基于基因组学的栎树生物学研究进展

doi:10.12302/j.issn.1000-2006.202208025

国家林草科技领军期刊
中国精品科技期刊
中国高校百佳科技期刊
江苏省新闻出版政府奖期刊奖
RCCSE林学权威期刊（A+）
CSCD核心期刊
Scopus数据库收录期刊
中文核心期刊
SCD核心期刊

作者加群：102861116

微信公众号：南京林业大学学报

高级检索

南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (6): 64-72.doi: 10.12302/j.issn.1000-2006.202208025

所属专题：南京林业大学120周年校庆特刊

基于基因组学的栎树生物学研究进展

方炎明(), 朱福远, 李垚, 李璇

南京林业大学,南方现代林业协同创新中心,国家林业和草原局亚热带森林生物多样性保护重点实验室,南京林业大学生物与环境学院,江苏南京 210037

收稿日期:2022-08-22 修回日期:2022-09-14 出版日期:2022-11-30 发布日期:2022-11-24
基金资助:
国家自然科学基金项目(31770699);国家自然科学基金项目(32201375);国家自然科学基金项目(31370666);江苏省林业三新工程项目(LYSX[2016]49)

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

摘要/Abstract

摘要：

栎树(Quercus spp.)是北半球重要的经济与生态树种。夏栎(Q. robur)、加州白栎(Q. lobata)、麻栎(Q. acutissima)等树种基因组的公布,对栎树生物学研究产生了深刻的影响。近5年来,栎树生物学出现了包括系统进化与物种鉴定、基因渐渗与适应进化、景观基因组学与生态保育、生物共存与互作机制、次生代谢与生长发育、DNA甲基化与表观遗传调控及基因与长寿机制等方面的研究热点。虽然基于基因组学的栎树生物学若干研究前沿已经形成,但尚处于起步阶段,笔者预期未来会向4个方面深入:①强调栎树基因组资源的深度应用。应用景观基因组学途径,探究栎树的杂交渐渗与适应进化;联合基因组、转录组、蛋白组等多组学技术,探究栎树生长发育与胁迫响应过程中的基因调控网络与信号通路;优化体细胞发生和遗传转化体系,攻克栎树遗传改良和基因资源开发技术瓶颈。②促进栎树研究体系的广度拓展。随着壳斗科其他树种全基因组序列的公布,基于从分子到群落的不同生物层次的模式系统,将对欧亚大陆和北美不同区域的栎树,包括白栎组、红栎组、冬青栎组、麻栎组等不同栎树类群,以及壳斗科其他属树种基因组生物学研究产生深远影响。③关注栎树资源利用的遗传与发育主题。用栎树基因组资源对其结构的、代谢的和农艺性状的差异及其优化加以解析,全基因组关联研究(GWAS)也将应用于栎树,从而为阐释木材发育和木栓形成的机制奠定基础。④聚焦栎林保育的生态与进化主题。在全球气候变化背景下,通过增加耐受胁迫的基因型,以缓解气候变化对森林生态系统的影响。同时维持和保护栎树在自然生态系统中的生态与进化过程,阐明栎树多样性、迁移与适应、趋异与趋同生态适应等方面进化成功的机制。

关键词: 栎树, 基因组, 基因渐渗, 景观基因组学, 资源保育

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

中图分类号:

S718

方炎明,朱福远,李垚,等. 基于基因组学的栎树生物学研究进展[J]. 南京林业大学学报（自然科学版）, 2022, 46(6): 64-72.

FANG Yanming, ZHU Fuyuan, LI Yao, LI Xuan. Advances and prospects of oak biology based on genomics[J].Journal of Nanjing Forestry University (Natural Science Edition), 2022, 46(6): 64-72.DOI: 10.12302/j.issn.1000-2006.202208025.

