scholarly journals Identification of shell-color-related microRNAs in the Manila clam Ruditapes philippinarum using high-throughput sequencing of small RNA transcriptomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jianfeng Ding ◽  
Qiang Wen ◽  
Zhongming Huo ◽  
Hongtao Nie ◽  
Yanjie Qin ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
High Throughput ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Color Polymorphism ◽  
Ruditapes Philippinarum ◽  
Manila Clam ◽  
Shell Color ◽  
Color Formation ◽  
Micro Rnas

AbstractShell-color polymorphism is a common phenomenon in several mollusk species and has been associated with thermal capacity, developmental stability, shell strength, and immunity. Shell-color polymorphism has been related to the differential expression of genes in several signal transduction pathways; however, the functions of micro-RNAs (miRNAs) in shell-color formation remain unclear. In the present study, we compared high-quality, small-RNA transcriptomes in three strains of the Manila clam Ruditapes philippinarum with specific shell-color patterns, artificially selected for six generations. Totals of 114 known and 208 novel miRNAs were identified by high-throughput sequencing, of which nine known and one novel miRNA were verified by stem-loop quantitative real time-polymerase chain reaction. Predicted miRNA targets were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. miR-137 and miR-216b and the Hedgehog signaling pathway and Wnt signaling pathway were identified as being potentially involved in pigment formation and regulation in R. philippinarum. These results may help to clarify the role of miRNAs in shell coloration and shed light on the mechanisms regulating color formation in bivalve shells.

scholarly journals Molecular cloning and expression analysis of tyrosinases (tyr) in four shell-color strains of Manila clam Ruditapes philippinarum

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8641 ◽  
Author(s):  
Kunyin Jiang ◽  
Liwen Jiang ◽  
Hongtao Nie ◽  
Zhongming Huo ◽  
Xiwu Yan
Keyword(s):  
Developmental Stages ◽  
Larval Growth ◽  
Negative Control ◽  
Ruditapes Philippinarum ◽  
Manila Clam ◽  
Cloning And Expression ◽  
Expression Level ◽  
Shell Color ◽  
Color Formation ◽  
Color Strains

The Manila clam (Ruditapes philippinarum) is an economically important molluscan bivalve with variation in pigmentation frequently observed in the shell. In nature, tyrosinase is widely distributed in invertebrates and vertebrates, and plays a crucial role in a variety of physiological activities. In this study, a tyrosinase gene (tyr 9) was cloned and the expression level of tyr genes (tyr 6, tyr 9, tyr 10, and tyr 11) were investigated in different shell colors. Quantitative real-time PCR showed that tyr genes were significantly expressed in the mantle, a shell formation and pigmentation-related tissue. Moreover, the expression pattern of the tyr genes in the mantle of different shell-color strains was different, suggesting that tyrosinases might be involved in different shell-color formation. In addition, the expression profile of tyr 6, tyr 9, tyr 10, and tyr 11 genes were detected at different early developmental stages and the expression level varied with embryonic and larval growth. RNA interference (RNAi) results showed that the expression level of tyr 9 in the RNAi group was significantly down-regulated compared to control and negative control groups, indicating that Rptyr 9 might participate in shell-color formation. Our results indicated that tyr genes were likely to play vital roles in the formation of shell and shell-color in R. philippinarum.

scholarly journals Transcriptomics of In Vitro Immune-Stimulated Hemocytes from the Manila Clam Ruditapes philippinarum Using High-Throughput Sequencing

PLoS ONE ◽  
2012 ◽  
Vol 7 (4) ◽  
pp. e35009 ◽  
Author(s):  
Rebeca Moreira ◽  
Pablo Balseiro ◽  
Josep V. Planas ◽  
Berta Fuste ◽  
Sergi Beltran ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Ruditapes Philippinarum ◽  
Manila Clam

scholarly journals Millet Could Be both a Weed and Serve as a Virus Reservoir in Crop Fields

