Status and Prospects Whole Genome Sequencing in Fruit Trees

doi:10.16420/j.issn.0513-353x.2020-0069

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (4): 733-748.doi: 10.16420/j.issn.0513-353x.2020-0069

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Status and Prospects Whole Genome Sequencing in Fruit Trees

HUANG Weijian, LI Meng()

College of Horticulture,Nanjing Agricultural University,Nanjing 210095,China

Received:2020-08-20 Online:2021-04-25 Published:2021-04-29
Contact: LI Meng E-mail:mli@njau.edu.cn

Abstract

Abstract:

Whole genome sequencing can obtain genome sequence information of species,which is very important for exploring the origin and evolution of the species,and fundamental for the development and utilization of genes. This article reviewed the progress of genome sequencing of seven important fruit trees（apple,citrus,grape,pear,strawberry,banana and peach）,discussed the currently existing problems of whole genome sequencing of fruit trees,and elaborated selection of DNA sequencing technology,openness of sequencing data,and research after sequencing and other issues in the future research.

Key words: whole genome sequencing, apple, citrus, grape, pear, strawberry, banana, peach

CLC Number:

HUANG Weijian, LI Meng. Status and Prospects Whole Genome Sequencing in Fruit Trees[J]. Acta Horticulturae Sinica, 2021, 48(4): 733-748.

Figures/Tables 2

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[47]	Zhang Y, Barthe G, Grosser J W, Wang N. 2016. Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome. BMC Genomics, 17:485. doi: 10.1186/s12864-016-2779-y URL
[48]	Zhou Y, Minio A, Massonnet M, Solares E A, Gaut B S. 2019. Structural variants,clonal propagation,and genome evolution in grapevine (Vitis vinifera). BioRxiv:508119.
[49]	Zhu C, Zheng X, Huang Y, Ye J, Chen P, Zhang C, Zhao F, Xie Z, Zhang S, Wang N, Li H, Wang L, Tang X, Chai L, Xu Q, Deng X. 2019. Genome sequencing and CRISPR/Cas9 gene editing of an early flowering Mini-Citrus (Fortunella hindsii). Plant Biotechnol J, 17 (11):2199-2210. doi: 10.1111/pbi.v17.11 URL

测序技术代数 Sequencing technolog generation	DNA扩增方式 DNA amplification method	测序平台 Sequencing platform	平均读长/bp Average read length	正确率/% Accuracy	成本/（$·Gb^-1） Cost	测序时间/h Sequencing time
一代1st	质粒扩增Plasmid amplification	Sanger	700	99.9	500 000.00	1
二代2nd	乳液PCR Emulsion PCR	Roche 454	700	99	9 500.00	23
	乳液PCR Emulsion PCR	SOLiD	120	99.9	50.00	144
	桥式PCR Bridge PCR	Solexa	300	99.9	20.00	19 ~ 40
三代3rd	单分子测序	PacBio RSⅡ	10 000	85 ~ 90	1 000.00	0.5 ~ 6
	Single molecule sequencing	MinION	200 ~ 500	70 ~ 90	1 000.00	48

测序技术代数 Sequencing technolog generation	DNA扩增方式 DNA amplification method	测序平台 Sequencing platform	平均读长/bp Average read length	正确率/% Accuracy	成本/（$·Gb^-1） Cost	测序时间/h Sequencing time
一代1st	质粒扩增Plasmid amplification	Sanger	700	99.9	500 000.00	1
二代2nd	乳液PCR Emulsion PCR	Roche 454	700	99	9 500.00	23
	乳液PCR Emulsion PCR	SOLiD	120	99.9	50.00	144
	桥式PCR Bridge PCR	Solexa	300	99.9	20.00	19 ~ 40
三代3rd	单分子测序	PacBio RSⅡ	10 000	85 ~ 90	1 000.00	0.5 ~ 6
	Single molecule sequencing	MinION	200 ~ 500	70 ~ 90	1 000.00	48

