Species	Country of origin	Voucher/accession no.	DNA quality	Type of library preparation	Probes used	No. of passed reads	Reference	% reads mapped reference	Average coverage depth	Standard deviation	% mismatch	% reference uncovered	% 10×	% 50×
Oryza sativa	Japan	(no voucher) NIP – IRD Montpellier	Band, >20 kbp	Chloroplast enrichment	Oryza sativa	17,129	KT289404.1	70.80	362.69	0.36	11.80	0.000	100.000	99.996
				Shotgun	None	151,234	KT289404.1	13.32	34.15	0.25	0.20	0.000	99.898	4.146
Oryza glaberrima	Senegal	(no voucher) CG14 – IRD Montpellier	Band, >20 kbp	Chloroplast enrichment	Oryza sativa	81,361	KM088021.1	98.23	2033.68	0.43	9.60	0.019	99.934	99.295
				Shotgun	None	1,201,104	KM088021.1	7.94	99.56	0.44	1.80	0.034	99.546	88.834
Pennisetum glaucum	Senegal	(no voucher) PE01455 – IRD Montpellier	Band, >20 kbp	Chloroplast enrichment	Oryza sativa	105,757	KJ490012.1	97.03	3318.44	0.39	10.20	0.000	99.992	99.981
				Shotgun	None	525,428	KJ490012.1	0.62	3.19	0.70	2.20	10.150	0.950	0.000
Digitaria exilis	Mali	(no voucher) CM05784 – IRD Montpellier	Band, >20 kbp	Chloroplast enrichment	Oryza sativa	141,248	NC_024176.1	94.42	3311.87	0.29	11.40	0.000	100.000	99.700
				Shotgun	None	8,665,102	NC_024176.1	6.85	593.29	0.33	0.50	0.045	99.846	99.462
Podococcus acaulis	Gabon	Couvreur TLP 556 (WAG)	Band, 15–20 kbp	Chloroplast enrichment	Podococcus barteri	249,416	NC_027276.1	15.72	497.68	0.47	10.20	0.454	96.163	93.096
				Shotgun	None	308,230	NC_027276.1	0.63	1.14	2.63	4.60	56.858	0.597	0.085
Raphia textilis	Angola	Lautenschläger 1086 (K)	Slight degradation, 5–16 kbp	Chloroplast enrichment	Podococcus barteri	83,832	NC_020365.1	87.49	893.98	0.47	12.00	0.352	96.068	91.972
				Shotgun	None	57,007,740	NC_020365.1	0.92	381.41	3.77	6.20	0.200	99.018	98.258
Phytelephas aequatorialis	Ecuador	Couvreur 1191 (QCA) – TAGUA F1	Smear, 1–10 kbp fragments	Chloroplast enrichment	Podococcus barteri	202,924	NC_029957.1	79.04	1713.58	0.53	10.30	0.004	99.522	96.383
				Shotgun	None	699,918	NC_029957.1	3.65	22.68	1.58	3.50	0.000	95.083	1.380