图/表 3

表1

叶绿体全基因组数据已完成测序的栎属植物"

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)

表1

表2

表3

参考文献 88

[1]	LEROY T, LOUVET J M, LALANNE C, et al. Adaptive introgression as a driver of local adaptation to climate in European white oaks[J]. New Phytol, 2020, 226(4):1171-1182.DOI:10.1111/nph.16095.
[2]	PLOMION C, AURY J M, AMSELEM J, et al. Decoding the oak genome:public release of sequence data,assembly,annotation and publication strategies[J]. Mol Ecol Resour, 2016, 16(1):254-265.DOI:10.1111/1755-0998.12425.
[3]	PLOMION C, AURY J M, AMSELEM J, et al. Oak genome reveals facets of long lifespan[J]. Nat Plants, 2018, 4(7):440-452.DOI:10.1038/s41477-018-0172-3.
[4]	SORK V L, FITZ-GIBBON S T, PUIU D, et al. First draft assembly and annotation of the genome of a California endemic oak Quercus lobata Née (Fagaceae)[J]. G3 ( Bethesda), 2016, 6(11):3485-3495.DOI:10.1534/g3.116.030411.
[5]	SORK V L, COKUS S J, FITZ-GIBBON S T, et al. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks[J]. Nat Commun, 2022, 13(1):2047.DOI:10.1038/s41467-022-29584-y.
[6]	FU R R, ZHU Y X, LIU Y, et al. Genome-wide analyses of introgression between two sympatric Asian oak species[J]. Nat Ecol Evol, 2022, 6(7):924-935.DOI:10.1038/s41559-022-01754-7.
[7]	郑万钧. 中国树木志(第2卷)[M]. 北京: 中国林业出版社,1985.
[8]	DENK T, GRIMM G W, MANOS P S, et al. An updated infrageneric classification of the oaks:review of previous taxonomic schemes and synthesis of evolutionary patterns[M]// Tree Physiology. Cham: Springer International Publishing, 2017:13-38.DOI:10.1007/978-3-319-69099-5_2.
[9]	KREMER A, CASASOLI M, BARRENECHE T, et al. Fagaceae trees[M]//Forest Trees.Berlin, Heidelberg:Springer, 2007:161-187.DOI:10.1007/978-3-540-34541-1_5.
[10]	WEI G M, LI X, FANG Y M. Sympatric genome size variation and hybridization of four oak species as determined by flow cytometry genome size variation and hybridization[J]. Ecol Evol, 2021, 11(4):1729-1740.DOI:10.1002/ece3.7163.
[11]	BODÉNÈS C, CHANCEREL E, EHRENMANN F, et al. High-density linkage mapping and distribution of segregation distortion regions in the oak genome[J]. DNA Res, 2016, 23(2):115-124.DOI:10.1093/dnares/dsw001.
[12]	RAMOS A M, USIÉ A, BARBOSA P, et al. The draft genome sequence of cork oak[J]. Sci Data, 2018, 5:180069.DOI:10.1038/sdata.2018.69.
[13]	AI W F, LIU Y Q, MEI M, et al. A chromosome-scale genome assembly of the Mongolian oak (Quercus mongolica)[J]. Mol Ecol Resour, 2022, 22(6):2396-2410.DOI:10.1111/1755-0998.13616.
[14]	HIPP A L, MANOS P S, GONZÁLEZ-RODRÍGUEZ A, et al. Sympatric parallel diversification of major oak clades in the Americas and the origins of Mexican species diversity[J]. New Phytol, 2018, 217(1):439-452.DOI:10.1111/nph.14773.
[15]	DENG M, JIANG X L, HIPP A L, et al. Phylogeny and biogeography of east Asian evergreen oaks (Quercus Section Cyclobalanopsis;Fagaceae):insights into the Cenozoic history of evergreen broad-leaved forests in subtropical Asia[J]. Mol Phylogenetics Evol, 2018, 119:170-181.DOI:10.1016/j.ympev.2017.11.003.
[16]	HIPP A L, MANOS P S, HAHN M, et al. Genomic landscape of the global oak phylogeny[J]. New Phytol, 2020, 226(4):1198-1212.DOI:10.1111/nph.16162.
[17]	MANOS P S, HIPP A L. An updated infrageneric classification of the north American oaks (Quercus subgenus Quercus):review of the contribution of phylogenomic data to biogeography and species diversity[J]. Forests, 2021, 12(6):786.DOI:10.3390/f12060786.
