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 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.
Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia.
Sim Lin
SL
Lim
Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia.
Haylee M
HM
D'Agui
School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia.
Neal J
NJ
Enright
Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia. Electronic address: Tianhua.He@curtin.edu.au.
Tianhua
T
He
D020451:Contig Mapping; D030562:Databases, Protein; D018895:Microsatellite Repeats; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D039105:Proteaceae / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
D018749:RNA, Plant
Banksia hookeriana; Gene annotation; RNA-seq; SSR marker; Transcriptome