ArticleGenomics, proteomics & bioinformatics2017
Characterization of Leaf Transcriptome in Banksia hookeriana.
Article in Genomics, proteomics & bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Gene Expression Divergence inPlants (Basel, Switzerland) · 2024Article
- Chromosome-Scale Assembly and Annotation of the Macadamia Genome (G3 (Bethesda, Md.) · 2020Article
- Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae.Frontiers in plant science · 2019Article
- Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Biotechnology for biofuels · 2019Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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=1098bp) through de novotranscriptome 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 5.6-7.1kb 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.
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