[18]	YANG Y C, ZHOU T, QIAN Z Q, et al. Phylogenetic relationships in Chinese oaks (Fagaceae,Quercus):evidence from plastid genome using low-coverage whole genome sequencing[J]. Genomics, 2021, 113(3):1438-1447.DOI:10.1016/j.ygeno.2021.03.013.
[19]	PANG X B, LIU H S, WU S R, et al. Species identification of oaks (Quercus L.,Fagaceae) from gene to genome[J]. Int J Mol Sci, 2019, 20(23):5940.DOI:10.3390/ijms20235940.
[20]	LI Y, WANG L, ZHANG X W, et al. Extensive sharing of chloroplast haplotypes among east Asian Cerris oaks:the imprints of shared ancestral polymorphism and introgression[J]. Ecol Evol, 2022, 12(8):e9142.DOI:10.1002/ece3.9142.
[21]	CANNON C H, PETIT R J. The oak syngameon:more than the sum of its parts[J]. New Phytol, 2020, 226(4):978-983.DOI:10.1111/nph.16091.
[22]	DEGEN B, YANBAEV Y, MADER M, et al. Impact of gene flow and introgression on the range wide genetic structure of Quercus robur (L.) in Europe[J]. Forests, 2021, 12(10): 1425. DOI:10.3390/f12101425.
[23]	LEROY T, PLOMION C, KREMER A. Oak symbolism in the light of genomics[J]. New Phytol, 2020, 226(4):1012-1017. DOI: 10.1111/nph.15987.
[24]	NAGAMITSU T, UCHIYAMA K, IZUNO A, et al. Environment-dependent introgression from Quercus dentata to a coastal ecotype of Quercus mongolica var.crispula in northern Japan[J]. New Phytol, 2020, 226(4):1018-1028.DOI:10.1111/nph.16131.
[25]	KHODWEKAR S, GAILING O. Evidence for environment-dependent introgression of adaptive genes between two red oak species with different drought adaptations[J]. Am J Bot, 2017, 104(7):1088-1098.DOI:10.3732/ajb.1700060.
[26]	LIND-RIEHL J, GAILING O. Adaptive variation and introgression of a CONSTANS-like gene in north American red oaks[J]. Forests, 2016, 8(1):3.DOI:10.3390/f8010003.
[27]	ORTEGO J, GUGGER P F, SORK V L. Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus)[J]. New Phytol, 2018, 218(2):804-818.DOI:10.1111/nph.14951.
[28]	LÓPEZ D E HEREDIA U, SÁNCHEZ H, SOTO A. Molecular evidence of bidirectional introgression between Quercus suber and Quercus ilex[J]. IForest, 2018, 11(2):338-343.DOI:10.3832/ifor2570-011.
[29]	LI X, WEI G M, EL-KASSABY Y A, et al. Hybridization and introgression in sympatric and allopatric populations of four oak species[J]. BMC Plant Biol, 2021, 21(1):266.DOI:10.1186/s12870-021-03007-4.
[30]	LI Y, ZHANG X W, WANG L, et al. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China[J]. Ann Bot, 2022, 129(2):231-245.DOI:10.1093/aob/mcab140.
[31]	BUCK R, FLORES-RENTERÍA L. The syngameon Enigma[J]. Plants (Basel), 2022, 11(7):895.DOI:10.3390/plants11070895.
[32]	BOECKLEN W J. Topology of syngameons[J]. Ecol Evol, 2017, 7(24):10486-10491.DOI:10.1002/ece3.3507.
[33]	SUAREZ-GONZALEZ A, LEXER C, CRONK Q C B. Adaptive introgression:a plant perspective[J]. Biol Lett, 2018, 14(3):20170688.DOI:10.1098/rsbl.2017.0688.
[34]	BURGARELLA C, BARNAUD A, KANE N A, et al. Adaptive introgression:an untapped evolutionary mechanism for crop adaptation[J]. Front Plant Sci, 2019, 10:4.DOI:10.3389/fpls.2019.00004.
[35]	BUFFALO V, COOP G. Estimating the genome-wide contribution of selection to temporal allele frequency change[J]. Proc Natl Acad Sci USA, 2020, 117(34):20672-20680.DOI:10.1073/pnas.1919039117.
[36]	SALEH D, CHEN J, LEPLÉ J C, et al. Genome-wide evolutionary response of European oaks during the Anthropocene[J]. Evol Lett, 2022, 6(1):4-20.DOI:10.1002/evl3.269.
[37]	LIANG Y Y, SHI Y, YUAN S, et al. Linked selection shapes the landscape of genomic variation in three oak species[J]. New Phytol, 2021, 233(1):555-568.DOI:10.1111/nph.17793.
