How the pan-genome is changing crop genomics and improvement

Della Coletta, Rafael; Qiu, Yinjie; Ou, Shujun; Hufford, Matthew B.; Hirsch, Candice N.

doi:10.1186/s13059-020-02224-8

Table 1 Summary of plant species with pan-genomes currently available

From: How the pan-genome is changing crop genomics and improvement

Species	Estimated mean DNA amount (C-value)^a	Method for pan-genome construction	Number of accessions	Sequencing method	Reference
Brachypodium distachyon	B. distachyon, 0.32 pg B. stacei, 0.28 pg B. hybridum, 0.63 pg	De novo assembly^b	54	Illumina HiSeq	[38]
B. distachyon, Brachypodium hybridum, Brachypodium stacei		De novo assembly^b	57	Illumina HiSeq PacBio	[39]
Medicago truncatula	0.47 pg	De novo assembly^b	15	Illumina HiSeq	[40]
Oryza sativa (Asian rice)	O. rufipogon, 0.46 pg O. nivara, 0.47 pg O. barthii, 0.60 pg O. glaberrima, 0.53 pg O. sativa, 0.50 pg	Iterative mapping and assembly^c	1483	Illumina HiSeq	[41]
O. sativa (Asian rice)		Map to pan^d	3010	Illumina HiSeq PacBio	[42]
O. sativa/Oryza rufipogon (Asian and common wild rice)		De novo assembly^b	66	Illumina HiSeq	[43]
O. sativa (Asian rice)		De novo assembly^b	12	PacBio	[44]
O. rufipogon/O. nivara/O. barthii/O. glaberrima (wild rice and African rice)		De novo assembly^b	4	PacBio	[45]
Juglans ssp. (walnuts)	0.64 pg	De novo assembly^b	6	Illumina HiSeq	[46]
Malus domestica/M. sieversii/M. sylvestris (apple and wild apple progenitors)	M. domestica, 0.88 pg M. sieversii, 0.75 pg M. sylvestris, 0.78 pg	Iterative mapping and assembly^c	91	Illumina HiSeq PacBio	[47]
Brassica oleracea, Brassica macrocarpa (cultivated and wild cabbage)	B. oleracea, 0.9 pg B. macrocarpa, not available B. napus, 1.10 pg	Iterative mapping and assembly^c	10	Illumina HiSeq	[48]
Brassica napus (oilseed)		Map to pan^d	9	Illumina Hiseq PacBio	[22]
Solanum lycopersicum (tomato)	1.06 pg	Map to pan^d	725	Illumina NextSeq	[49]
Solanum lycopersicum (tomato)	1.06 pg	De novo assembly^b	100 (14 assembled)	Illumina NextSeq Nanopore	[23]
Glycine soja (wild soybean)	G. soja, 1.10 pg G. max, 1.13 pg	De novo assembly^b	7	Illumina HiSeq	[12]
Glycine max (soybean)	G. soja, 1.10 pg G. max, 1.13 pg	De novo assembly^b	29	Illumina HiSeq PacBio	[24]
Zea mays (maize)	2.7 pg	Novel transcript assembly^e	503	Illumina HiSeq	[10]
Zea mays (maize)	2.7 pg	De novo assembly^b	6	Illumina HiSeq	[50]
Capsicum annuum (pepper)	3.16 pg	Iterative mapping and assembly^c	383	Illumina HiSeq	[51]
Helianthus annuus (sunflower)	3.67 pg	Map to pan^d	493	Illumina HiSeq	[52]
Triticum aestivum (bread wheat)	24.65 pg	Iterative mapping and assembly^c	19	Illumina HiSeq	[53]

^aThe mean 1C (pg) value was obtained from the plant DNA C-values Database (https://cvalues.science.kew.org), 1 pg = 978 Mb [54]
^bAssemble and annotate each genome separately and identify the variable regions
^cDe novo assemble individual genome and then compare the assembled genome to the reference genome to capture the gene information that is not present in the reference genome
^dMap reads to the reference genome, perform de novo assembly using unmapped reads, and incorporate the information into the reference genome
^eDe novo assembly of short reads to capture transcript diversity

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ISSN: 1474-760X

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