Advances on whole genome sequencing in Triticeae

doi:10.3785/j.issn.1008-9209.2022.05.161

Journal of Zhejiang University (Agriculture and Life Sciences)

2023, Vol. 49

Issue (1): 1-13 DOI: 10.3785/j.issn.1008-9209.2022.05.161

Reviews

Advances on whole genome sequencing in Triticeae

Liuhui KUANG(

),Qi LI,Guoping ZHANG(

)

College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China

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Abstract

The Triticeae provides the important cereal crops, such as wheat, barley, and rye, which produces approximately 9×10⁸ t annually, accounting for about 30% of the total global cereal production. However, Triticeae genomes are relatively difficult to be de novo sequenced and assembled due to their large genome size, a high proportion of repeat sequences, and different ploidy levels. With the rapid development of third-generation long read sequencing technologies and assembly algorithms designed for complex genomes, and also the falling cost of genome sequencing in recent years, more and more Triticeae species have been successfully sequenced. In this study, we reviewed the advances on the whole genome sequencing of 17 Triticeae species (including subspecies), including Triticum, Hordeum, Secale, Elytrigia, and Aegilops, in aspects of sequencing technology, assembly strategy and quality, and the major research contents associated with genomes and gene functions. This review may provide the references for sequencing strategies and genomic studies of other more complex plant genomes.

Key words： Triticeae genome whole genome sequencing Triticum Hordeum Secale Elytrigia Aegilops

Received: 16 May 2022 Published: 07 March 2023

CLC:

S512.1

Corresponding Authors: Guoping ZHANG E-mail: kuangliuhui@zju.edu.cn;Zhanggp@zju.edu.cn

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Cite this article:

Liuhui KUANG,Qi LI,Guoping ZHANG. Advances on whole genome sequencing in Triticeae. Journal of Zhejiang University (Agriculture and Life Sciences), 2023, 49(1): 1-13.

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https://www.zjujournals.com/agr/10.3785/j.issn.1008-9209.2022.05.161 OR https://www.zjujournals.com/agr/Y2023/V49/I1/1

小麦族全基因组测序研究进展

小麦族是禾本科植物中最重要的粮食作物来源之一，包括小麦、大麦、黑麦等麦类作物，全球年产量高达9亿t，约占全部谷类产量的30%。小麦族物种基因组庞大，重复序列比例高，且倍性水平多样，因此其从头测序和组装难度相对较大。近年来，随着三代长读长测序技术和针对复杂基因组的组装算法不断发展，以及测序成本显著下降，越来越多的小麦族物种的全基因组测序工作相继完成。本文综述了小麦族中小麦属、大麦属、黑麦属、偃麦草属和山羊草属共计17个物种（包括亚种）的全基因组研究进展，包括测序技术、拼装策略、组装质量、基因组和基因功能的主要分析内容等，旨在为更复杂的植物基因组测序和基因组学研究提供一定的理论与技术参考。

