Genome sequence and evolution of Betula platyphylla

AbstractBetula L. (birch) is a pioneer hardwood tree species with ecological, economic, and evolutionary importance in the Northern Hemisphere. We sequenced the Betula platyphylla genome and assembled the sequences into 14 chromosomes. The Betula genome lacks evidence of recent whole-genome duplication and has the same paleoploidy level as Vitis vinifera and Prunus mume. Phylogenetic analysis of lignin pathway genes coupled with tissue-specific expression patterns provided clues for understanding the formation of higher ratios of syringyl to guaiacyl lignin observed in Betula species. Our transcriptome analysis of leaf tissues under a time-series cold stress experiment revealed the presence of the MEKK1–MKK2–MPK4 cascade and six additional mitogen-activated protein kinases that can be linked to a gene regulatory network involving many transcription factors and cold tolerance genes. Our genomic and transcriptome analyses provide insight into the structures, features, and evolution of the B. platyphylla genome. The chromosome-level genome and gene resources of B. platyphylla obtained in this study will facilitate the identification of important and essential genes governing important traits of trees and genetic improvement of B. platyphylla.

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Identification, Characterization, and Expression Analysis Reveal Diverse Regulated Roles of Three MAPK Genes in Chlamys farreri Under Heat Stress

Frontiers in Physiology ◽

10.3389/fphys.2021.688626 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhi Liu ◽

Xiaoting Huang ◽

Zujing Yang ◽

Cheng Peng ◽

Haitao Yu ◽

...

Keyword(s):

Heat Stress ◽

Expression Patterns ◽

Chlamys Farreri ◽

Mitogen Activated Protein Kinase ◽

Specific Expression ◽

Temperature Changes ◽

Mapk Cascades ◽

Mitogen Activated Protein ◽

As Stress ◽

Eukaryotic Organisms

Mitogen-activated protein kinase (MAPK) cascades are fundamental signal transduction modules in all eukaryotic organisms, participating growth and development, as well as stress response. In the present study, three MAPK genes were successfully identified from the genome of Chlamys farreri, respectively, named CfERK1/2, CfJNK, and Cfp38, and only one copy of ERK, JNK, and p38 were detected. Domain analysis indicated that CfMAPKs possessed the typical domains, including S_TKc, Pkinase, and PKc_like domain. Phylogenetic analysis showed that three CfMAPKs of MAPK subfamilies exists in the common ancestor of vertebrates and invertebrates. All CfMAPKs specifically expressed during larval development and in adult tissues, and the expression level of CfERK1/2 and Cfp38 was apparently higher than that of CfJNK. Under heat stress, the expression of CfERK1/2 and Cfp38 were significantly downregulated and then upregulated in four tissues, while the expression of CfJNK increased in all tissues; these different expression patterns suggested a different molecular mechanism of CfMAPKs for bivalves to adapt to temperature changes. The diversity of CfMAPKs and their specific expression patterns provide valuable information for better understanding of the functions of MAPK cascades in bivalves.

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Genome edited colorectal cancer organoid models reveal distinct microRNA activity patterns across different mutation profiles

10.1101/2021.12.13.472432 ◽

2021 ◽

Author(s):

Jonathan W Villanueva ◽

Lawrence Kwong ◽

Teng Han ◽

Salvador Alonso Martinez ◽

Fong Cheng Pan ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Genetically Modified ◽

Activity Patterns ◽

Expression Patterns ◽

Regulatory Mechanisms ◽

Oncogenic Mutations ◽

Gene Regulatory ◽

Insight Into

Somatic mutations drive colorectal cancer (CRC) by disrupting gene regulatory mechanisms. Distinct combinations of mutations can result in unique changes to regulatory mechanisms leading to variability in the efficacy of therapeutics. MicroRNAs are important regulators of gene expression, and their activity can be altered by oncogenic mutations. However, it is unknown how distinct combinations of CRC-risk mutations differentially affect microRNAs. Here, using genetically-modified mouse intestinal organoid (enteroid) models, we identify ten different modules of microRNA expression patterns across distinct combinations of mutations common in CRC. We also show that miR-24-3p, which is aberrant in genetically-modified mouse enteroids and human colonoids irrespective of mutational context, is a master regulator of gene expression in CRC. In follow-up experiments, we also demonstrate that miR-24 promotes CRC cell survival. These findings offer insight into the mechanisms that drive inter-tumor heterogeneity and highlight candidate microRNA therapeutic targets for the advancement of precision medicine for CRC.