[38]	BALKENHOL N, DUDANIEC R Y, KRUTOVSKY K V, et al. Landscape genomics:understanding relationships between environmental heterogeneity and genomic characteristics of populations[M]// Population Genomics. Cham: Springer International Publishing, 2017:261-322.DOI:10.1007/13836_2017_2.
[39]	STORFER A, PATTON A, FRAIK A K. Navigating the interface between landscape genetics and landscape genomics[J]. Front Genet, 2018, 9:68.DOI:10.3389/fgene.2018.00068.
[40]	FENG L, DU F K. Landscape genomics in tree conservation under a changing environment[J]. Front Plant Sci, 2022, 13:822217.DOI:10.3389/fpls.2022.822217.
[41]	DU F K, WANG T R, WANG Y Y, et al. Contrasted patterns of local adaptation to climate change across the range of an evergreen oak,Quercus aquifolioides[J]. Evol Appl, 2020, 13(9):2377-2391.DOI:10.1111/eva.13030.
[42]	GUGGER P F, FITZ-GIBBON S T, ALBARRÁN-LARA A, et al. Landscape genomics of Quercus lobata reveals genes involved in local climate adaptation at multiple spatial scales[J]. Mol Ecol, 2021, 30(2):406-423.DOI:10.1111/mec.15731.
[43]	VANHOVE M, PINA-MARTINS F, COELHO A C, et al. Using gradient forest to predict climate response and adaptation in Cork oak[J]. J Evol Biol, 2021, 34: 910-923. DOI: 10.1111/jeb.13765.
[44]	SORK V L, AITKEN S N, DYER R J, et al. Putting the landscape into the genomics of trees:approaches for understanding local adaptation and population responses to changing climate[J]. Tree Genet Genomes, 2013, 9(4):901-911.DOI:10.1007/s11295-013-0596-x.
[45]	BROWNE L, WRIGHT J W, FITZ-GIBBON S, et al. Adaptational lag to temperature in valley oak (Quercus lobata) can be mitigated by genome-informed assisted gene flow[J]. Proc Natl Acad Sci USA, 2019, 116(50):25179-25185.DOI:10.1073/pnas.1908771116.
[46]	MARTINS K, GUGGER P F, LLANDERAL-MENDOZA J, et al. Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa[J]. Evol Appl, 2018, 11(10):1842-1858.DOI:10.1111/eva.12684.
[47]	GAO J, LIU Z L, ZHAO W, et al. Combined genotype and phenotype analyses reveal patterns of genomic adaptation to local environments in the subtropical oak Quercus acutissima[J]. J Syst Evol, 2021, 59(3):541-556.DOI:10.1111/jse.12568.
[48]	PINA-MARTINS F, BAPTISTA J, PAPPAS G J, et al. New insights into adaptation and population structure of cork oak using genotyping by sequencing[J]. Glob Change Biol, 2018, 25(1):337-350.DOI:10.1111/gcb.14497.
[49]	ZHOU B F, SHI Y, CHEN X Y, et al. Linked selection,ancient polymorphism,and ecological adaptation shape the genomic landscape of divergence in Quercus dentata[J]. J Sytematics Evolution, 2022, 19.DOI:10.1111/jse.12817.
[50]	TEDERSOO L, BRUNDRETT M C. Evolution of ectomycorrhizal symbiosis in plants[M]// Biogeography of Mycorrhizal Symbiosis. Cham: Springer International Publishing, 2017:407-467.DOI:10.1007/978-3-319-56363-3_19.
[51]	BOUFFAUD M L, HERRMANN S, TARKKA M T, et al. Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi[J]. BMC Genomics, 2020, 21(1):399.DOI:10.1186/s12864-020-06806-5.
[52]	ABDELFATTAH A, WISNIEWSKI M, SCHENA L, et al. Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root[J]. Environ Microbiol, 2021, 23(4):2199-2214.DOI:10.1111/1462-2920.15392.
[53]	FORT T, PAUVERT C, ZANNE A E, et al. Maternal effects shape the seed mycobiome in Quercus petraea[J]. New Phytol, 2021, 230(4):1594-1608.DOI:10.1111/nph.17153.
[54]	U’REN J M, ZIMMERMAN N B. Oaks provide new perspective on seed microbiome assembly[J]. New Phytol, 2021, 230(4):1293-1295.DOI:10.1111/nph.17305.
