scholarly journals Gene Expressing and sRNA Sequencing Show That Gene Differentiation Associates with a YellowAcer palmatumMutant Leaf in Different Light Conditions

2015 ◽  
Vol 2015 ◽  
pp. 1-10
Author(s):  
Shu-Shun Li ◽  
Qian-Zhong Li ◽  
Li-Ping Rong ◽  
Ling Tang ◽  
Bo Zhang
Keyword(s):  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Light Condition ◽  
Low Density ◽  
Physiological Changes ◽  
Potential Mechanism ◽  
Light Conditions ◽  
Pigment Synthesis ◽  
Leaf Coloration ◽  
Gene Expressing

Acer palmatumThunb., like other maples, is a widely ornamental-use small woody tree for leaf shapes and colors. Interestingly, we found a yellow-leaves mutant “Jingling Huangfeng” turned to green when grown in shade or low-density light condition. In order to study the potential mechanism, we performed high-throughput sequencing and obtained 1,082 DEGs in leaves grown in different light conditions that result inA. palmatumsignificant morphological and physiological changes. A total of 989 DEGs were annotated and clustered, of which many DEGs were found associating with the photosynthesis activity and pigment synthesis. The expression of CHS and FDR gene was higher while the expression of FLS gene was lower in full-sunlight condition; this may cause more colorful substance like chalcone and anthocyanin that were produced in full-light condition, thus turning the foliage to yellow. Moreover, this is the first available miRNA collection which contains 67 miRNAs ofA. palmatum, including 46 conserved miRNAs and 21 novel miRNAs. To get better understanding of which pathways these miRNAs involved, 102 Unigenes were found to be potential targets of them. These results will provide valuable genetic resources for further study on the molecular mechanisms ofAcer palmatumleaf coloration.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Discovery of MicroRNAs and Their Target Genes Related to Drought in Paulownia “Yuza 1” by High-Throughput Sequencing

2017 ◽  
Vol 2017 ◽  
pp. 1-11 ◽  
Author(s):  
Minjie Deng ◽  
Yabing Cao ◽  
Zhenli Zhao ◽  
Lu Yang ◽  
Yanfang Zhang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Plant Hormone ◽  
Target Genes ◽  
Reference Data ◽  
Relevant Information ◽  
Putative Target

Understanding the role of miRNAs in regulating the molecular mechanisms responsive to drought stress was studied in Paulownia “yuza 1.” Two small RNA libraries and two degradome libraries were, respectively, constructed and sequenced in order to detect miRNAs and their target genes associated with drought stress. A total of 107 miRNAs and 42 putative target genes were identified in this study. Among them, 77 miRNAs were differentially expressed between drought-treated Paulownia “yuza 1” and the control (60 downregulated and 17 upregulated). The predicted target genes were annotated using the GO, KEGG, and Nr databases. According to the functional classification of the target genes, Paulownia “yuza 1” may respond to drought stress via plant hormone signal transduction, photosynthesis, and osmotic adjustment. Furthermore, the expression levels of seven miRNAs (ptf-miR157b, ptf-miR159b, ptf-miR398a, ptf-miR9726a, ptf-M2153, ptf-M2218, and ptf-M24a) and their corresponding target genes were validated by quantitative real-time PCR. The results provide relevant information for understanding the molecular mechanism of Paulownia resistance to drought and reference data for researching drought resistance of other trees.

Control of browning during seed germination of Meizotropis pellita: a rare and an endangered plant

2021 ◽  
Vol 16 (8) ◽  
pp. 118-120
Author(s):  
Renu Chandola ◽  
Anshulika Upadhyaya
Keyword(s):  
Seed Germination ◽  
Culture Media ◽  
Light Condition ◽  
Endangered Plant ◽  
In Vitro Germination ◽  
Light Conditions ◽  
Low Intensity ◽  
Browning Reaction ◽  
Threatened Plant Species