物种 Species	测序材料 Sequencing material	测序方法 Sequencing method	基因组/ Mb Genome size	组装全长/Mb Assembly	基因数量 Number of gene	重复序列比率 /% Repeat	总序列骨架数 Scaffold Total	Contig N50/kb	基因组杂合度/% Genomic Hetero- zygosity	测序深度 Sequencing depth	倍性 Ploidy	参考文献 Reference
苹果Apple （Malus× domestica）	金冠Golden Delicious	Sanger, Roche454	742.3	603.9	57 386	67	1 629	16.7	缺失 Deficiency	16.9×	二倍体 Diploid	Velasco et al.,2010
	金冠Golden Delicious	Illumina HiSeq, PacBio RS II	701	632.4	53 922	60	缺失 Deficiency	111.6	缺失 Deficiency	131×	二倍体 Diploid	Li et al.2016
	金冠双单倍体 GDDH13	Illumina HiSeq, PacBio RS II	651	649.7	42 140	57.3	280	699	缺失 Deficiency	835×	双单倍体 Double haploid	Daccord et al.,2017
	寒富HFTH1	Illumina HiSeq, PacBio RS II	708.5	658.9	44 677	59.8	502	6 990	缺失 Deficiency	552×	三倍体 Triploid	Zhang et al.,2019
柑橘 Citrus	甜橙Sweet Orange （C.sinensis）	Illumina GAII	367	320.5	29 445	20	4 811	49.89	50	214×	二倍体 Diploid	Xu et al.2013
	克里曼丁橘 Clemenules （C. clementina）	Sanger	302	310	24 533	44.7	2 931	115.9	缺失 Deficiency	6.94×	单倍体 Haploid	Wu et al.2014
	枳柚 Swingle Citrumelo （C. paradise Macf. × Poncirus trifoliata（L.） Raf.）	Illumina HiSeq	380	280.6	29 054	16.8	66 319	11.4	缺失 Deficiency	15×	不可用 Not Available	Zhang et al.,2016
	柚Pummelo （C. grandis）	Illumina HiSeq, PacBio RS II	380.8	344.8	30 123	45.8	1 612	2 180	缺失 Deficiency	427×	单倍体 Haploid	Wang et al.,2017
	温州蜜橘 Satsuma（C. unshiuMarc.）	Illumina HiSeq, PacBio RS II	不可用 Not Available	359	29 024	39.5	20 876	缺失 Deficiency	0.44	缺失 Deficiency	二倍体 Diploid	Shimizu et al.,2017
	莽山野柑 Mangshan Mandarin （C. reticulata）	Illumina HiSeq	344.3	334	28 820	50.1	42 714	24.7	缺失 Deficiency	199.7×	二倍体 Diploid	Wang et al.,2018
	香港金橘 Hongkong Kumquat （Fortunella hindsii）	Illumina HiSeq, PacBio	389	373.6	32 257	14.3	900	2 200	0.8	145×	二倍体 Diploid	Zhu et al.2019
葡萄Grape （Vitis vinifera）	黑皮诺 PN40024	Sanger	475	487.1	30 434	41.4	3 514	65.9	2.6	8.4×	单倍体 Haploid	Jaillon et al.,2007
	赤霞珠 Cabernet Sauvignon	PacBio RS II	633	591.4	36 687	51.1	1 314	2 170	缺失 Deficiency	缺失 Deficiency	二倍体 Diploid	Chin et al.,2016
	霞多丽 Chardonnay	Illumina HiSeq, PacBio RS II, MiSeq	580	490	29 675	38.7	缺失 Deficiency	935	缺失 Deficiency	115×	二倍体 Diploid	Roach et al.,2018
	霞多丽 FPS 04	Illumina HiSeq, PacBio RS II	600	606	38 020	47.3	684	1 240	缺失 Deficiency	220×	二倍体 Diploid	Zhou et al.,2019
梨 Pear	砀山酥梨 Dangshan Suli （Pyrus bretschneideriRehd.）	Illumina HiSeq	527	512	42 812	53.1	2 103	35.7	1.99	194×	二倍体 Diploid	Wu et al.2013
	西洋梨 Bartlett （P. communisL.）	Roche 454	600	577.3	43 419	34.1	142 083	6.53	缺失 Deficiency	11.4×	单倍体 Haploid	Chagne et al.,2014
	西洋梨 BartlettDHv2.0 （P. communisL.）	PacBio SII	528	496.9	37 445	49.7	494	5 300	缺失 Deficiency	63×	双单倍体 Double haploid	Linsmith et al.,2019
	山西杜梨 Shanxi Duli （P. betuleafolia）	Illumina HiSeq, PacBio	511	532.7	59 522	46.4	139	1 570	1.54	缺失 Deficiency	缺失 Deficiency	Dong et al.,2020
草莓 Strawberry	森林草莓 Hawaii 4 （Fragaria vesca）	Roche 454, SOLiD, Illumina HiSeq	240	209.8	34 809	23	3 263	13 000	缺失 Deficiency	39×	二倍体 Diploid	Shulaev et al.,2011
	Reikou （F. ananassa）	Roche 454, Illumina HiSeq	692	698	45 377	5	7 598	46.8	缺失 Deficiency	缺失 Deficiency	八倍体 Octoploid	Hirakawa et al.2014
	卡麦罗莎草莓 Camarosa （F. ananassa）	Illumina HiSeq, PacBio RS II	813.4	660	108 087	36	25 426	79.9	缺失 Deficiency	615×	八倍体 Octoploid	Edger et al.,2019
	黄毛草莓 Ruegen（F. nilgerrensis）	Illumina HiSeq, PacBio SMRT	276	270.3	28 780	43.4	257	85 000	缺失 Deficiency	152×	二倍体 Diploid	Zhang et al.,2020
香蕉 Banana	彭亨香蕉 DH-Pahang （Musa acuminata）	Sanger, Roche454, Illumina GAIIx	523	472.2	36 542	44	7 513	43.1	缺失 Deficiency	50×	双单倍体 Double haploid	D'Hont et al.,2012
	Pisang Klutuk Wulung（M. balbisiana）	Illumina HiSeq	432.7	341.4	36 638	29.5	63 245	7.9	缺失 Deficiency	41.4×	二倍体 Diploid	Davey et al.,2013
	阿宽蕉（M. itinerans）	Illumina HiSeq	615.2	462.1	32 456	38.9	7 194	33.9	0.25	120.7×	二倍体 Diploid	Wu et al.2016
	DH-PKW（M. balbisiana）	Illumina HiSeq, PacBio,	492	430	35 148	55.8	294	1 830	缺失 Deficiency	417×	双单倍体 Double haploid	Wang et al.,2019
桃Peach （Prunus persica）	Lovell	Sanger	265	224.6	27 852	37.14	202	294	缺失 Deficiency	8.47×	二倍体 Diploid	Verde et al.,2013