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 954
Author(s):  
György Pasztor ◽  
Zsuzsanna Galbacs N. ◽  
Tamas Kossuth ◽  
Emese Demian ◽  
Erzsebet Nadasy ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Seed Dormancy ◽  
High Throughput ◽  
Small Rna ◽  
Diagnostic Method ◽  
High Throughput Sequencing ◽  
Infection Risk ◽  
Viral Diseases ◽  
Crop Fields ◽  
Special Control

Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study, we focused on visual symptoms and detected the presence of several viruses in millet using serological methods, which can only detect the presence of the investigated pathogen. In this current work, we used small RNA high-throughput sequencing as an unbiased virus diagnostic method to uncover presenting viruses in randomly sampled millet grown as a volunteer weed in two maize fields, showing stunting, chlorosis, and striped leaves. Our results confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G, neither of which had been previously described in Hungary, were also identified. As these viruses can cause severe diseases in wheat and other cereals, their presence in a weed implies a potential infection risk. Our study indicates that the presence of millet in fields requires special control to prevent the emergence of new viral diseases in crop fields.

scholarly journals Accurate detection for a wide range of mutation and editing sites of microRNAs from small RNA high-throughput sequencing profiles

2016 ◽  
Vol 44 (14) ◽  
pp. e123-e123 ◽  
Author(s):  
Yun Zheng ◽  
Bo Ji ◽  
Renhua Song ◽  
Shengpeng Wang ◽  
Ting Li ◽  
...  
Keyword(s):  
High Throughput ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Accurate Detection ◽  
Wide Range

scholarly journals High-Throughput Sequencing of Small RNA Transcriptome Reveals Salt Stress Regulated MicroRNAs in Sugarcane

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e59423 ◽  
Author(s):  
Mariana Carnavale Bottino ◽  
Sabrina Rosario ◽  
Clicia Grativol ◽  
Flávia Thiebaut ◽  
Cristian Antonio Rojas ◽  
...  
Keyword(s):  
Salt Stress ◽  
High Throughput ◽  
Small Rna ◽  
High Throughput Sequencing

scholarly journals Transcriptome analysis reveals the pigmentation related genes in four different shell color strains of the Manila clam Ruditapes philippinarum

Genomics ◽  
2020 ◽  
Vol 112 (2) ◽  
pp. 2011-2020 ◽  
Author(s):  
Hongtao Nie ◽  
Kunyin Jiang ◽  
Liwen Jiang ◽  
Zhongming Huo ◽  
Jianfeng Ding ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Ruditapes Philippinarum ◽  
Manila Clam ◽  
Shell Color ◽  
Color Strains

scholarly journals Differential Expression of Maize and Teosinte microRNAs under Submergence, Drought, and Alternated Stress

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1367
Author(s):  
Edgar Baldemar Sepúlveda-García ◽  
José Francisco Pulido-Barajas ◽  
Ariana Arlene Huerta-Heredia ◽  
Julián Mario Peña-Castro ◽  
Renyi Liu ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Zea Mays ◽  
High Throughput ◽  
Small Rna ◽  
Abiotic Stresses ◽  
Crop Production ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Evolutionary Divergence ◽  
Rna Profiling

Submergence and drought stresses are the main constraints to crop production worldwide. MicroRNAs (miRNAs) are known to play a major role in plant response to various stresses. In this study, we analyzed the expression of maize and teosinte miRNAs by high-throughput sequencing of small RNA libraries in maize and its ancestor teosinte (Zea mays ssp. parviglumis), under submergence, drought, and alternated stress. We found that the expression patterns of 67 miRNA sequences representing 23 miRNA families in maize and other plants were regulated by submergence or drought. miR159a, miR166b, miR167c, and miR169c were downregulated by submergence in both plants but more severely in maize. miR156k and miR164e were upregulated by drought in teosinte but downregulated in maize. Small RNA profiling of teosinte subject to alternate treatments with drought and submergence revealed that submergence as the first stress attenuated the response to drought, while drought being the first stress did not alter the response to submergence. The miRNAs identified herein, and their potential targets, indicate that control of development, growth, and response to oxidative stress could be crucial for adaptation and that there exists evolutionary divergence between these two subspecies in miRNA response to abiotic stresses.

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