[55]	PASCUAL-ALVARADO E, CASTILLEJOS-LEMUS D E, CUEVAS-REYES P, et al. Diversity of galls induced by wasps (Hymenoptera:Cynipidae,Cynipini) associated with oaks (Fagaceae:Quercus) in Mexico[J]. Bot Sci, 2017, 95(3):461.DOI:10.17129/botsci.1215.
[56]	SCHULTZ J C, STONE G N. A tale of two tissues:probing gene expression in a complex insect-induced gall[J]. Mol Ecol, 2022, 31(11):3031-3034.DOI:10.1111/mec.16482.
[57]	HEARN J, BLAXTER M, SCHÖNROGGE K, et al. Genomic dissection of an extended phenotype:oak galling by a cynipid gall wasp[J]. PLoS Genet, 2019, 15(11):e1008398.DOI:10.1371/journal.pgen.1008398.
[58]	MARTINSON E O, WERREN J H, EGAN S P. Tissue-specific gene expression shows a cynipid wasp repurposes oak host gene networks to create a complex and novel parasite-specific organ[J]. Mol Ecol, 2022, 31(11):3228-3240.DOI:10.1111/mec.16159.
[59]	LEBOLDUS J M, NAVARRO S M, KLINE N, et al. Repeated emergence of sudden oak death in Oregon:chronology,impact,and management[J]. Plant Dis, 2022:2022Apr29.DOI:10.1094/PDIS-02-22-0294-FE.
[60]	GALLARDO A, MORCUENDE D, SOLLA A, et al. Regulation by biotic stress of tannins biosynthesis in Quercus ilex: crosstalk between defoliation and Phytophthora cinnamomi infection[J]. Physiol Plant, 2019, 165(2):319-329.DOI:10.1111/ppl.12848.
[61]	BARTHOLOMÉ J, BRACHI B, MARÇAIS B, et al. The genetics of exapted resistance to two exotic pathogens in pedunculate oak[J]. New Phytol, 2020, 226(4):1088-1103.DOI:10.1111/nph.16319.
[62]	COELHO A C, PIRES R, SCHÜTZ G, et al. Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots:a long-term proteomics approach[J]. PLoS One, 2021, 16(1):e0245148.DOI:10.1371/journal.pone.0245148.
[63]	CRISTINA A C, SCHÜTZ G. Protein markers for the identification of cork oak plants infected with Phytophthora cinnamomi by applying an (α,β)-k-feature set approach[J]. Forests, 2022, 13(6):940.DOI:10.3390/f13060940.
[64]	CUNHA E, SILVA M, CHAVES I, et al. iEC7871 Quercus suber model:the first multi-tissue diel cycle genome-scale metabolic model of a woody tree[J]. bioRxiv, 2021, DOI:10.1101/2021.03.09.434537.
[65]	LEAL A R, SAPETA H, BEECKMAN T, et al. Spatiotemporal development of suberized barriers in cork oak taproots[J]. Tree Physiol, 2021, 42(6):1269-1285.DOI:10.1093/treephys/tpab176.
[66]	LOPES S T, SOBRAL D, COSTA B, et al. Phellem versus xylem:genome-wide transcriptomic analysis reveals novel regulators of cork formation in cork oak[J]. Tree Physiol, 2019, 40(2):129-141.DOI:10.1093/treephys/tpz118.
[67]	FERNÁNDEZ-PIÑÁN S, BOHER P, SOLER M, et al. Transcriptomic analysis of cork during seasonal growth highlights regulatory and developmental processes from phellogen to phellem formation[J]. Sci Rep, 2021, 11:12053.DOI:10.1038/s41598-021-90938-5.
[68]	LIN L M, GUO H Y, SONG X, et al. Adaptive evolution of Chalcone isomerase superfamily in Fagaceae[J]. Biochem Genet, 2021, 59(2):491-505.DOI:10.1007/s10528-020-10012-z.
[69]	MOSELER A, SELLES B, ROUHIER N, et al. Novel insights into the diversity of the sulfurtransferase family in photosynthetic organisms with emphasis on oak[J]. New Phytol, 2020, 226(4):967-977.DOI:10.1111/nph.15870.
[70]	ZHANG J, LIN L M, CHENG W W, et al. Genome-wide identification and expression analysis of glycosyltransferase gene family 1 in Quercus robur L[J]. J Appl Genetics, 2021, 62(4):559-570.DOI:10.1007/s13353-021-00650-3.