Meizotropis pellita is a rare, endangered and threatened plant species found in Patwadanger forest. In nature this species grows from rootstock in precise and sensitive habitats. However, phenolic compounds provoke browning reaction which is responsible for lethal browning in plant tissue culture and hindering in vitro germination. The aim of this study was to minimize the effect of phenolic compound during seed germination. We evaluate different antibrowning treatments in Meizotropis pellita seeds. The seeds were pretreated in Polyvinylpyrrolidone and then treated seeds were cultured on MS media and sterilized seeds were directly inoculated on PVP containing MS media. These culture media incubate under dark and light conditions at different durations respectively. Our results showed that addition of antibrowning agent, PVP inhibit onset of browning. Dark and light condition also played a crucial role on onset of browning. Delayed and low intensity of browning were observed in case of seeds that were inoculated on MS media containing PVP and were kept in dark. The present research offers a positive in vitro seed germination protocol for Meizotropis pellita conservation.

scholarly journals Germination and seedling structure of Ruprechtia laxiflora Meissn. (Polygonaceae)

2017 ◽  
Vol 39 (2) ◽  
pp. 243
Author(s):  
Rafael Espanhol Müller ◽  
Luiz Antonio De Souza ◽  
Lindamir Hernandez Pastorini ◽  
Mariza Barion Romagnolo
Keyword(s):  
Experimental Design ◽  
Light Condition ◽  
Cotyledonary Node ◽  
Plant Anatomy ◽  
Light Conditions ◽  
Continuous Darkness ◽  
Germination Speed ◽  
Forest Remnants ◽  
Mean Time ◽  
Germination Parameters

Germination of diaspores and the seedling structure of Ruprechtia laxiflora Meissn. (Polygonaceae) which is a secondary species frequent in forest remnants are described. Seedlings were embedded in hydroxymethacrylate and sectioned in a rotary microtome according to usual techniques in plant anatomy. For bioassays of germination, the experimental design was completely randomized in a 3x2 bifactorial arrangement, corresponding to three temperatures (20, 25 and 30°C) and two light conditions (photoperiod and continuous darkness) for the diaspores newly harvested and in a 4x2 bifactorial arrangement, corresponding to four temperatures (15, 20, 25 and 30°C) and two light conditions (photoperiod and continuous darkness) for diaspores analyzed after storage. There was no interaction between the factors light condition and temperature for germination parameters analyzed. However, the temperature affected the germination and diaspores maintained at 25°C showed a shorter mean time and higher germination speed index. Seedlings are phanerocotylar and epigeal with tetrarch root, intermediate-low type of root-stem transition and trilacunar cotyledonary node.

scholarly journals Gene Annotation and Transcriptome Delineation on a De Novo Genome Assembly for the Reference Leishmania major Friedlin Strain

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1359
Author(s):  
Esther Camacho ◽  
Sandra González-de la Fuente ◽  
Jose C. Solana ◽  
Alberto Rastrojo ◽  
Fernando Carrasco-Ramiro ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Leishmania Major ◽  
De Novo ◽  
Gene Annotation ◽  
Leishmania Species ◽  
De Novo Genome Assembly ◽  
Sequencing Platforms

Leishmania major is the main causative agent of cutaneous leishmaniasis in humans. The Friedlin strain of this species (LmjF) was chosen when a multi-laboratory consortium undertook the objective of deciphering the first genome sequence for a parasite of the genus Leishmania. The objective was successfully attained in 2005, and this represented a milestone for Leishmania molecular biology studies around the world. Although the LmjF genome sequence was done following a shotgun strategy and using classical Sanger sequencing, the results were excellent, and this genome assembly served as the reference for subsequent genome assemblies in other Leishmania species. Here, we present a new assembly for the genome of this strain (named LMJFC for clarity), generated by the combination of two high throughput sequencing platforms, Illumina short-read sequencing and PacBio Single Molecular Real-Time (SMRT) sequencing, which provides long-read sequences. Apart from resolving uncertain nucleotide positions, several genomic regions were reorganized and a more precise composition of tandemly repeated gene loci was attained. Additionally, the genome annotation was improved by adding 542 genes and more accurate coding-sequences defined for around two hundred genes, based on the transcriptome delimitation also carried out in this work. As a result, we are providing gene models (including untranslated regions and introns) for 11,238 genes. Genomic information ultimately determines the biology of every organism; therefore, our understanding of molecular mechanisms will depend on the availability of precise genome sequences and accurate gene annotations. In this regard, this work is providing an improved genome sequence and updated transcriptome annotations for the reference L. major Friedlin strain.