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Overexpression of BplERD15 Enhances Drought Tolerance in Betula platyphylla Suk.

Forests ◽

10.3390/f11090978 ◽

2020 ◽

Vol 11 (9) ◽

pp. 978

Author(s):

Kaiwen Lv ◽

Hairong Wei ◽

Jing Jiang

Keyword(s):

Expression Patterns ◽

Functional Characterization ◽

Early Response ◽

Growth Media ◽

Betula Platyphylla ◽

Specific Expression ◽

Growth Deficiency ◽

Young Leaves ◽

Betula Platyphylla Suk ◽

Responsive Gene

In this study, we report the cloning and functional characterization of an early responsive gene, BplERD15, from Betula platyphylla Suk to dehydration. BplERD15 is located in the same branch as Morus indica Linnaeus ERD15 and Arabidopsis Heynh ERD15 in the phylogenetic tree built with ERD family protein sequences. The tissue-specific expression patterns of BplERD15 were characterized using qRT-PCR and the results showed that the transcript levels of BplERD15 in six tissues were ranked from the highest to the lowest levels as the following: mature leaves (ML) > young leaves (YL) > roots (R) > buds (B) > young stems (YS) > mature stems (MS). Multiple drought experiments were simulated by adding various osmotica including polyethylene glycol, mannitol, and NaCl to the growth media to decrease their water potentials, and the results showed that the expression of BplERD15 could be induced to 12, 9, and 10 folds, respectively, within a 48 h period. However, the expression level of BplERD15 was inhibited by the plant hormone abscisic acid in the early response and then restored to the level of control. The BplERD15 overexpression (OE) transgenic birch lines were developed and they did not exhibit any phenotypic anomalies and growth deficiency under normal condition. Under drought condition, BplERD15-OE1, 3, and 4 all displayed some drought tolerant characteristics and survived from the drought while the wild type (WT) plants withered and then died. Analysis showed that all BplERD15-OE lines had significant lower electrolyte leakage levels as compared to WT. Our study suggests that BplERD15 is a drought-responsive gene that can reduce mortality under stress condition.

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Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes

BMC Genomic Data ◽

10.1186/s12863-021-00973-4 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Lin Yuan ◽

Kun Pan ◽

Yonghui Li ◽

Bo Yi ◽

Bingmiao Gao

Keyword(s):

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Genetically Engineered ◽

Flavonoid Biosynthesis ◽

Specific Gene ◽

Specific Expression ◽

Tissue Specific ◽

Alpinia Oxyphylla ◽

Leaf Tissues

Abstract Background Alpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. Results In all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3110 differentially expressed genes (DEGs) and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes associated with flavonoid biosynthesis. In particular, 9 DEGs were significantly up-regulated in fruits, whereas expression of 11 DEGs were highly up-regulated in roots, compared with those in leaves. Conclusion The DEGs and metabolic pathway related to flavonoids biosynthesis were identified in root, leaf, and different stages of fruits from A. oxyphylla. These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla.

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Insight into the B3Transcription Factor Superfamily and Expression Profiling of B3 Genes in Axillary Buds after Topping in Tobacco(Nicotiana tabacum L.)

Genes ◽

10.3390/genes10020164 ◽

2019 ◽

Vol 10 (2) ◽

pp. 164 ◽

Cited By ~ 3

Author(s):

Fei Xia ◽

Tingting Sun ◽

Shuangjuan Yang ◽

Xiao Wang ◽

Jiangtao Chao ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Expression Patterns ◽

