Identification of miRNAs and their targets in transgenic Brassica napus and its acceptor (Westar) by high-throughput sequencing and degradome analysis

RSC Advances ◽  
2015 ◽  
Vol 5 (104) ◽  
pp. 85383-85394 ◽  
Author(s):  
Cheng-Yi Tang ◽  
Min-Kai Yang ◽  
Feng-Yao Wu ◽  
Hua Zhao ◽  
Yan-Jun Pang ◽  
...  
Keyword(s):  
Stress Response ◽  
Brassica Napus ◽  
Plant Growth ◽  
High Throughput ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Degradome Analysis ◽  
Growth Development

MicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that play many roles in plant growth, development, and the stress response.

scholarly journals High throughput sequencing of two celery varieties small RNAs identifies microRNAs involved in temperature stress response

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 242 ◽  
Author(s):  
Meng-Yao Li ◽  
Feng Wang ◽  
Zhi-Sheng Xu ◽  
Qian Jiang ◽  
Jing Ma ◽  
...  
Keyword(s):  
Stress Response ◽  
Temperature Stress ◽  
High Throughput ◽  
Small Rnas ◽  
High Throughput Sequencing

scholarly journals Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 421 ◽  
Author(s):  
Miao Y Xu ◽  
Yun Dong ◽  
Qiu X Zhang ◽  
Lan Zhang ◽  
Yan Z Luo ◽  
...  
Keyword(s):  
Brassica Napus ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Degradome Analysis

scholarly journals Identifying the Active Microbiome Associated with Roots and Rhizosphere Soil of Oilseed Rape

2017 ◽  
Vol 83 (22) ◽  
Author(s):  
Konstantia Gkarmiri ◽  
Shahid Mahmood ◽  
Alf Ekblad ◽  
Sadhna Alström ◽  
Nils Högberg ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Stable Isotope ◽  
Oilseed Rape ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Stable Isotope Probing ◽  
Biofuel Production ◽  
Content Type ◽  
Bacteria And Fungi

ABSTRACT RNA stable isotope probing and high-throughput sequencing were used to characterize the active microbiomes of bacteria and fungi colonizing the roots and rhizosphere soil of oilseed rape to identify taxa assimilating plant-derived carbon following 13CO2 labeling. Root- and rhizosphere soil-associated communities of both bacteria and fungi differed from each other, and there were highly significant differences between their DNA- and RNA-based community profiles. Verrucomicrobia, Proteobacteria, Planctomycetes, Acidobacteria, Gemmatimonadetes, Actinobacteria, and Chloroflexi were the most active bacterial phyla in the rhizosphere soil. Bacteroidetes were more active in roots. The most abundant bacterial genera were well represented in both the 13C- and 12C-RNA fractions, while the fungal taxa were more differentiated. Streptomyces, Rhizobium, and Flavobacterium were dominant in roots, whereas Rhodoplanes and Sphingomonas (Kaistobacter) were dominant in rhizosphere soil. “Candidatus Nitrososphaera” was enriched in 13C in rhizosphere soil. Olpidium and Dendryphion were abundant in the 12C-RNA fraction of roots; Clonostachys was abundant in both roots and rhizosphere soil and heavily 13C enriched. Cryptococcus was dominant in rhizosphere soil and less abundant, but was 13C enriched in roots. The patterns of colonization and C acquisition revealed in this study assist in identifying microbial taxa that may be superior competitors for plant-derived carbon in the rhizosphere of Brassica napus. IMPORTANCE This microbiome study characterizes the active bacteria and fungi colonizing the roots and rhizosphere soil of Brassica napus using high-throughput sequencing and RNA-stable isotope probing. It identifies taxa assimilating plant-derived carbon following 13CO2 labeling and compares these with other less active groups not incorporating a plant assimilate. Brassica napus is an economically and globally important oilseed crop, cultivated for edible oil, biofuel production, and phytoextraction of heavy metals; however, it is susceptible to several diseases. The identification of the fungal and bacterial species successfully competing for plant-derived carbon, enabling them to colonize the roots and rhizosphere soil of this plant, should enable the identification of microorganisms that can be evaluated in more detailed functional studies and ultimately be used to improve plant health and productivity in sustainable agriculture.

scholarly journals The high-throughput sequencing of small RNAs profiling in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra

Genomics Data ◽  
2015 ◽  
Vol 3 ◽  
pp. 1-3 ◽  
Author(s):  
Muhammad Awais Ghani ◽  
Junxing Li ◽  
Linli Rao ◽  
Muhammad Ammar Raza ◽  
Liwen Cao ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
High Throughput ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Brassica Nigra ◽  
Wide Hybridisation

Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis

Planta ◽  
2016 ◽  
Vol 245 (1) ◽  
pp. 161-182 ◽  
Author(s):  
Dhananjay Kumar ◽  
Summi Dutta ◽  
Dharmendra Singh ◽  
Kumble Vinod Prabhu ◽  
Manish Kumar ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Leaf Rust ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Triticum Aestivum L ◽  
Degradome Analysis
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