scholarly journals Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
S. Le Guillou ◽  
A. Leduc ◽  
J. Laubier ◽  
S. Barbey ◽  
M.-N. Rossignol ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Milk Production ◽  
High Throughput ◽  
Genetic Background ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Whole Milk ◽  
Mammary Morphogenesis ◽  
Regulatory Properties

AbstractThe concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.

scholarly journals Approach to the Adult Acute Lymphoblastic Leukemia Patient

2019 ◽  
Vol 8 (8) ◽  
pp. 1175 ◽  
Author(s):  
Valentina Sas ◽  
Vlad Moisoiu ◽  
Patric Teodorescu ◽  
Sebastian Tranca ◽  
Laura Pop ◽  
...  
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Kinase Inhibitors ◽  
Lymphoblastic Leukemia ◽  
Survival Rates ◽  
High Risk Patient ◽  
Late Relapse ◽  
Published Data ◽  
Hematopoietic Stem

During recent decades, understanding of the molecular mechanisms of acute lymphoblastic leukemia (ALL) has improved considerably, resulting in better risk stratification of patients and increased survival rates. Age, white blood cell count (WBC), and specific genetic abnormalities are the most important factors that define risk groups for ALL. State-of-the-art diagnosis of ALL requires cytological and cytogenetical analyses, as well as flow cytometry and high-throughput sequencing assays. An important aspect in the diagnostic characterization of patients with ALL is the identification of the Philadelphia (Ph) chromosome, which warrants the addition of tyrosine kinase inhibitors (TKI) to the chemotherapy backbone. Data that support the benefit of hematopoietic stem cell transplantation (HSCT) in high risk patient subsets or in late relapse patients are still questioned and have yet to be determined conclusive. This article presents the newly published data in ALL workup and treatment, putting it into perspective for the attending physician in hematology and oncology.

scholarly journals Metabolomic and transcriptomic analyses of mutant yellow leaves provide insights into pigment synthesis and metabolism in Ginkgo biloba

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yaqiong Wu ◽  
Jing Guo ◽  
Tongli Wang ◽  
Fuliang Cao ◽  
Guibin Wang
Keyword(s):  
Ginkgo Biloba ◽  
Color Variation ◽  
Differentially Expressed ◽  
Flavonoid Pathway ◽  
Pigment Synthesis ◽  
Normal Green ◽  
Leaf Coloration ◽  
Photosynthesis Pathway ◽  
Different Color ◽  
Leaf Mutants

Abstract Background Ginkgo (Ginkgo biloba L.) is an excellent landscape species. Its yellow-green leaf mutants are ideal materials for research on pigment synthesis, but the regulatory mechanism of leaf coloration in these ginkgo mutants remains unclear. Results We compared the metabolomes and transcriptomes of green and mutant yellow leaves of ginkgo over the same period in this study. The results showed that the chlorophyll content of normal green leaves was significantly higher than that of mutant yellow leaves of ginkgo. We obtained 931.52M clean reads from different color leaves of ginkgo. A total of 283 substances in the metabolic profiles were finally detected, including 50 significantly differentially expressed metabolites (DEMs). We identified these DEMs and 1361 differentially expressed genes (DEGs), with 37, 4, 3 and 13 DEGs involved in the photosynthesis, chlorophyll, carotenoid, and flavonoid biosynthesis pathways, respectively. Moreover, integrative analysis of the metabolomes and transcriptomes revealed that the flavonoid pathway contained the upregulated DEM (−)-epicatechin. Fourteen DEGs from the photosynthesis pathway were positively or negatively correlated with the DEMs. Conclusions Our findings suggest a complex metabolic network in mutant yellow leaves. This study will provide a basis for studies of leaf color variation and regulation.

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