Characterization of Leaf Transcriptome in Banksia hookeriana
Banksia is a significant element in vegetation of southwestern Australia, a biodiversity hotspot with global significance. In particular, Banksia hookeriana represents a species with significant economic and ecological importance in the region. For better conservation and management, we reported an...
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| Format: | Article |
| Language: | English |
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Elsevier
2017-02-01
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| Series: | Genomics, Proteomics & Bioinformatics |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S1672022917300013 |
| _version_ | 1797369957316558848 |
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| author | Sim Lin Lim Haylee M. D'Agui Neal J. Enright Tianhua He |
| author_facet | Sim Lin Lim Haylee M. D'Agui Neal J. Enright Tianhua He |
| author_sort | Sim Lin Lim |
| collection | DOAJ |
| description | Banksia is a significant element in vegetation of southwestern Australia, a biodiversity hotspot with global significance. In particular, Banksia hookeriana represents a species with significant economic and ecological importance in the region. For better conservation and management, we reported an overview of transcriptome of B. hookeriana using RNA-seq and de novo assembly. We have generated a total of 202.7 million reads (18.91 billion of nucleotides) from four leaf samples in four plants of B. hookeriana, and assembled 59,063 unigenes (average size = 1098 bp) through de novo transcriptome assembly. Among them, 39,686 unigenes were annotated against the Swiss-Prot, Clusters of Orthologous Groups (COG), and NCBI non-redundant (NR) protein databases. We showed that there was approximately one single nucleotide polymorphism (SNP) per 5.6–7.1 kb in the transcriptome, and the ratio of transitional to transversional polymorphisms was approximately 1.82. We compared unigenes of B. hookeriana to those of Arabidopsis thaliana and Nelumbo nucifera through sequence homology, Gene Ontology (GO) annotation, and KEGG pathway analyses. The comparative analysis revealed that unigenes of B. hookeriana were closely related to those of N. nucifera. B. hookeriana, N. nucifera, and A. thaliana shared similar GO annotations but different distributions in KEGG pathways, indicating that B. hookeriana has adapted to dry-Mediterranean type shrublands via regulating expression of specific genes. In total 1927 potential simple sequence repeat (SSR) markers were discovered, which could be used in the genotype and genetic diversity studies of the Banksia genus. Our results provide valuable sequence resource for further study in Banksia. |
| first_indexed | 2024-03-08T17:55:28Z |
| format | Article |
| id | doaj.art-a05d144b876b4852a88e1f674cc262d8 |
| institution | Directory Open Access Journal |
| issn | 1672-0229 |
| language | English |
| last_indexed | 2024-03-08T17:55:28Z |
| publishDate | 2017-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics, Proteomics & Bioinformatics |
| spelling | doaj.art-a05d144b876b4852a88e1f674cc262d82024-01-02T05:35:48ZengElsevierGenomics, Proteomics & Bioinformatics1672-02292017-02-01151495610.1016/j.gpb.2016.11.001Characterization of Leaf Transcriptome in Banksia hookerianaSim Lin Lim0Haylee M. D'Agui1Neal J. Enright2Tianhua He3Department of Environment and Agriculture, Curtin University, Perth, WA 6845, AustraliaDepartment of Environment and Agriculture, Curtin University, Perth, WA 6845, AustraliaSchool of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, AustraliaDepartment of Environment and Agriculture, Curtin University, Perth, WA 6845, AustraliaBanksia is a significant element in vegetation of southwestern Australia, a biodiversity hotspot with global significance. In particular, Banksia hookeriana represents a species with significant economic and ecological importance in the region. For better conservation and management, we reported an overview of transcriptome of B. hookeriana using RNA-seq and de novo assembly. We have generated a total of 202.7 million reads (18.91 billion of nucleotides) from four leaf samples in four plants of B. hookeriana, and assembled 59,063 unigenes (average size = 1098 bp) through de novo transcriptome assembly. Among them, 39,686 unigenes were annotated against the Swiss-Prot, Clusters of Orthologous Groups (COG), and NCBI non-redundant (NR) protein databases. We showed that there was approximately one single nucleotide polymorphism (SNP) per 5.6–7.1 kb in the transcriptome, and the ratio of transitional to transversional polymorphisms was approximately 1.82. We compared unigenes of B. hookeriana to those of Arabidopsis thaliana and Nelumbo nucifera through sequence homology, Gene Ontology (GO) annotation, and KEGG pathway analyses. The comparative analysis revealed that unigenes of B. hookeriana were closely related to those of N. nucifera. B. hookeriana, N. nucifera, and A. thaliana shared similar GO annotations but different distributions in KEGG pathways, indicating that B. hookeriana has adapted to dry-Mediterranean type shrublands via regulating expression of specific genes. In total 1927 potential simple sequence repeat (SSR) markers were discovered, which could be used in the genotype and genetic diversity studies of the Banksia genus. Our results provide valuable sequence resource for further study in Banksia.http://www.sciencedirect.com/science/article/pii/S1672022917300013Banksia hookerianaGene annotationRNA-seqSSR markerTranscriptome |
| spellingShingle | Sim Lin Lim Haylee M. D'Agui Neal J. Enright Tianhua He Characterization of Leaf Transcriptome in Banksia hookeriana Genomics, Proteomics & Bioinformatics Banksia hookeriana Gene annotation RNA-seq SSR marker Transcriptome |
| title | Characterization of Leaf Transcriptome in Banksia hookeriana |
| title_full | Characterization of Leaf Transcriptome in Banksia hookeriana |
| title_fullStr | Characterization of Leaf Transcriptome in Banksia hookeriana |
| title_full_unstemmed | Characterization of Leaf Transcriptome in Banksia hookeriana |
| title_short | Characterization of Leaf Transcriptome in Banksia hookeriana |
| title_sort | characterization of leaf transcriptome in banksia hookeriana |
| topic | Banksia hookeriana Gene annotation RNA-seq SSR marker Transcriptome |
| url | http://www.sciencedirect.com/science/article/pii/S1672022917300013 |
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