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Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis.

Huang A, He L, Wang G - BMC Genomics (2011)

Bottom Line: They were probable P. tricornutum-specific novel miRNAs.These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on.Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, China.

ABSTRACT

Background: Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions.

Results: A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on.

Conclusions: Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.

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Small RNA (redundant sequences) distribution across different chromosomes. Y axis, number of small RNA tags that located on each chromosomes. X axis, chromosomes. Bars above the axis represent matches to the plus strand; bars below the axis represent those to the minus strand. (A) PT1. (B) PT2. (C) PT3.
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Figure 2: Small RNA (redundant sequences) distribution across different chromosomes. Y axis, number of small RNA tags that located on each chromosomes. X axis, chromosomes. Bars above the axis represent matches to the plus strand; bars below the axis represent those to the minus strand. (A) PT1. (B) PT2. (C) PT3.

Mentions: To determine the likely roles of miRNAs in nitrogen and silicon metabolism in P. tricornutum, we constructed and sequenced small RNA libraries from P. tricornutum grown in normal (PT1), nitrogen-free (PT2) and silicon-free (PT3) media, respectively. After removing adaptor sequences and filtering out low quality data (see Additional file 1 for flow chart of the procedure for processing of reads), we obtained small RNAs with size range of 10-30 nt, with an enrichment in 20-22 nt (Figure 1). After removing sequences shorter than 18 nt, we obtained 8 924 476, 5 609 466 and 6 982 282 total sequences, representing 718 770, 596 498 and 672 323 unique, although sometimes partially overlapping, clean reads from PT1, PT2 and PT3, respectively (Table 1). Of these unique sequences, about 73% (521 761), 74% (441 959) and 73% (491 748) were only sequenced once. There were 4 105 629, 2 492 000 and 2 908 127 total; and 221 523, 262 038 and 250 371 unique sequences with at least one perfect match in the P. tricornutum nuclear genome - whereas 3 076 974, 1 503 395 and 2 410 100 total; and 68 048, 43 151 and 55 321 unique sequences matched the chloroplast genome, in PT1, PT2 and PT3, respectively (Table 1). It was quite unexpected that a majority of sRNAs were located in the minus strand of chromosome 13 and both strands of the chloroplast genome (Figure 2). The usual preference for a U at the 5' - end of plant small RNA sequences [40] was not observed (see Additional file 2 for redundant small RNA nucleotide bias at each position). The four types of bases appeared equally in each locus.


Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis.

Huang A, He L, Wang G - BMC Genomics (2011)

Small RNA (redundant sequences) distribution across different chromosomes. Y axis, number of small RNA tags that located on each chromosomes. X axis, chromosomes. Bars above the axis represent matches to the plus strand; bars below the axis represent those to the minus strand. (A) PT1. (B) PT2. (C) PT3.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3141676&req=5

Figure 2: Small RNA (redundant sequences) distribution across different chromosomes. Y axis, number of small RNA tags that located on each chromosomes. X axis, chromosomes. Bars above the axis represent matches to the plus strand; bars below the axis represent those to the minus strand. (A) PT1. (B) PT2. (C) PT3.
Mentions: To determine the likely roles of miRNAs in nitrogen and silicon metabolism in P. tricornutum, we constructed and sequenced small RNA libraries from P. tricornutum grown in normal (PT1), nitrogen-free (PT2) and silicon-free (PT3) media, respectively. After removing adaptor sequences and filtering out low quality data (see Additional file 1 for flow chart of the procedure for processing of reads), we obtained small RNAs with size range of 10-30 nt, with an enrichment in 20-22 nt (Figure 1). After removing sequences shorter than 18 nt, we obtained 8 924 476, 5 609 466 and 6 982 282 total sequences, representing 718 770, 596 498 and 672 323 unique, although sometimes partially overlapping, clean reads from PT1, PT2 and PT3, respectively (Table 1). Of these unique sequences, about 73% (521 761), 74% (441 959) and 73% (491 748) were only sequenced once. There were 4 105 629, 2 492 000 and 2 908 127 total; and 221 523, 262 038 and 250 371 unique sequences with at least one perfect match in the P. tricornutum nuclear genome - whereas 3 076 974, 1 503 395 and 2 410 100 total; and 68 048, 43 151 and 55 321 unique sequences matched the chloroplast genome, in PT1, PT2 and PT3, respectively (Table 1). It was quite unexpected that a majority of sRNAs were located in the minus strand of chromosome 13 and both strands of the chloroplast genome (Figure 2). The usual preference for a U at the 5' - end of plant small RNA sequences [40] was not observed (see Additional file 2 for redundant small RNA nucleotide bias at each position). The four types of bases appeared equally in each locus.

Bottom Line: They were probable P. tricornutum-specific novel miRNAs.These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on.Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences (IOCAS), Qingdao, China.

ABSTRACT

Background: Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatoms' mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions.

Results: A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were sequenced from P. tricornutum under normal, nitrogen-limited and/or silicon-limited conditions, and their potential targets were involved in various processes, such as signal transduction, protein amino acid phosphorylation, fatty acid biosynthetic process, regulation of transcription and so on.

Conclusions: Our results indicated that P. tricornutum contained novel miRNAs that have no identifiable homologs in other organisms and that they might play important regulator roles in P. tricornutum metabolism.

Show MeSH
Related in: MedlinePlus