[71]	GUGGER P F, FITZ-GIBBON S, PELLEGRINI M, et al. Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients[J]. Mol Ecol, 2016, 25(8):1665-1680.DOI:10.1111/mec.13563.
[72]	BROWNE L, MEAD A, HORN C, et al. Experimental DNA demethylation associates with changes in growth and gene expression of oak tree seedlings[J]. G3 Genes\|Genomes\|Genetics, 2020, 10(3):1019-1028.DOI:10.1534/g3.119.400770.
[73]	SILVA H G, SOBRAL R S, MAGALHÃES A P, et al. Genome-wide identification of epigenetic regulators in Quercus suber L[J]. Int J Mol Sci, 2020, 21(11):3783.DOI:10.3390/ijms21113783.
[74]	INÁCIO V, BARROS P M, COSTA A, et al. Differential DNA methylation patterns are related to phellogen origin and quality of Quercus suber cork[J]. PLoS One, 2017, 12(1):e0169018.DOI:10.1371/journal.pone.0169018.
[75]	BROWNE L, MACDONALD B, FITZ-GIBBON S, et al. Genome-wide variation in DNA methylation predicts variation in leaf traits in an ecosystem-foundational oak species[J]. Forests, 2021, 12(5):569.DOI:10.3390/f12050569.
[76]	ROSSI F, CRNJAR A, COMITANI F, et al. Extraction and high-throughput sequencing of oak heartwood DNA:assessing the feasibility of genome-wide DNA methylation profiling[J]. PLoS One, 2021, 16(11):e0254971.DOI:10.1371/journal.pone.0254971.
[77]	MUNNÉ-BOSCH S. Limits to tree growth and longevity[J]. Trends Plant Sci, 2018, 23(11):985-993.DOI:10.1016/j.tplants.2018.08.001.
[78]	TOBIAS P A, GUEST D I. Tree immunity:growing old without antibodies[J]. Trends Plant Sci, 2014, 19(6):367-370.DOI:10.1016/j.tplants.2014.01.011.
[79]	SCHMID-SIEGERT E, SARKAR N, ISELI C, et al. Low number of fixed somatic mutations in a long-lived oak tree[J]. Nat Plants, 2017, 3(12):926-929.DOI:10.1038/s41477-017-0066-9.
[80]	CHEN M X, ZHANG Y J, FERNIE A R, et al. SWATH-MS-based proteomics:strategies and applications in plants[J]. Trends Biotechnol, 2021, 39(5):433-437.DOI:10.1016/j.tibtech.2020.09.002.
[81]	MARTÍNEZ M T, SAN-JOSÉ M, ARRILLAGA I, et al. Holm oak somatic embryogenesis:current status and future perspectives[J]. Front Plant Sci, 2019, 10:239.DOI:10.3389/fpls.2019.00239.
[82]	SERRA O, MÄHÖNEN A P, HETHERINGTON A J, et al. The making of plant armor:the periderm[J]. Annu Rev Plant Biol, 2022, 73:405-432.DOI:10.1146/annurev-arplant-102720-031405.
[83]	CAVENDER-BARES J. Diversification,adaptation,and community assembly of the American oaks (Quercus),a model clade for integrating ecology and evolution[J]. New Phytol, 2019, 221(2):669-692.DOI:10.1111/nph.15450.
[84]	XING Y, LIU Y, ZHANG Q, et al. Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)[J]. Gigascience, 2019, 8(9):giz112.DOI:10.1093/gigascience/giz112.
[85]	SUN Y, GUO J L, ZENG X R, et al. Chromosome-scale genome assembly of Castanopsis tibetana provides a powerful comparative framework to study the evolution and adaptation of Fagaceae trees[J]. Mol Ecol Resour, 2022, 22(3):1178-1189.DOI:10.1111/1755-0998.13539.
[86]	VINHA A F, BARREIRA J C M, COSTA A S G, et al. A new age for Quercus spp.fruits:review on nutritional and phytochemical composition and related biological activities of acorns[J]. Compr Rev Food Sci Food Saf, 2016, 15(6):947-981.DOI:10.1111/1541-4337.12220.
[87]	SCHROEDER H, NOSENKO T, GHIRARDO A, et al. Oaks as beacons of hope for threatened mixed forests in central Europe[J]. Front For Glob Change, 2021, 4:670797. DOI: 10.3389/ffgc.2021.670797.
[88]	KREMER A, HIPP A L. Oaks: an evolutionary success story[J]. New Phytol, 2020, 226(4): 987-1011. DOI: 10.1111/nph.16274.

