Advances and prospects of oak biology based on genomics

doi:10.12302/j.issn.1000-2006.202208025

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (6): 64-72.doi: 10.12302/j.issn.1000-2006.202208025

Special Issue: 南京林业大学120周年校庆特刊

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Advances and prospects of oak biology based on genomics

FANG Yanming(), ZHU Fuyuan, LI Yao, LI Xuan

Co-Innovation Center for Sustainable Forestry in Southern China,Key Laboratory of state Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation,College of Biology and the Environment, Nanjing Forestry University,Nanjing 210037,China

Received:2022-08-22 Revised:2022-09-14 Online:2022-11-30 Published:2022-11-24

Abstract

Abstract:

Oaks are important economic and ecological tree species in the northern Hemisphere, and are colloquially known as the “tree of life” or the “frame of civilization”. The publication of several oak genomes, such as those of Quercus robur, Q. lobata and Q. acutissima, has a profound impact on oak biology. In the past five years,numerous topics in oak biology have been investigated, including the systematic evolution and species identification, gene introgression and adaptive evolution, landscape genomics and ecological conservation, biological coexistence and interaction mechanism, secondary metabolism and growth and development, DNA methylation and epigenetic regulation, genes and longevity mechanisms. The expected development trends include four aspects: highlighting the in-depth application of oak genome resources, promoting extension of oak study systems, emphasizing topics in genetics and development for utilization of oak resources, and highlighting themes in ecology and evolution for conservation of oak forests.

Key words: oak, genome, gene introgression, landscape genomics, resource conservation

CLC Number:

S718

FANG Yanming, ZHU Fuyuan, LI Yao, LI Xuan. Advances and prospects of oak biology based on genomics[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2022, 46(6): 64-72.

Figures/Tables 3

Table 1

List of complete chloroplast genome sequences of oaks had been sequenced"

亚属 subgen.	组 Sect.	树种(首次报道的GenBank序列号) tree species(first reported GenBank accession No.)
栎亚属 Quercus	弗吉尼亚栎组 Virentes	弗吉尼亚栎Q. virginiana (MT916773)
	白栎组 Quercus	槲栎Q. aliena (KP301144);锐齿槲栎Q. aliena var. acutiserrata (KU240008);槲树Q. dentata (MG967555);黄山栎Q. dentata subsp. stewardii (MG678022);白栎Q. fabri (MG678031);凤城栎Q. fenchengensis (MN095295);深裂叶栎Q. gambelii (MK105457);大叶栎Q. griffithii (MG678034);大果栎Q. macrocarpa (MK105459);蒙古栎Q. mongolica (MG678033);皱叶栎Q. mongolica subsp. crispula (MK860969);无梗花栎 Q. petraea (LT996899);夏栎Q. robur (LT996900);枹栎Q. serrata (MG678024);短柄枹栎Q. serrata var. brevipetiolata (MG678032);星毛栎Q. stellata (MK105467);辽东栎Q. wutaishanica (MG678027)和云南波罗栎Q. yunnanensis (MG678028)
	红栎组 Lobatae	海滨常绿栎Q. agrifolia (OK634019);猩红栎Q. coccinea (MN308055);加州黑栎Q. kelloggii (OM541584);沼生栎Q. palustris (MK105461);柳叶栎Q. phellos (MZ196210);红槲栎Q. rubra (JX970937)和山地常绿栎Q. wislizeni (OM541583)
麻栎亚属 Cerris	青冈组 Cyclobalanopsis	赤栎Q. acuta (MT742291);细叶青冈Q. ciliaris (MN199024);福建青冈Q. chungii (MW401633);黄毛青冈Q. delavayi (MW450870);华南青冈Q. edithiae (KU382355);饭甑青冈Q. fleuryi (MG678008);赤皮青冈Q. gilva (MG678009);青冈Q. glauca (KX852399);大叶青冈Q. jenseniana (MG678011);木姜叶青冈Q. litseoides (ON598394);多脉青冈Q. multinervis (MG678004);小叶青冈Q. myrsinifolia (MG678005);竹叶青冈Q. neglecta (MG678010);宁冈青冈Q. ningangensis (MG678013);倒卵叶青冈Q. obovatifolia (MG356785);薄叶青冈Q. saravanensis (MW411183);滇青冈Q. schottkyana (=Q.glaucoides, MW450872);云山青冈Q. sessilifolia (MG678012);西畴青冈Q. sichourensis (MF787253)和褐叶青冈Q. stewardiana (MN199023)
	冬青栎组 Ilex	岩栎Q. acrodonta (MG678019);川滇高山栎Q. aquifolioides (KP340971);橿子栎Q. baronii (KT963087);坝王栎Q. bawanglingensis (MK449426);铁橡栎Q. cocciferoides (MG678016);匙叶栎Q. dolicholepis (KU240010);巴东栎Q. engleriana (MG678029);锥连栎Q. franchetii (MG678018);川西栎Q. gilliana (MG678007);帽斗栎Q. guyavifolia (MG678020);矮高山栎Q. monimotricha (MG678006);尖叶栎Q. oxyphylla (MG678021);黄背栎Q. pannosa (MG678025);乌冈栎Q. phillyraeoides (MG678026);毛脉高山栎Q. rehderiana (MG678037);光叶高山栎Q. pseudosemecarpifolia (MG678014);高山栎Q. semecarpifolia (MG678017);灰背栎Q. senescens (MG678023);刺叶高山栎Q. spinosa (KM841421);太鲁阁栎Q. tarokoensis (MF135621);通麦栎Q. tungmaiensis (MF593893)和炭栎Q. utilis (MG678015)
	麻栎组 Cerris	麻栎Q. acutissima (MF593895);小叶栎Q. chenii (MF593894)和栓皮栎Q. variabilis (KU240009)

