Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Research article

MicroRNAs of Bombyx mori identified by Solexa sequencing

Shiping Liu1, Dong Li1, Qibin Li2, Ping Zhao1, Zhonghuai Xiang1 and Qingyou Xia13*

Author Affiliations

1 The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Tiansheng Road, Beibei, Chongqing 400715, PR China

2 Beijing Genomics Institute, Beishan Road, Yantian District, Shenzhen 518083, PR China

3 Institute of Agricultural and Life Sciences, Chongqing University, Shazhengjie, Shapingba, Chongqing 400030, PR China

For all author emails, please log on.

BMC Genomics 2010, 11:148  doi:10.1186/1471-2164-11-148

Published: 3 March 2010

Additional files

Additional file 1:

The flow results of data filtration and distribution of sequenced small RNAs across different categories. After sequential filtration, the raw data in each library were separated into low and high quality reads. High quality reads with at least 18 nt were differentiated into categories of short sequencing reads, including rRNA, tRNA, snoRNA, fragments of sense and antisense exons and introns of coding genes, repeat sequences in transposable elements, unannotated short sequencing reads and some annotated miRNAs. Novel miRNAs were screened from unannotated sequencing reads and repeated sequences in transposable elements. Final miRNA data in each library are highlighted in blue. (A) Yield of whole body. (B) Yield of anterior-middle silk gland. (C) Yield of posterior silk gland.

Format: XLS Size: 29KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Distribution of clean tag reads from whole body and silk gland batches. As shown in Additional file 1, the total high quality reads in each library (2,619,505 in the whole silkworm body) minus reads of adapters and inserts represent the clean tag reads in this Additional file. However, only sequences equal to and longer than 10 nt in each library were summed up for total reads in the respective tables (to the left of this file). Graphs on the right are derived from data from the table (left).

Format: XLS Size: 297KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3:

Silkworm miRNAs identified by Solexa sequencing. In all, 324 miRNA genes (loci) were identified in the silkworm genome, responsible for 209 unique miRNAs and 87 star sequences, which were screened from the raw data through flow data filtration. All known and novel miRNAs have been submitted to the international public DataBase, miRBase. The temporal names of novel miRNAs were replaced by the assigned names. The bmo-mir-276 well mapped to Build 1, but not to the Build2 genome sequence (blast 1e-5). Three new miRNAs, bmo-mir-100, bmo-mir-92b and bmo-mir-216, did not pass the filtering threshold due to their uncanonical hairpin structures, but were finally identified through homolog searches. Another two annotated miRNAs, bmo-mir-1920 and bmo-mir-1921, were not included in this file, since they showed sequential processing in generating mature sequences and no more accumulated reads were observed (Additional file 10). Several novel miRNA genes have duplicated loci within the silkworm genome. The U in the sequence was replaced with T, and sequences presented in the DNA form.

Format: XLS Size: 167KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Sequence reads and hairpin structures of all sequenced miRNAs in the whole body. (A) Known silkworm miRNAs further identified using Solexa sequencing in the whole body. (B) Novel miRNAs of whole body predicted with mireap based on Solexa sequencing reads. (C) Repeat-associated novel miRNAs of whole body predicted as above.

Format: XLS Size: 225KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 5:

Sequence reads and hairpin structures of sequenced miRNAs in the anterior-middle silk gland. (A) Known silkworm miRNAs further identified in the anterior-middle silk gland using Solexa sequencing. (B) Novel miRNAs of the anterior-middle silk gland predicted with mireap based on Solexa sequencing reads. (C) Repeat-associated novel miRNAs of the anterior-middle silk gland predicted using mireap based on Solexa sequencing reads.

Format: XLS Size: 513KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 6:

Sequence reads and hairpin structures of all sequenced miRNAs in the posterior silk gland. (A) Known silkworm miRNAs in the posterior silk gland further identified using Solexa sequencing. (B) Novel miRNAs of the posterior silk gland predicted with mireap based on Solexa sequencing reads. (C) Repeat-associated novel miRNAs of the posterior silk gland predicted using mireap based on Solexa sequencing reads.

Format: XLS Size: 335KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 7:

Conservation analysis of silkworm miRNAs. All known miRNAs and their orthologs were downloaded from miRBase 14.0. Abbreviations: inv-ver, widely identified in invertebrates and vertebrates; inv, identified in invertebrates; ins, identified in insects; sw, reported only in the silkworm. The colors in 'conservation' only highlight the differences in their conservation for easier viewing. Three miRNAs, bmo-mir-9b, bmo-mir-1924 and bmo-mir-1926, had no sequencing reads corresponding to previously reported miRNA sequences across the three libraries but the star sequence of bmo-mir-9b, miR-9b*, was identified in the anterior-middle and posterior silk glands (highlighted in blue). Nucleotides in red in some mature sequences were confirmed by Solexa sequencing.

Format: XLS Size: 52KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 8:

Insight into phylogenetic relationships among species from categorization of conserved silkworm miRNAs. To know about phylogenetic relationships among diverse species on the basis of conservation of miRNAs, we used all known and novel silkworm miRNAs to BLASTN against the localized mature sequence data downloaded from the latest miRBase database. Only those miRNAs and miRNA*s with high sequence similarity to the mature sequences of silkworm are left in this file. The first miRNA in each group (highlighted in blue) is the silkworm miRNAs identified in this study or previously reported.

Format: XLS Size: 346KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 9:

Known silkworm miRNAs refined based on Solexa sequencing results. Different nucleotides in sequences from miRBase 14.0 are highlighted in blue and different nucleotides in the Solexa sequencing reads highlighted in red. Annotated mature sequences of 9 miRNAs (green in the 'name' column) were significantly fewer than those from other arms of the hairpin precursors. The reported mature sequences of bmo-mir-1920 and bmo-mir-1921 (purple) should be refined on the basis of Solexa sequencing reads. Annotated sequences from miRBase 14.0 and sequences with the highest reads are presented in bold.

Format: XLS Size: 30KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 10:

Heterogeneity of mature sequences of bmo-mir-1920 and mir-1921. (A) Heterogeneity in the whole body. (B) Heterogeneity in the anterior-middle silk gland. (C) Heterogeneity in the posterior silk gland.

Format: XLS Size: 229KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11:

Closely clustered miRNAs of the silkworm. For our analysis, groups of miRNA genes located within 2.5 kb of each other are defined as clusters. The close proximity of these miRNA genes in each cluster implies that they are likely to be transcribed as a single polycistronic transcript. Actually, more clusters can be identified when the space region is extended to a wider region than 2.5 kb.

Format: XLS Size: 72KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 12:

Paralogous miRNA genes of the silkworm. Shown here are 45 groups of paralogous miRNA genes identified on the similarity of mature sequences, miRNAs or miRNA*s. Repeats of some miRNA genes in the genome are also considered paralogs since they are responsible for high similar (even identical) mature sequences. For the convenience of comparison and description, much information shown in Additional file 3 was also presented in this file.

Format: XLS Size: 95KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 13:

The reads count of conserved and silkworm-specific miRNAs. The existence (+) or not (-) of miRNAs in the three libraries were clearly summarized in the samples' columns, WB, AMSG, PSG. Other information maintained only for the convenience of comparative analysis.

Format: XLS Size: 108KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data