关键词： 小麦族, 基因组, 全基因组测序, 小麦属, 大麦属, 黑麦属, 偃麦草属, 山羊草属

物种/基因组 Species/genome	品种 Cultivar	组装大小 Assembly size/Gb	染色体序列大小 Chromosome sequence size/ Gb	Contig N50/kb	Scaffold N50/kb	HC基因数量 HC gene number	BUSCO 评估指数 BUSCO assessment index/%	测序方法 Sequencing strategy	发表年份 Year published	文献 Reference
普通小麦/AABBDD T. aestivum/AABBDD	中国春	5.42	NA	NA	NA	94 000～ 96 000	NA	全基因组鸟枪法/Roche 454测序	2012	[11]
	中国春	10.24	NA	NA	2.3	124 201	95.4	分染色体测序、BAC测序、Illumina PE	2014	[12]
	中国春	13.43	NA	16.7	88.8	104 091	NA	Illumina PE/MP、链特异性RNA-Seq、 PacBio全长转录组	2017	[13]
	中国春	15.34	NA	232.7	NA	NA	98.3	Illumina PE、PacBio SMRT	2017	[14]
	中国春	14.50	14.07	51.8	22 800	107 891	99.0	BAC测序、Illumina PE/MP、 DeNovoMAGIC2、10×Genomics、 BioNano光学图谱、Hi-C、POPSEQ遗传图谱	2018	[10]
	W7984	9.12	7.10	8.3	24.8	NA	NA	全基因组鸟枪法/Illumina PE/MP、 POPSEQ遗传图谱	2015	[16]
	Fielder	15.00	14.70	NA	20 700	116 480	97.1	PacBio循环共识测序（CCS）、Omni-C 染色体构象捕获	2021	[17]
	泛基因组	14.3～14.9	13.9～14.2	48.9～ 83.5	10 200～ 49 700	118 734～ 120 967	97.6～98.4	Illumina PE/MP、DeNovoMAGIC3、10× Genomics、Nanopore、Hi-C、POPSEQ遗传图谱	2020	[18]
西藏半野生小麦/AABBDD T. aestivum ssp. tibetanum/ AABBDD	藏1817	14.71	14.05	66.3	37 600	118 078	99.5	Illumina PE/MP、DeNovoMAGIC3、10× Genomics、借助‘中国春’参考基因组（2018）进行染色体挂载	2020	[19]
乌拉尔图小麦/AA T. urartu/AA	G1812	4.66	NA	3.4	63.7	34 879	86.3	全基因组鸟枪法/Illumina PE	2013	[22]
乌拉尔图小麦/AA T. urartu/AA	G1812	4.86	4.67	344.0	3 700	37 516	NA	BAC测序、PacBio SMRT、10× Genomics、BioNano光学图谱	2018	[23]
粗山羊草/DD A. tauschii/DD	AL8/78	4.23	1.72	4.5	57.6	34 498	NA	全基因组鸟枪法/Illumina PE、Roche 454测序、遗传图谱	2013	[24]
	AL8/78	4.79	4.03	NA	NA	17 093	NA	全基因组鸟枪法、BAC测序、遗传图谱	2013	[25]
	AL8/78	4.34	NA	486.8	521.7	NA	NA	MaSuRCA混合拼装（Illumina PE/MP、PacBio SMRT）	2017	[26]
	AL8/78	4.31	3.99	112.6	12 100	42 828	97.0	Illumina PE/MP、DeNovoMAGIC2、 PacBio SMRT、高密度SNP遗传图谱	2017	[27]
	AL8/78	4.23	4.03	93.1	31 700	39 622	97.8	BAC测序、全基因组鸟枪法、PacBio SMRT、BioNano光学图谱	2017	[28]
野生二粒小麦/AABB T. turgidum var. dicoccoides/AABB	Zavitan	10.50	10.10	57.4	7 000	65 012	98.4	Illumina PE、DeNovoMAGIC2、 Hi-C、遗传图谱	2017	[4]
硬粒小麦/AABB T. turgidum var. durum/ AABB	Svevo	10.45	9.96	56.2	6 000	66 559	98.1	Illumina PE/MP、DeNovoMAGIC2、 Hi-C、高密度SNP遗传图谱	2019	[29]
大麦/HH H. vulgare/HH	Morex	1.87	NA	1.4	NA	26 159	NA	全基因组鸟枪法/Illumina PE/MP、 Roche 454测序、RNA-Seq	2012	[30]
	Morex	4.79	4.54/4.63	79.0	1 900	39 734	92.5	BAC测序、Illumina PE/MP、Roche 454测序、BioNano光学图谱，Hi-C、POPSEQ遗传图谱	2017	[31]
	Morex	4.65	4.34	NA	40 200	32 787	98.9	TRITEX（Illumina PE/MP、10× Genomics、Hi-C）	2019	[32]
	Morex	4.50	4.20	69 600	118 900	35 827	98.6	TRITEX（IIllumina PE/MP、10× Genomics、Hi-C）、PacBio SMRT、 PacBio CCS、Nanopore	2021	[33]
