Sequencing report of the rRNA amplicons of Echinochloa crus-galli in Iraq

Abstract

This study was conducted to identify the genetic polymorphisms of one wild grass sample species and assess the phylogenetic distribution these isolates occupy based on their internal transcribed (ITS) ribosomal sequences. This study amplified one genetic locus covering a portion of the ITS rRNA sequences. A direct sequencing strategy was performed for the observed PCR amplicons in the amplified genetic locus. Subsequently, a comprehensive phylogenetic tree was constructed in the observed variants for these sequences to reveal the accurate phylogenetic distances alongside other relative sequences. Our results indicated the identity of the investigated wild grass samples (assigned S1 and S2). Sequencing reactions indicated that our investigated samples belonged to Echinochloa crusgalli var. crus-galli (panicum grass), a common wild grass dominated in tropical Asia. Two ribosomal variations were identified in the investigated wild grass samples, 61C>T, observed in the S2 sample and 408C>A, observed in both the S1 and S2 samples. According to the identified results, the investigated samples were positioned within one distinct phylogenetic clade of these identified wild grass sequences in the currently generated comprehensive tree. These positionings were observed within the main clade of Echinochloa crus-galli. Based on the identified ribosomal sequences, it was found that the currently investigated samples may exhibit variable extents of diversities originating from several Asian and South American ancestors. Also, the currently constructed tree revealed that the investigated wild grass sequences belonged to one distinct clade of Echinochloa crus-galli, having many sequences of close phylogenetic connections. This clade occupied far away phylogenetic positions from the other comparable grasses within the same tree. Keywords: rRNA amplicons, Echinochloa crus-galli, Rice