Welcome to msRepDB database

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msRepDB - a comprehensive multi-species repetitive sequence database

Authors: Xingyu Liao, Kang Hu, Adil Salhi1, Jianxin Wang and Xin Gao

Corresponding Author: Prof. Xin Gao (xin.gao@kaust.edu.sa)

Repetitive sequences are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the human genome (01,02). Repetitive sequences play indispensable roles in the evolution, inheritance, variation, genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations (03,04,05,06,07). For example, the number and types of repetitive sequences vary between organisms and may reflect how rapidly an organism evolves to changes in its environment (08,09). Comprehensive identification, classification and annotation of repetitive elements in genomes can provide accurate and targeted solutions for research and diagnosis of complex diseases, optimization of plant properties, development of new drugs, and individual health management. RepBase (10) and Dfam (11) libraries are two most frequently used repeat databases, but they are not sufficiently complete. For instance, in the Drosophila genome, when the combination of RepBase and Dfam is used as the repetitive sequence database, only 4.04% of bases can be accurately annotated as repetitive sequences, as compared to 23.39% for msRepDB. However, it is well known that the proportion of repeat in Drosophila genome should be about 22%, which means that there are a large number of repeats cannot be annotated. Due to the lack of a comprehensive repetitive sequence database of multiple species, the current research in this field is far from being satisfactory.

LongRepMarker (12, DOI:10.1093/nar/gkab563) is a new framework developed recently by our group for comprehensive identification of genomic repetitive sequences. By integrating the detection results of LongRepMarker and existing databases (i.e, RepBase and Dfam), we here propose msRepDB, which is currently the most comprehensive multi-species repetitive sequence database (i.e., it contains 61,347 species). msRepDB takes the reference sequence or assembly of species as the input, and generates the masked sequence and comprehensive annotation report as the output. When the input data are reference sequences or assemblies, it should be in the fasta format (https://en.wikipedia.org/wiki/FASTA_format), and msRepDB takes out all the sequences and matches them with the database to find out the repeated elements contained in the sequences, as well as their locations and types, and finally masks the repeated elements in the input sequence and generates an annotation report. msRepDB also provides query and download functions. Users can retrieve and download the repetitive elements and their annotation reports from msRepDB according to the axon name or family name. On the other hand, if the user does not have any data, but just a taxon name or a repeat family name, msRepDB will also retrieve all relevant contents from the database and provide download links.

We deployed the first working version of msRepDB on the university intranet in October, 2020. Since then, msRepDB has handled more than 100 jobs to evaluate its performance and functionality, as well as its compatibility with major web browsers. We have had six individuals outside of our group with different background to test the database. We have conducted various experimental evaluations on the comprehensiveness of the msRepDB database. For example, we used the latest version of RepeatMasker (V.4.1.2) to classify and annotate the repeats of rice and drosophila based on msRepDB and the combination of the latest RepBase (V.26.06) and Dfam (V.3.3). The experimental results show that RepeatMasker annotated 315,702 DNA-type repeats (17,435.133kb in length) on the rice genome based on msRepDB, as compared to 8,008 DNA-type repeats (247.292kb in length) for the combination of the state-of-the-art databases. All the experimental data will be shown in the manuscript.

Main improvements of msRepDB

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Compared with the existing repeat databases, the major improvements of msRepDB are as follows:

1. msRepDB contains more species than RepBase and Dfam databases

RepBase and Dfam libraries are the two most frequently used repeat databases, but they are not sufficiently complete, because most of the repetitive sequences collected in these two libraries are obtained through some existing detection methods (such as RepeatMasker, RepeatScout, RepeatModeler and RepeatModeler2). Due to the limitations of sequencing data and the defects in design of the detection principle, existing detection methods cannot accurately and comprehensively obtain the repetitive sequences of species.

LongRepMarker (DOI:10.1093/nar/gkab563, https://github.com/BioinformaticsCSU/LongRepMarker) is a new framework developed recently by our group for comprehensive identification of genomic repetitive sequences. The comprehensive experiments carried out in the study of LongRepMarker not only show that LongRepMarker can achieve more satisfactory results than the existing detection methods (Table 1), but also can discover a large number of new repeat sequences and families (Table 2). By integrating the detection results of LongRepMarker and existing databases (i.e, RepBase and Dfam), we here propose msRepDB, which is currently the most comprehensive multi-species repetitive sequence database (i.e., it contains more than 62,000 species).

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Table 1. Comparison of the proportion and detailed classification of detection results generated by three tools on Human(hg38) dataset covering the corresponding RepBase library.


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Table 2. Compared with RepeatMasker, LongRepMarker found repeat families and their detailed numbers on the Drosophila dataset.



2. For a single species, msRepDB contains more complete repeats and families than the existing repeat databases

We have conducted various experimental evaluations on the comprehensiveness of the msRepDB database. For example, we used the latest version of RepeatMasker (V.4.1.2) to classify and annotate the repeats of rice and drosophila based on msRepDB and the combination of the latest RepBase (V.26.06) and Dfam (V.3.3). The experimental results show that RepeatMasker annotated 80,003 LINE-type repeats (8,110.286kb in length) on the drosophila genome based on msRepDB, as compared to 49,524 LINE-type repeats (82.968kb in length) for the combination of the state-of-the-art databases (Table 3), and annotated 315,702 DNA-type repeats (17,435.133kb in length) on the rice genome based on msRepDB, as compared to 8,008 DNA-type repeats (247.292kb in length) for the combination of the state-of-the-art databases (Table 4). All the experimental data will be shown in the manuscript.

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Table 3. Partial comparison of the proportion and detailed classification of detected repeats generated based on two databases of drosophila genome.


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Table 4. Partial comparison of the proportion and detailed classification of detected repeats generated based on two databases of rice genome.


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   (A) Drosophila                                                                                                                             (B) Rice

Fig. 1 Comparison of the length occupied of repeat families based on two databases. Sub-figure(A) shows the comparison of the length occupied of repeat families of the two databases on the drosophila genome; Sub-figure(B) shows the comparison of the length occupied of repeat families of the two databases on the rice genome.

It can be seen from the experimental results shown above that msRepDB is the most complete multi-species repetitive sequence database at present because it integrates the detection results of longrepmarker, RepBase and Dfam libraries. We hope to be able to release the database for many species to the scientific community soon to benefit the genome research.



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