	Haruna Nijo	2.00	NA	NA	3.5	30 606	80.2	Illumina PE、Roche 454测序	2016	[34]
	Haruna Nijo	4.28	4.13	NA	18 900	49 524	96.0	TRITEX（Illumina PE/MP、10× Genomics、Hi-C）	2022	[35]
	AAC Synergy	4.85	4.14	40.0	2 300	46 845	93.9	TRITEX（Illumina PE/MP、10× Genomics、Hi-C）、PacBio SMRT	2021	[36]
	Golden Promise	4.13	4.13	22.4	4 100	45 154	95.2	Illumina PE/MP、Dovetail Chicago、 Hi-C	2020	[37]
	泛基因组	3.8～4.5	3.8～4.5	NA	5 000～ 42 700	35 859～ 40 044	NA	Minia+SOAPdenovo+TRITEX（Illumina PE/MP、10×Genomics、Hi-C）、DeNovoMAGIC3、POPSEQ遗传图谱	2020	[38]
青稞/HH H. vulgare var. coeleste/HH	拉萨钩芒	3.89	3.48	18.1	242.0	36 151	NA	全基因组鸟枪法/Illumina PE、Morex 基因组（2012）和遗传图谱进行染色体挂载	2015	[39]
	藏青320	3.73/ 4.84	4.59	5.9	171.1	46 787	NA	Illumina PE/MP、PacBio SMRT、Morex V1基因组（2017）进行染色体挂载	2018	[40]
	拉萨钩芒	4.00	NA	1 600	4 000	40 457	95.7	Illumina MP、PacBio SMRT、遗传图谱	2020	[41]
钝稃野大麦/HH H. spontaneum/HH	AWCS276/WB1	4.28	NA	35.4	724.9	36 395	95.3	全基因组鸟枪法/Illumina PE	2020	[5]
钝稃野大麦/HH H. spontaneum/HH	OUH602	4.50	4.32	NA	11 300	43 375	97.1	TRITEX（Illumina PE/MP、10× Genomics、Hi-C）	2021	[6]
海大麦/XaXa H. marinum/XaXa	H559	3.82	3.69	6 830	524 470	41 045	98.4	Illumina PE、PacBio SMRT、10× Genomics、Hi-C	2022	[46]
黑麦/RR S. cereale/RR	Lo7	2.80	NA	1.7	9.5	27 784	89.0	Illumina PE/MP	2017	[48]
黑麦/RR S. cereale/RR	威宁黑麦	7.74	7.25	480.4	1 000 000	45 596	96.7	TRITEX（Illumina PE/MP、10× Genomics、Hi-C）、PacBio SMRT、遗传图谱、BioNano光学图谱	2021	[47]
长穗偃麦草/EE E. elongatum/EE	NA	4.63	4.54	2 200	73 200	44 474	97.6	Illumina PE/MP、DeNovoMAGIC3、 PacBio SMRT、10×Genomics、 BioNano光学图谱、Hi-C	2020	[7]
二角山羊草/S^S^ A. bicornis/S^S^	TB01	5.64	5.38	8 700	NA	40 222	95.1	Nanopore、Hi-C、Illumina短读长测序	2022	[21]
高大山羊草/S^S^ A. longissima/S^S^	TL05	5.80	5.23	1 100	NA	37 201	94.0	Nanopore、Hi-C、Illumina短读长测序	2022	[21]
高大山羊草/S^S^ A. longissima/S^S^	AEG-6782-2	6.70	5.92	8.7	3 800	31 183	97.5	TRITEX（Illumina PE/MP、10× Genomics、Hi-C）	2022	[49]
西尔斯山羊草/S^S^ A. searsii/S^S^	searsii	5.34	4.66	600	NA	37 995	92.9	Nanopore、Hi-C、Illumina短读长测序	2022	[21]
沙融山羊草/S^S^ A. sharonensis/S^S^	TH02	5.89	5.14	1 000	NA	38 440	93.2	Nanopore、Hi-C、Illumina短读长测序	2022	[21]
沙融山羊草/S^S^ A. sharonensis/S^S^	AS_1644	6.70	6.30	NA	12 300	30 626	96.5	全基因组鸟枪法/Illumina MP、10× Genomics、Hi-C	2022	[50]
拟斯卑尔脱山羊草/SS A. speltoides/SS	TS01	4.11	3.76	1 800	NA	37 607	93.8	Nanopore、Hi-C、Illumina短读长测序	2022	[21]
拟斯卑尔脱山羊草/SS A. speltoides/SS	AEG-9674-1	5.14	4.02	15.6	3 100	36 928	96.4	TRITEX（Illumina PE/MP、10× Genomics、Hi-C）	2022	[49]

Table 1 Whole genome sequenced species from Triticeae


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