Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

Table 2 Reference plastome hits in the mitogenomes of Cuscuta australis and C. campestris

Hit	Species	Location: (contig) coordinate	Length (bp)	% identity	Putative origin^a	Note
1	C. australis C. campestris	(1) 36,607..36,722 60,410..60,295; 248,718..248,603	116	90–94	homology	trnD-GUC; identical to Ipomoea nil
2	C. australis	(1) 84,001..84,148	148	71–78	intracellular	unresolved but close to Solanum, Ipomoea and Cuscuta africana
3	C. australis C. campestris	(1) 119,219..119,360 106,543..106,402	142	69–75	homology	portion of nad5 hitting portion of ndhF
4	C. australis C. campestris	(2) 16,249..15,698 144,976..145,546	552 571	71–82	HGT?	portion of ndhB and intron
5	C. australis C. campestris	(2) 17,873..17,432 143,582..143,960	442 379	63–96	HGT?	portion of psbB
6	C. australis C. campestris	(5) 990..1101 156,265..156,376	112	74–79	mitogenome	hits within ycf2; 100% identical to Solanales mitogenomes
7	C. campestris	61,212..62,827	1616	82–96	intracellular	resolved closest to Cuscuta spp.
8	C. campestris	166,948..167,125	178	73	mitogenome	hits unannotated; > 98% identical to Solanales mitogenomes

Table shows the locations and features of reference plastome hits in the mitogenomes of Cuscuta australis and C. campestris. Notes indicate further detail and phylogenetic placements or NCBI BLASTN results
^aPutative origins are listed as explanations for the presence of the hit and are as follows: 1) homology: the hit likely arises from ancient similarity/transfer between plastomes and mitogenomes; 2) intracellular: the hit likely represents a transfer from the plastome to the mitogenome within the lineage; 3) HGT: the hit likely represents a transfer from another lineage, either plastome to mitogenome (intra) then mitogenome to mitogenome (HGT), or plastome to mitogenome (HGT); 4) mitogenome: the hit likely represents mitogenome sequence with some similarity to the plastome, possibly by chance, and not differing from related mitogenomes

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