Protein Structures ◽

Axillary Buds ◽

Comparative Genome Analysis ◽

Specific Expression ◽

Protein Motifs ◽

Nicotiana Tabacum L ◽

Gene Structures ◽

Insight Into

Members of the plant-specific B3 transcription factor superfamily play important roles in various growth and developmental processes in plants. Even though there are many valuable studies on B3 genes in other species, little is known about the B3 superfamily in tobacco. We identified 114 B3 proteins from tobacco using comparative genome analysis. These proteins were classified into four subfamilies based on their phylogenetic relationships, and include the ARF, RAV, LAV, and REM subfamilies. The chromosomal locations, gene structures, conserved protein motifs, and sub-cellular localizations of the tobacco B3 proteins were analyzed. The patterns of exon-intron numbers and arrangement and the protein structures of the tobacco B3 proteins were in general agreement with their phylogenetic relationships. The expression patterns of 114 B3 genes revealed that many B3 genes show tissue-specific expression. The expression levels of B3 genes in axillary buds after topping showed that the REM genes are mainly up-regulated in response to topping, while the ARF genes are down-regulated after topping.

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Transcriptome Analyses Reveal Circadian-Related Expression Features in the Visual Systems of Two Snakes

Diversity ◽

10.3390/d13120621 ◽

2021 ◽

Vol 13 (12) ◽

pp. 621

Author(s):

Chen-Yang Tang ◽

Meng-Huan Song ◽

Zhong-Liang Peng ◽

Wei Wu ◽

Changjun Peng ◽

...

Keyword(s):

Expression Patterns ◽

Genetic Research ◽

Retinal Cell ◽

Biological Functions ◽

Specific Expression ◽

Expression Of Genes ◽

Opsin Genes ◽

Phototransduction Pathway ◽

Circadian Patterns ◽

Insight Into

The visual characteristics of animals with different circadian habits, especially colubrid snakes, exhibit highly variable photoreceptor morphology. While studies have reported on the diversity in retinal cell morphology among snakes with different circadian patterns, few studies have examined the expression of genes related to vision. To explore gene expression patterns in the eyes between diurnal and nocturnal snakes, we carried out RNA sequencing of six tissues (eye, heart, liver, lung, kidney, and muscle) in two colubrids with disparate circadian activities, i.e., diurnal Ahaetulla prasina and nocturnal Lycodon flavozonatum, followed by weighted gene co-expression network analysis (WGCNA). The genes in the two most correlated modules were primarily enriched in different functional pathways, thus suggesting different biological functions. Three opsin genes (RH1, LWS, and SWS) were differentially expressed between the two species. Moreover, in the phototransduction pathway, different genes were highly expressed in the eyes of both species, reflecting specific expression patterns in the eyes of snakes with different circadian activity. We also confirmed the dominance of cone- and rod-related genes in diurnal and nocturnal adaptation, respectively. This work provides an important foundation for genetic research on visual adaptation in snakes and provides further insight into the adaptive evolution of such species.

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Tissue-specific expression patterns of nuclear receptors

NURSA Datasets ◽

10.1621/datasets.02001 ◽

2013 ◽

Author(s):

AL Bookout ◽

Y Jeong ◽

M Downes ◽

RT Yu ◽

RM Evans ◽

...

Keyword(s):

Nuclear Receptors ◽

Expression Patterns ◽

Specific Expression ◽

Tissue Specific ◽

Tissue Specific Expression

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Overexpression of the Oral Mucosa-Specific microRNA-31 Promotes Skin Wound Closure

International Journal of Molecular Sciences ◽

10.3390/ijms20153679 ◽

2019 ◽

Vol 20 (15) ◽

pp. 3679 ◽

Cited By ~ 3

Author(s):

Lin Chen ◽

Alyne Simões ◽

Zujian Chen ◽

Yan Zhao ◽

Xinming Wu ◽

...

Keyword(s):

Wound Healing ◽

Oral Mucosa ◽

Wound Closure ◽

Expression Patterns ◽

Skin Wound ◽

Skin Wound Healing ◽

Specific Expression ◽

Keratinocyte Proliferation

Wounds within the oral mucosa are known to heal more rapidly than skin wounds. Recent studies suggest that differences in the microRNAome profiles may underlie the exceptional healing that occurs in oral mucosa. Here, we test whether skin wound-healing can be accelerating by increasing the levels of oral mucosa-specific microRNAs. A panel of 57 differentially expressed high expresser microRNAs were identified based on our previously published miR-seq dataset of paired skin and oral mucosal wound-healing [Sci. Rep. (2019) 9:7160]. These microRNAs were further grouped into 5 clusters based on their expression patterns, and their differential expression was confirmed by TaqMan-based quantification of LCM-captured epithelial cells from the wound edges. Of these 5 clusters, Cluster IV (consisting of 8 microRNAs, including miR-31) is most intriguing due to its tissue-specific expression pattern and temporal changes during wound-healing. The in vitro functional assays show that ectopic transfection of miR-31 consistently enhanced keratinocyte proliferation and migration. In vivo, miR-31 mimic treatment led to a statistically significant acceleration of wound closure. Our results demonstrate that wound-healing can be enhanced in skin through the overexpression of microRNAs that are highly expressed in the privileged healing response of the oral mucosa.