物种 Species	测序材料 Sequencing material	测序方法 Sequencing method	基因组/ Mb Genome size	组装全长/Mb Assembly	基因数量 Number of gene	重复序列比率 /% Repeat	总序列骨架数 Scaffold Total	Contig N50/kb	基因组杂合度/% Genomic Hetero- zygosity	测序深度 Sequencing depth	倍性 Ploidy	参考文献 Reference
苹果Apple （Malus× domestica）	金冠Golden Delicious	Sanger, Roche454	742.3	603.9	57 386	67	1 629	16.7	缺失 Deficiency	16.9×	二倍体 Diploid	Velasco et al.,2010
	金冠Golden Delicious	Illumina HiSeq, PacBio RS II	701	632.4	53 922	60	缺失 Deficiency	111.6	缺失 Deficiency	131×	二倍体 Diploid	Li et al.2016
	金冠双单倍体 GDDH13	Illumina HiSeq, PacBio RS II	651	649.7	42 140	57.3	280	699	缺失 Deficiency	835×	双单倍体 Double haploid	Daccord et al.,2017
	寒富HFTH1	Illumina HiSeq, PacBio RS II	708.5	658.9	44 677	59.8	502	6 990	缺失 Deficiency	552×	三倍体 Triploid	Zhang et al.,2019
柑橘 Citrus	甜橙Sweet Orange （C.sinensis）	Illumina GAII	367	320.5	29 445	20	4 811	49.89	50	214×	二倍体 Diploid	Xu et al.2013
	克里曼丁橘 Clemenules （C. clementina）	Sanger	302	310	24 533	44.7	2 931	115.9	缺失 Deficiency	6.94×	单倍体 Haploid	Wu et al.2014
	枳柚 Swingle Citrumelo （C. paradise Macf. × Poncirus trifoliata（L.） Raf.）	Illumina HiSeq	380	280.6	29 054	16.8	66 319	11.4	缺失 Deficiency	15×	不可用 Not Available	Zhang et al.,2016
	柚Pummelo （C. grandis）	Illumina HiSeq, PacBio RS II	380.8	344.8	30 123	45.8	1 612	2 180	缺失 Deficiency	427×	单倍体 Haploid	Wang et al.,2017
	温州蜜橘 Satsuma（C. unshiuMarc.）	Illumina HiSeq, PacBio RS II	不可用 Not Available	359	29 024	39.5	20 876	缺失 Deficiency	0.44	缺失 Deficiency	二倍体 Diploid	Shimizu et al.,2017
	莽山野柑 Mangshan Mandarin （C. reticulata）	Illumina HiSeq	344.3	334	28 820	50.1	42 714	24.7	缺失 Deficiency	199.7×	二倍体 Diploid	Wang et al.,2018
	香港金橘 Hongkong Kumquat （Fortunella hindsii）	Illumina HiSeq, PacBio	389	373.6	32 257	14.3	900	2 200	0.8	145×	二倍体 Diploid	Zhu et al.2019
葡萄Grape （Vitis vinifera）	黑皮诺 PN40024	Sanger	475	487.1	30 434	41.4	3 514	65.9	2.6	8.4×	单倍体 Haploid	Jaillon et al.,2007
	赤霞珠 Cabernet Sauvignon	PacBio RS II	633	591.4	36 687	51.1	1 314	2 170	缺失 Deficiency	缺失 Deficiency	二倍体 Diploid	Chin et al.,2016
