Your lab uses the annelid worm Lumbriculus variegatus as a model organism to study regeneration. Your studies would be helped by knowing which genes are present in this organism, but its genome has not been sequenced. A recent technique for gene determination is RNA-Seq, in which RNAs are directly isolated and sequenced. What is a disadvantage of using RNA-Seq for gene identification?

a. RNA-Seq may miss genes transcribed in a very tissue- and temporal-limited fashion.
b. RNA-Seq relies on genes being homologous across species, but not all genes have homologs.
c. RNA-Seq works only in mammalian cells and therefore cannot be used with model organisms such as Lumbriculus or Drosophila.
d. RNA-Seq may selectively miss noncoding RNAs as compared to mRNAs.

RNA-Seq is a methodology used in molecular biology to identify RNA transcripts by using deep-sequencing techniques. RNA-Seq has shown that the genome is often transcribed in the form of non-coding RNA sequences such as, for example, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), etc., thereby redefining our vision about transcription in eukaryotic organisms. This methodology is based on the conversion of RNAs to cloned cDNA (complementary DNA) fragments that are further sequenced to be mapped against the reference genome. In consequence, tissue-specific-transcripts are not detected by RNA-Seq in cells in which these sequences are not transcribed.