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Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals

Scientific Reports ◽

10.1038/s41598-021-95082-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Leyla A. Erozenci ◽

Sander R. Piersma ◽

Thang V. Pham ◽

Irene V. Bijnsdorp ◽

Connie R. Jimenez

Keyword(s):

Expression Patterns ◽

Interaction Network ◽

Extracellular Vesicle ◽

Protein Signaling ◽

Protein Patterns ◽

Specific Expression ◽

Non Invasive ◽

Data Independent Acquisition ◽

Time Period ◽

Using Data

AbstractThe protein content of urinary extracellular vesicles (EVs) is considered to be an attractive non-invasive biomarker source. However, little is known about the consistency and variability of urinary EV proteins within and between individuals over a longer time-period. Here, we evaluated the stability of the urinary EV proteomes of 8 healthy individuals at 9 timepoints over 6 months using data-independent-acquisition mass spectrometry. The 1802 identified proteins had a high correlation amongst all samples, with 40% of the proteome detected in every sample and 90% detected in more than 1 individual at all timepoints. Unsupervised analysis of top 10% most variable proteins yielded person-specific profiles. The core EV-protein-interaction network of 516 proteins detected in all measured samples revealed sub-clusters involved in the biological processes of G-protein signaling, cytoskeletal transport, cellular energy metabolism and immunity. Furthermore, gender-specific expression patterns were detected in the urinary EV proteome. Our findings indicate that the urinary EV proteome is stable in longitudinal samples of healthy subjects over a prolonged time-period, further underscoring its potential for reliable non-invasive diagnostic/prognostic biomarkers.

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Longitudinal Expression of Testicular TAS1R3 from Prepuberty to Sexual Maturity in Congjiang Xiang Pigs

Animals ◽

10.3390/ani11020437 ◽

2021 ◽

Vol 11 (2) ◽

pp. 437

Author(s):

Ting Gong ◽

Weiyong Wang ◽

Houqiang Xu ◽

Yi Yang ◽

Xiang Chen ◽

...

Keyword(s):

Sexual Maturity ◽

Cell Function ◽

Expression Patterns ◽

Taste Receptor ◽

Receptor Type ◽

Mrna Levels ◽

Early Puberty ◽

Specific Expression

Testicular expression of taste receptor type 1 subunit 3 (T1R3), a sweet/umami taste receptor, has been implicated in spermatogenesis and steroidogenesis in mice. We explored the role of testicular T1R3 in porcine postnatal development using the Congjiang Xiang pig, a rare Chinese miniature pig breed. Based on testicular weights, morphology, and testosterone levels, four key developmental stages were identified in the pig at postnatal days 15–180 (prepuberty: 30 day; early puberty: 60 day; late puberty: 90 day; sexual maturity: 120 day). During development, testicular T1R3 exhibited stage-dependent and cell-specific expression patterns. In particular, T1R3 levels increased significantly from prepuberty to puberty (p < 0.05), and expression remained high until sexual maturity (p < 0.05), similar to results for phospholipase Cβ2 (PLCβ2). The strong expressions of T1R3/PLCβ2 were observed at the cytoplasm of elongating/elongated spermatids and Leydig cells. In the eight-stage cycle of the seminiferous epithelium in pigs, T1R3/PLCβ2 levels were higher in the spermatogenic epithelium at stages II–VI than at the other stages, and the strong expressions were detected in elongating/elongated spermatids and residual bodies. The message RNA (mRNA) levels of taste receptor type 1 subunit 1 (T1R1) in the testis showed a similar trend to levels of T1R3. These data indicate a possible role of T1R3 in the regulation of spermatid differentiation and Leydig cell function.

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