Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef)

BMC Genomics

Table 1 Summary of genome annotation

Type		Number or copies	Total size (bp)	Percent of genome
A. Repetitive Elements
Masked with WindowMasker			95556652	14.2
Masked with RepeatMasker			39352657	6.6
MITEs		77908	10783061	1.6
B. Noncoding RNAs
rRNA		80	13580
tRNA		1184	88295
miRNA		570	73999
snRNA		834	95690
C. Proteins
Dataset	Number of clusters (unigene)	Number of transcripts	Average length of CDS (bp)	Percentage of Genome
454Isotig	27756	38333	285	1.8
Extended	28113	88078	331	4.7
Maker prediction		42052	395	3.3

Number and size of A) repetitive elements, B) noncoding RNAs, and C) proteins. Repetitive elements were quantified using WindowMasker, RepeatMasker and MITE-Hunter. The non-coding RNAs were found using the Infernal software with the Rfam database. The transcripts in two assemblies (454Isotigs, Extended) and the predicted genes in the genome (Maker) are also compared.

ISSN: 1471-2164