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Table 1 De novo assembly and annotation of C. reflexa , C. japonica, and I. balsamina contigs

From: A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads

 

C. reflexa (Cr_contigs)

C. japonica (Cj_contigs_ci1)

I. balsamina (Ib_contigs)

Library type

Illumina, 90 bp paired-end

Illumina, 101 bp paired-end

Illumina, 101 bp paired-end

Assembler

Trinity

Velvet/Oases

Velvet/Oases

Assembled reads

308,147,540

182,703,208

95,704,104

Number of contigs

165,213

60,124

27,594

Median contig length

377 bp

599 bp

1,026 bp

Average contig length

620 bp

980 bp

1,276 bp

ORF predicted

89,456 (54%)

59,768 (99%)

27,507 (99%)

Full-length ORF

64,442 (39%)

33,313 (55%)

18,118 (66%)

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Plant Methods

ISSN: 1746-4811