of L. chinensis to cyhalofop-butyl, although the exact mechanisms require further study.

Whole Transcriptome Analysis Resulted in the Identification of Chinese Sprangletop (Leptochloa Chinensis) Genes Involved in Cyhalofop-Butyl Resistance

2021 ◽  
Author(s):  
Ke Chen ◽  
Yajun Peng ◽  
Liang Zhang ◽  
Long Wang ◽  
Donghai Mao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Herbicide Tolerance ◽  
Differentially Expressed ◽  
Metabolic Resistance ◽  
Invasive Weed ◽  
P450 Monooxygenase ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Background Chinese sprangletop [Leptochloa chinensis (L.) Nees] is an annual invasive weed, which can often be found in paddy fields. Cyhalofop-butyl is a specialized herbicide which is utilized to control L. chinensis. However, in many areas, L. chinensis has become resistant to this key herbicide due to its continuous long-term use. Results In this study, we utilized a resistant (LC18002) and a sensitive (LC17041) L. chinensis populations previously identified in our laboratory, which were divided into nine different treatment groups. We then employed whole transcriptome analysis to identify candidate genes which may be involved in cyhalofop-butyl tolerance. This analysis resulted in the identification of eight possible candidate genes, including six cytochrome P450 monooxygenase genes and two ATP-binding cassette transporter genes. We then carried out a phylogenetic analysis to identify homologs of the differentially expressed P450 genes. This phylogenetic analysis indicated that every genes have close homologs in pattern species, some of which have been implicated in non-target site resistance (NTSR). Conclusions This study is the first to use whole transcriptome analysis to identify herbicide non-target resistance genes in L. chinensis. The differentially expressed genes represent promising targets for better understanding herbicide tolerance in L. chinensis. The eight genes belonging to classes already associated in herbicide tolerance may play important roles in the metabolic resistance of L. chinensis to cyhalofop-butyl, although the exact mechanisms require further study.

scholarly journals Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium

2020 ◽  
Author(s):  
Hua Liu ◽  
Chang Luo ◽  
Dongliang Chen ◽  
Yaqin Wang ◽  
Shuang Guo ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Analysis ◽  
Anthocyanin Biosynthesis ◽  
Floral Organ ◽  
Chrysanthemum Morifolium ◽  
Differentially Expressed ◽  
Vegetative Buds ◽  
Ray Florets ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

Abstract Background Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils. Results We conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds . Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding. Conclusions The whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.

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