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Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan ( Daemonorops jenkinsiana )

View Article: PubMed Central - PubMed

ABSTRACT

Rattan is an important group of regenerating non-wood climbing palm in tropical forests. The cirrus is an essential climbing organ and provides morphological evidence for evolutionary and taxonomic studies. However, limited data are available on the molecular mechanisms underlying the development of the cirrus. Thus, we performed in-depth transcriptomic sequencing analyses to characterize the cirrus development at different developmental stages of Daemonorops jenkinsiana. The result showed 404,875 transcripts were assembled, including 61,569 high-quality unigenes were identified, of which approximately 76.16% were annotated and classified by seven authorized databases. Moreover, a comprehensive analysis of the gene expression profiles identified differentially expressed genes (DEGs) concentrated in developmental pathways, cell wall metabolism, and hook formation between the different stages of the cirri. Among them, 37 DEGs were validated by qRT-PCR. Furthermore, 14,693 transcriptome-based microsatellites were identified. Of the 168 designed SSR primer pairs, 153 were validated and 16 pairs were utilized for the polymorphic analysis of 25 rattan accessions. These findings can be used to interpret the molecular mechanisms of cirrus development, and the developed microsatellites markers provide valuable data for assisting rattan taxonomy and expanding the understanding of genomic study in rattan.

No MeSH data available.


Summary of the sequence annotations.(a) BLAST analysis of the non-redundant unigenes against seven public databases. (b) Pie-charts showing the distributions of BLAST matches of D. jenkinsiana transcriptome unigenes with respect to similarity, match percentage, and e-value. (c) GO classification. (d) COG annotation of the putative proteins. (e) KEGG annotation of the putative proteins. (f) Pie-chart showing distributions of the BLAST match of D. jenkinsiana transcriptome unigenes with respect to species containing the homologous genes.
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f1: Summary of the sequence annotations.(a) BLAST analysis of the non-redundant unigenes against seven public databases. (b) Pie-charts showing the distributions of BLAST matches of D. jenkinsiana transcriptome unigenes with respect to similarity, match percentage, and e-value. (c) GO classification. (d) COG annotation of the putative proteins. (e) KEGG annotation of the putative proteins. (f) Pie-chart showing distributions of the BLAST match of D. jenkinsiana transcriptome unigenes with respect to species containing the homologous genes.

Mentions: Based on the unigenes of the rattan, we performed a series of functional analyses to help researchers to expand the knowledge in rattan by protein sequence similarity searches among seven authorized databases. These databases included the non-redundant NCBI protein database (NR)20, UniProtKB/SwissProt database21, Clusters of Orthologous Groups (COG) database22, Gene Ontology (GO) database23, Kyoto Encyclopedia of Genes and Genomes (KEGG) database24, Conserved Domain Database for protein classification (CDD)25 and the InterPro database26. Thus, the integrated result (Fig. 1a) indicated that 46,890 unigenes (76.16%) can translate to relative protein sequences and then these were annotated, whereas the remaining unigenes (23.84%) as non-coding protein sequences were filtered in further analyses. The genes of the missing annotation may be due to the relatively short length of the query sequences and the lack of information on the rattan genome. Moreover, the percentage of the missing annotation (23.84%) by seven authorized databases was higher than the that of BUSCO (11.3%), which was likely caused by different alignment databases.


Transcriptome-based investigation of cirrus development and identifying microsatellite markers in rattan ( Daemonorops jenkinsiana )
Summary of the sequence annotations.(a) BLAST analysis of the non-redundant unigenes against seven public databases. (b) Pie-charts showing the distributions of BLAST matches of D. jenkinsiana transcriptome unigenes with respect to similarity, match percentage, and e-value. (c) GO classification. (d) COG annotation of the putative proteins. (e) KEGG annotation of the putative proteins. (f) Pie-chart showing distributions of the BLAST match of D. jenkinsiana transcriptome unigenes with respect to species containing the homologous genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382692&req=5

f1: Summary of the sequence annotations.(a) BLAST analysis of the non-redundant unigenes against seven public databases. (b) Pie-charts showing the distributions of BLAST matches of D. jenkinsiana transcriptome unigenes with respect to similarity, match percentage, and e-value. (c) GO classification. (d) COG annotation of the putative proteins. (e) KEGG annotation of the putative proteins. (f) Pie-chart showing distributions of the BLAST match of D. jenkinsiana transcriptome unigenes with respect to species containing the homologous genes.
Mentions: Based on the unigenes of the rattan, we performed a series of functional analyses to help researchers to expand the knowledge in rattan by protein sequence similarity searches among seven authorized databases. These databases included the non-redundant NCBI protein database (NR)20, UniProtKB/SwissProt database21, Clusters of Orthologous Groups (COG) database22, Gene Ontology (GO) database23, Kyoto Encyclopedia of Genes and Genomes (KEGG) database24, Conserved Domain Database for protein classification (CDD)25 and the InterPro database26. Thus, the integrated result (Fig. 1a) indicated that 46,890 unigenes (76.16%) can translate to relative protein sequences and then these were annotated, whereas the remaining unigenes (23.84%) as non-coding protein sequences were filtered in further analyses. The genes of the missing annotation may be due to the relatively short length of the query sequences and the lack of information on the rattan genome. Moreover, the percentage of the missing annotation (23.84%) by seven authorized databases was higher than the that of BUSCO (11.3%), which was likely caused by different alignment databases.

View Article: PubMed Central - PubMed

ABSTRACT

Rattan is an important group of regenerating non-wood climbing palm in tropical forests. The cirrus is an essential climbing organ and provides morphological evidence for evolutionary and taxonomic studies. However, limited data are available on the molecular mechanisms underlying the development of the cirrus. Thus, we performed in-depth transcriptomic sequencing analyses to characterize the cirrus development at different developmental stages of Daemonorops jenkinsiana. The result showed 404,875 transcripts were assembled, including 61,569 high-quality unigenes were identified, of which approximately 76.16% were annotated and classified by seven authorized databases. Moreover, a comprehensive analysis of the gene expression profiles identified differentially expressed genes (DEGs) concentrated in developmental pathways, cell wall metabolism, and hook formation between the different stages of the cirri. Among them, 37 DEGs were validated by qRT-PCR. Furthermore, 14,693 transcriptome-based microsatellites were identified. Of the 168 designed SSR primer pairs, 153 were validated and 16 pairs were utilized for the polymorphic analysis of 25 rattan accessions. These findings can be used to interpret the molecular mechanisms of cirrus development, and the developed microsatellites markers provide valuable data for assisting rattan taxonomy and expanding the understanding of genomic study in rattan.

No MeSH data available.