	霞多丽 Chardonnay	Illumina HiSeq, PacBio RS II, MiSeq	580	490	29 675	38.7	缺失 Deficiency	935	缺失 Deficiency	115×	二倍体 Diploid	Roach et al.,2018
	霞多丽 FPS 04	Illumina HiSeq, PacBio RS II	600	606	38 020	47.3	684	1 240	缺失 Deficiency	220×	二倍体 Diploid	Zhou et al.,2019
梨 Pear	砀山酥梨 Dangshan Suli （Pyrus bretschneideriRehd.）	Illumina HiSeq	527	512	42 812	53.1	2 103	35.7	1.99	194×	二倍体 Diploid	Wu et al.2013
	西洋梨 Bartlett （P. communisL.）	Roche 454	600	577.3	43 419	34.1	142 083	6.53	缺失 Deficiency	11.4×	单倍体 Haploid	Chagne et al.,2014
	西洋梨 BartlettDHv2.0 （P. communisL.）	PacBio SII	528	496.9	37 445	49.7	494	5 300	缺失 Deficiency	63×	双单倍体 Double haploid	Linsmith et al.,2019
	山西杜梨 Shanxi Duli （P. betuleafolia）	Illumina HiSeq, PacBio	511	532.7	59 522	46.4	139	1 570	1.54	缺失 Deficiency	缺失 Deficiency	Dong et al.,2020
草莓 Strawberry	森林草莓 Hawaii 4 （Fragaria vesca）	Roche 454, SOLiD, Illumina HiSeq	240	209.8	34 809	23	3 263	13 000	缺失 Deficiency	39×	二倍体 Diploid	Shulaev et al.,2011
	Reikou （F. ananassa）	Roche 454, Illumina HiSeq	692	698	45 377	5	7 598	46.8	缺失 Deficiency	缺失 Deficiency	八倍体 Octoploid	Hirakawa et al.2014
	卡麦罗莎草莓 Camarosa （F. ananassa）	Illumina HiSeq, PacBio RS II	813.4	660	108 087	36	25 426	79.9	缺失 Deficiency	615×	八倍体 Octoploid	Edger et al.,2019
	黄毛草莓 Ruegen（F. nilgerrensis）	Illumina HiSeq, PacBio SMRT	276	270.3	28 780	43.4	257	85 000	缺失 Deficiency	152×	二倍体 Diploid	Zhang et al.,2020
香蕉 Banana	彭亨香蕉 DH-Pahang （Musa acuminata）	Sanger, Roche454, Illumina GAIIx	523	472.2	36 542	44	7 513	43.1	缺失 Deficiency	50×	双单倍体 Double haploid	D'Hont et al.,2012
	Pisang Klutuk Wulung（M. balbisiana）	Illumina HiSeq	432.7	341.4	36 638	29.5	63 245	7.9	缺失 Deficiency	41.4×	二倍体 Diploid	Davey et al.,2013
	阿宽蕉（M. itinerans）	Illumina HiSeq	615.2	462.1	32 456	38.9	7 194	33.9	0.25	120.7×	二倍体 Diploid	Wu et al.2016
	DH-PKW（M. balbisiana）	Illumina HiSeq, PacBio,	492	430	35 148	55.8	294	1 830	缺失 Deficiency	417×	双单倍体 Double haploid	Wang et al.,2019
桃Peach （Prunus persica）	Lovell	Sanger	265	224.6	27 852	37.14	202	294	缺失 Deficiency	8.47×	二倍体 Diploid	Verde et al.,2013

Status and Prospects Whole Genome Sequencing in Fruit Trees

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