Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

Pont, Caroline; Wagner, Stefanie; Kremer, Antoine; Orlando, Ludovic; Plomion, Christophe; Salse, Jerome

doi:10.1186/s13059-019-1627-1

Table 2 Ancient plant DNA

From: Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA

Species	Dating^a	Site	Sample	Characterization^b	Extraction^c	Reference
Oak	500–9800 BP	Europe	Waterlogged wood	NGS	TrisHCL SDS CaCl₂ EDTA DTT PK/Phchlo/Column	[142]
Japanese cedar	3600 BP	Japan	Buried tree	PCR/sequencing	Column	[133]
Maize	1100–6000 BP	New World	Desiccated cob	PCR/sequencing	CTAB TrisHCL NaCl EDTA/Chlo	[111] [112]
Maize	360–1320 BP	New World	Desiccated cob	PCR/sequencing	Column	[114]
Maize	670–5280 BP	New World	Desiccated cob	Capture, NGS	SDS DTT PK/Phchlo/Column	[115]
Maize	650–4300 BP	New World	–	PCR/sequencing	SDS DTT PK/Phchlo/EDTA PTB/Column	[113]
Maize	4700 BP	Chile, Peru	Charred and non-charred grain	PCR/sequencing	SDS DTT PK/Phchlo	[110]
Maize	5310 BP	Mexico	Desiccated grain	NGS	TrisHCL SDS CaCl₂ EDTA DTT PK/Phchlo/Column	[116]
Maize	5300 BP	Mexico	Desiccated cob	NGS	–	[117]
Sunflower	3100 BP	USA	Desiccated disk fragment, pericarp, kernel	NGS	TrisHCl NaCl SDS CaCl₂ EDTA DTT PK/Phchlo/Column	[119]
Radish	350–550 AD	Egypt	Desiccated seed	Chemical analysis/PCR/sequencing	CTAB TrisHCL NaCl EDTA/Chlo	[124]
Sorghum	2800 BP	Egypt	Desiccated seed	PCR/sequencing	–	[125]
Rice	1200–2400 BC	China	Desiccated seed and chaff	PCR/sequencing	Magnetic beads	[127]
Grape	1600–2500 BP	Europe	Waterlogged and charred pip	PCR/sequencing	DTAB /Chlo/CTAB	[120]
Grape	7^th–15^th century AD	Italy	Waterlogged pip	PCR	SDS DTT PK/Phchlo/Column	[121]
Grape, maize, olive, dogwood, cotton	400–2400 BP	New World, Europe	Non-carbonized remain	PCR/sequencing	SDS DTT PK/Phchl	[122]
Barley	6200–5800 BP	Israel	Desiccated seed	NGS	CTAB TrisHCL PVP βME/Phchlo/Column	[104]
Barley	3000 BP	Egypt	Desiccated grain	PCR/sequencing	SDS DTT PK EDTA PTB/Column	[103]
Barley, wheat	150–5250 BC	Spain	Charred, partially charred, waterlogged seed	PCR/sequencing	TrisHCL SDS EDTA PK/Phchlo or Column	[105]
Wheat	700 AD–8400 BP	Anatolia	Charred grain	PCR/sequencing	CTAB TrisHCL NaCl EDTA/Chlo	[109]
Wheat	340–3500 BP	Spain	Charred and desiccated seed	PCR/sequencing	Tris EDTA CTAB βME/Column	[108]
Cotton	750–3750 BP	Brazil, Peru, Egypt	Desiccated seed	NGS	CTAB/Column	[132]
Arabidopsis	300 BP	USA	Herbarium	NGS	CTAB or PTB DTT/Column	[131]

Summary of ancient plant nuclear DNA recovery listing species, dating, location site, sample type, characterization method, extraction protocol, and associated references. ^aDatings are referenced as in the publication concerned using BC, AD, or BP. ^bPCR/sequencing polymerase chain reaction and sequence capture, NGS next-generation sequencing. ^cDDT dithiothreitol proteinase K, Phchlo phenol-chloroform, Ph phenol, Chlo chloroform, SDS sodium dodecyl sulphate, EDTA ethylene-diamine-tetraacetic acid, CTAB cetyltrimethylammonium-bromide, PTB phenacylthiazolium bromide, DTAB dodecyltrimethylammonium bromide, βME β-mercaptoethanol, Tris tris(hydroxymethyl) aminomethane, PK proteinase K

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ISSN: 1474-760X

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