Dataset from: The origin and fate of fungal mitochondrial horizontal gene transferred sequences in orchids (Orchidaceae)

The transfer of DNA among distantly related organisms is relatively common in bacteria but less prevalent in eukaryotes. Among fungi and plants, few of these events have been reported. Two segments of fungal mitochondrial DNA have been discovered in the mitogenome of orchids. Here, we build on their work to understand the timing of those transfer events, which orchids retain the fungal DNA, and the fate of the foreign DNA during orchid evolution. We update the content of the large DNA fragment and establish that it was transferred to the most recent common ancestor of a highly diverse clade of epidendroid orchids that lived ~28–43 Mya. Also, we present hypotheses of the origin of the small transferred fragment. Our findings deepen the knowledge of these interesting DNA transfers among organelles and we formulate a probable mechanism for these horizontal gene transfer events., We sampled 61 taxa from across Orchidaceae of which two were taken from available data on GenBank (mitochondrial sequences of Erycina pusilla: KJ501971, KJ501972, KJ501991, KJ501994, and Gastrodia elata: MF070088 and MF070090). The HGT regions of Apostasia shenzhenica and Triphora wagneri were taken from Sinn & Barrett (2020). 
DNA extractions, sequencing, and data assembly were performed as in Valencia-D. et al. (2021). In short, total DNA was extracted following a modified Doyle and Doyle (1987) procedure (Neubig et al., 2014). Sequencing of total DNA without enrichment was performed using Illumina HiSeq or NovaSeq technologies, generating paired-end read sequences of 100, 150, or 250 bp length. The data was processed using Geneious Prime 2020.3 (Kearse et al., 2012).  
To capture the HGT region, the sequences found in other orchids by Sinn and Barrett (2020) we used. Geneious mapper and Bowtie2 (Langmead & Salzberg, 2012) were used with low sensitive parameters to capture rea...,