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Dernière mise à jour : Mai 2018

Menu Logo Principal AgroParisTech Université Paris-Saclay

INRA GABI Unit

GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

RumimiR : a database including all bovine, caprine and ovine microRNA

@Rumimir
The massive use of high-throughput sequencing techniqus has generated a large quantity of data. Many publications have described several hundreds of microRNA sequences. We created a new database, RumimiR, containing a detailed description of microRNA in bovines, caprines and ovines.

MOTS-CLES : microARN, ruminants, database

Ruminir-2
To date, 2 887, 2 733 and 5 095 bovine, caprine and ovine microRNA have respectively been included. In addition to their positions on the genome and their sequences, this database contains information concerning the animals, tissues and experimental conditions; microRNA may be selected according to different criteria. The information in RumimiR is more complete than the reference database miRBase since it provides important information on the studies performed in animal production such as breed and nutrition of the animals studied.

 

The main objective of this database is to be able to easily access all microRNA of ruminants described in the literature.

Genomic selection, which is based on the prediction of the genetic value of animal candidates for selection, based on the information provided by a large number of neutral markers, is a relevant and sustainable lever. The search for causal mutations and their integration in genomic evaluations provides an important gain in precision. It is therefore necessary to improve the characterizations of the causal mutations responsible for the variability of quantitative traits associated with production efficiency and product quality such as milk.

The high-throughput technological evolutions have allowed the fine identification of genomic regions having an effect on quantitative traits (QTL) in livestock. Some causal mutations have been identified in the coding regions of genes. However, in most of the QTL, candidate mutations have been identified in non-coding regions, amongst which the genes that code for microRNA are located.

Thus, we have developed a projet with the objective to perform fine mapping of dairy QTL in three ruminant species in order to identify microRNA located in these regions, to establish a complete catalogue of variants located in these microRNA, to study all the dairy microRNA-variants-QTL, and to evaluate the effect of these variants on microRNA function.

In order to carry out this project well, it was necessary to have access to all the microRNA described in the literature for cattle, goats and sheep. Classically scientists use the miRBase database that contains a catalogue of all the microRNA known in many species. However, upon its latest update in 2018, it was found that microRNA obtained by high-throughput sequencing are not included. In addition, miRBase does not contain information on the origin of microRNA such as breed, lactation stages of the animals, which are important elements to be considered in our project. We therefore decided to make this information collected in the literature available to scientists worldwide by creating the RumimiR database, thanks to partnerships between GaLac (GABI), GenROC (GenPhySE) and Sigenae.

Data from 78 articles were collected. Thus 2 887, 2 733 and 5 059 microRNA from cattle, goats and sheep respectively were recorded in RumimiR. The detailed information of the animals (age, breed, etc.), the reason of the study (health, nutrition,etc.), the samples (tissues), the sequencing technique present in each publication are recorded in RumimiR. In order to homogenize the information, the microRNA sequences were aligned according to the latest versions of the reference genomes available in 2018, that is UMD3.1.1 for cattle, ARS1 for goats and Oar v4.0 for sheep. MicroRNA sequences are systematically compared with sequences of small RNA already described (ribosomal, transfer, nuclear RNA, ....) and their identity with human and murine microRNA were also sought. These complementary analyses allowed us to propose a code for false-positives for each microRNA entered in the database, providing users with additional information on the nature of the microRNA.

For each microRNA, 29 characteristics are provided. The database filters microRNA according to several of these characteristics and the results obtained are downloadable as different formats (Excel, Fasta, etc.).

The database contains all the microRNA known to this day in three species. New microRNA that will be described in the literature will be introduced into the database. Two updates are planned each year, with access to the archives of the previous versions. The reference genomes will also be considered for the updates. This database will be able to inlcude microRNA from other species if needed.
  

Contact(s)

Scientific Contact(s):

Associated Division(s): Animal Genetics

Associated Center(s): Jouy-en-josas

 

OpenScience

INRAE priority in the guidance document

#OpenScience-2:  Data organisation for sharing and reuse.

See also

Valorisation

This database is in open acces on internet: http://rumimir.sigenae.org/

Bibliography

Bourdon, C., Bardou, P., Aujean, E., Le Guillou, S., Tosser-Klopp, G., Le Provost, F. RumimiR: a detailed microRNA database focused on ruminant species. Database (2019) Vol. 2019: article ID baz099; doi:10.1093/database/baz099