Table 1

Table 2

Table 3

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组 Sect.	树种 species	遗传标记 genetic markers	文献 reference
麻栎组Cerris	麻栎Q. acutissima、栓皮栎Q. variabilis	nSNPs	[6]
白栎组 Quercus	夏栎Q. robur、无梗花栎Q. petraea	nSNPs、cpSNPs、mtSNPs	[22]
	夏栎Q. robur、无梗花栎Q. petraea	nSNPs	[23]
	槲树Q. dentata、皱叶栎Q. mongolica subsp. crispula	nSNPs	[24]
红栎组 Lobatae	北方针栎Q. ellipsoidalis、红槲栎Q. rubra	EST-SSRs	[25]
红栎组 Lobatae	猩红栎Q. coccinea、北方针栎Q. ellipsoidalis、红槲栎Q. rubra和黑栎Q. velutina	SSRs、EST-SSRs	[26]
中间栎组Protobalanus	金杯栎Q. chrysolepis、岛屿栎Q. tomentella	nSNPs	[27]
麻栎组和冬青栎组 Cerris and Ilex	冬青栎Q. ilex、欧洲栓皮栎Q. suber	nSSRs	[28]
麻栎组和白栎组 Cerris and Quercus	麻栎Q. acutissima、白栎Q. fabri、枹栎Q. serrata和栓皮栎Q. variabilis	nSSRs	[29]

树种 species	个体数 number of individuals	测序方法 sequencing method	SNP数 number of SNPs	参考基因组 reference genome	主要发现 main findings	文献 reference
川滇高山栎 Q. aquifolioides	587	Pool-seq	381	夏栎 Q. robur	RONA分析表明有一个谱系适应能力更强;在长寿广布栎树中检测到自然选择和分子适应相关的遗传印记;物种在异质生境中发生了不同的种内适应过程	[41]
加州白栎 Q. lobata	436	GBS	11 019	加州白栎 Q. lobata	许多位点可能是多空间尺度或多地理环境局域适应的基础,新候选基因与气候适应关联	[42]
网叶栎 Q. rugosa	103	GBS	5 354	加州白栎 Q. lobata	遗传变异的空间模式与降水季节性和地理距离密切相关,预测了种群未来面临风险的区域	[46]
麻栎 Q. acutissima	167	RAD-seq	55 361	加州白栎 Q. lobata	环境对非中性SNP的影响大于中性SNP,环境与表型分化显著相关;同质园试验与景观基因组学数据相结合可验证栎树局域适应假设	[47]
欧洲栓皮栎 Q. suber	95	GBS	1 996	加州白栎 Q. lobata	RONA分析途径可以应用于物种响应气候变化与适应研究	[48]
槲树 Q. dentata	38	WGS	16 654 671	夏栎 Q. robur	发现一个500 kb基因组区域,含12个环境相关单核苷酸多态性位点;单核苷酸多态性密度比基因组背景高160倍;群体遗传分析揭示了该基因组区域的各种选择迹象	[49]

Advances and prospects of oak biology based on genomics

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