STRATEGIES FOR TRANSCRIPTOME ANALYSIS IN NONMODEL PLANTS

被引:108
作者
Ward, Judson A. [1 ]
Ponnala, Lalit [2 ]
Weber, Courtney A. [1 ]
机构
[1] Cornell Univ, Dept Hort, New York State Agr Expt Stn, Geneva, NY 14456 USA
[2] Cornell Univ, Computat Biol Serv Unit, Ithaca, NY 14853 USA
关键词
de novo transcriptome assembly; gene expression; nonmodel organisms; reference genome independent; RNA-seq; Rosaceae; Rubus idaeus; GENE-EXPRESSION ANALYSIS; RNA-SEQ DATA; MESSENGER-RNA; GLOBAL CHARACTERIZATION; DIFFERENTIAL DISPLAY; FLORAL TRANSCRIPTOME; ROOT TRANSCRIPTOME; HUMAN GENOME; NOVO; ALGORITHMS;
D O I
10.3732/ajb.1100334
中图分类号
Q94 [植物学];
学科分类号
071001 ;
摘要
Even with recent reductions in sequencing costs, most plants lack the genomic resources required for successful short-read transcriptome analyses as performed routinely in model species. Several approaches for the analysis of short-read transcriptome data are reviewed for nonmodel species for which the genome of a close relative is used as the reference genome. Two approaches using a data set from Phytophthora-challenged Rubus idaeus (red raspberry) are compared. Over 70000000 86-nt Illumina reads derived from R. idaeus roots were aligned to the Fragaria vesca genome using publicly available informatics tools (Bowtie/TopHat and Cufflinks). Alignment identified 16956 putatively expressed genes. De novo assembly was performed with the same data set and a publicly available transcriptome assembler (Trinity). A BLAST search with a maximum e-value threshold of 1.0 x 10(-3) revealed that over 36000 transcripts had matches to plants and over 500 to Phytophthora. Gene expression estimates from alignment to F vesca and de novo assembly were compared for raspberry (Pearson's correlation = 0.730). Together, alignment to the genome of a close relative and de novo assembly constitute a powerful method of transcriptome analysis in nonmodel organisms. Alignment to the genome of a close relative provides a framework for differential expression testing if alignments are made to the predefined gene-space of a close relative and de novo assembly provides a more robust method of identifying unique sequences and sequences from other organisms in a system. These methods are considered experimental in nonmodel systems, but can be used to generate resources and specific testable hypotheses.
引用
收藏
页码:267 / 276
页数:10
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