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]

基于基因组学的栎树生物学研究进展

Advances and prospects of oak biology based on genomics

RichHTML

PDF

可视化

摘要/Abstract

引用本文

使用本文

图/表 3

参考文献 88

相关文章 15

编辑推荐

Metrics

本文评价

作者

读者

审稿

[1]	邓演文, 田淑意, 刘世晗, 梁建, 陶家璐, 邓小梅. 广东含笑和诗琳通含笑叶绿体基因组结构及系统发育分析[J]. 南京林业大学学报（自然科学版）, 2025, 49(1): 69-77.
[2]	欧阳泽怡, 李志辉, 牟虹霖, 姜小龙, 程勇, 吴际友. 基于简化基因组开发青冈和滇青冈微卫星引物[J]. 南京林业大学学报（自然科学版）, 2024, 48(6): 62-70.
[3]	翟学昌, 彭丽, 颜海飞, 朱柯帆, 张淑燕, 张彩云, 鲁显楷. 资源植物黑老虎的比较叶绿体基因组学研究[J]. 南京林业大学学报（自然科学版）, 2024, 48(6): 71-78.
[4]	马建慧, 陈昕, 耿礼阳, 汤晨茜, 魏雪妍. 蔷薇科花楸属白毛系的系统发生分析[J]. 南京林业大学学报（自然科学版）, 2024, 48(4): 25-36.
[5]	刘莉, 瞿印权, 余延浩, 王倩, 洑香香. 青钱柳全基因组SSR位点分析及多态性引物开发[J]. 南京林业大学学报（自然科学版）, 2024, 48(4): 67-75.
[6]	杨永. 裸子植物的系统分类:历史、现状和展望[J]. 南京林业大学学报（自然科学版）, 2024, 48(3): 14-26.
[7]	尹增芳, 欧香, 陈瑶, 杨爱香, 孙李勇. 望春玉兰生物学基础研究进展与展望[J]. 南京林业大学学报（自然科学版）, 2024, 48(2): 256-262.
[8]	邱靖, 李嘉宝, 朱大海, 陈昕. 花楸属直脉组7种/变种基因组大小及叶表皮微形态特征的分类学意义[J]. 南京林业大学学报（自然科学版）, 2023, 47(3): 77-86.
[9]	马秋月, 王玉虓, 李倩中, 李淑顺, 闻婧, 朱璐, 颜坤元, 杜一鸣, 解志军, 李淑娴, 欧阳芳群, 鲁成代. 基于流式细胞术和K-mer方法测定6种槭属植物基因组大小[J]. 南京林业大学学报（自然科学版）, 2023, 47(1): 163-170.
[10]	陈赢男, 韦素云, 曲冠正, 胡建军, 王军辉, 尹佟明, 潘惠新, 卢孟柱, 康向阳, 李来庚, 黄敏仁, 王明庥. 现代林木育种关键核心技术研究现状与展望[J]. 南京林业大学学报（自然科学版）, 2022, 46(6): 1-9.
[11]	储陈辰, 孙明升, 吴雨涵, 言震宇, 李婷, 冯洋帆, 国颖, 尹佟明, 薛良交. 杨树泛基因组构建与基因组变异分析[J]. 南京林业大学学报（自然科学版）, 2022, 46(6): 251-260.
[12]	何旭东, 隋德宗, 王红玲, 黄瑞芳, 郑纪伟, 王保松. 中国柳树遗传育种研究进展[J]. 南京林业大学学报（自然科学版）, 2022, 46(6): 51-63.
[13]	王子玥, 甄艳, 刘光欣, 席梦利. 染色质转座酶可及性测序及其在木本植物中的应用前景[J]. 南京林业大学学报（自然科学版）, 2022, 46(5): 1-10.
[14]	丁晓磊, 张悦, 林司曦, 叶建仁. 基于高通量测序技术的松材线虫研究进展[J]. 南京林业大学学报（自然科学版）, 2022, 46(4): 1-7.
[15]	汪青桐, 丁晓磊, 叶建仁, 史秀峰. 基于SNP分子标记的华东地区松材线虫种群遗传分化研究[J]. 南京林业大学学报（自然科学版）, 2022, 46(4): 21-28.