Using RNA-seq to characterize responses to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

Table 1 Comparison of waterhemp transcriptome assemblies

		v1 (k-mer = 25)	v2 (k-mer = 29)	v3 (k-mer = 32)	v4
	Total ‘gene’ count	269,388	238,782	226,402	42,040
	Total transcript count	512,945	471,767	451,199	113,893
All Transcripts	Contig N50	762	926	1029	1709
	Median Contig Length	390	424	448	1094
	Average Contig Length	598.54	669.21	713.94	1317.45
Longest Isoform	Contig N50	662	747	792	1816
	Median Contig Length	359	371	375	998
	Average Contig Length	549.32	590.09	609.47	1301.70

Trinity (version 2.0.6, [24]) was used to generate three unique de novo waterhemp transcriptome assemblies: v1, v2, and v3 based on different kmer length requirements. With each assembly, the number of total transcripts decreased while average contig length increased (see Additional file 1). A total of 2.3 billion reads representing different genotypes, treatments and time points were used in the assembly. The v4 assembly is a subset of the v3 assembly, with transcripts that were redundant, lacking open reading frames or expressed at low levels removed

ISSN: 1471-2229