Estimation of genome sizes of six Acer species by flow cytometry and K-mer analysis

MA Qiuyue, WANG Yuxiao, LI Qianzhong, LI Shushun, WEN Jing, ZHU Lu, YAN Kunyuan, DU Yiming, XIE Zhijun, LI Shuxian, OUYANG Fangqun, LU Chengdai

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2023, Vol. 47 ›› Issue (1) : 163-170.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2023, Vol. 47 ›› Issue (1) : 163-170. DOI: 10.12302/j.issn.1000-2006.202110030

Estimation of genome sizes of six Acer species by flow cytometry and K-mer analysis

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Abstract

【Objective】 There are variety species in the genus Acer, which have broad prospects for development and application in the ornamental, oil and medicinal fields. To provide an important theoretical reference for molecular biology and cytology studies of Acer, the genome sizes of six species of Acer were estimated using flow cytometry and K-mer analysis. 【Method】 Fresh leaves of six species of Acer were collected, and woody plant buffer(WPB) was used as a nuclear dissociation solution, Glycine max ‘Polanka’ and Zea mays CE-777 as internal standard. Six genome sizes were estimated by flow cytometry and K-mer analysis. 【Result】 The results of flow cytometry showed that the genomes of Acer henryi, A. buergerianum, A. elegantulum, A. griseum, A. pentaphyllum and A. tegmentosum were successfully estimated. The genome sizes of those were (691.12±8.69),(863.90±8.69), (896.50±4.35), (893.24±8.69), (766.10±8.69) and (1 154.04±13.04) Mb, respectively. The K-mer analysis showed that they were 561.72, 743.00, 777.87, 771.51, 650.64 and 1 103.46 Mb, respectively. The hybridity rate was about 1.00%、1.24%、1.31%、1.08%、0.28% and 0.81%, respectively,which were slightly smaller than that flow cytometry. 【Conclusion】 The results of this study could enrich the Acer gene database and provide important foundations for genomic and molecular cytogenetics studies within this genus.

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Acer / genome size / flow cytometry / K-mer analysis

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MA Qiuyue , WANG Yuxiao , LI Qianzhong , et al . Estimation of genome sizes of six Acer species by flow cytometry and K-mer analysis[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2023, 47(1): 163-170 https://doi.org/10.12302/j.issn.1000-2006.202110030

References

List( Publishing order | Descend order by publishing year | Descend order by cited within ) Chart analysis
[1]
方文培. 中国植物志: 46卷[M]. 北京: 科学出版社, 1981.
FANG W P. Chinese bulletin of botany:Vol.46[M]. Beijing: Science Press, 1981.
Cited in this article [1]
[2]
MA Q Y, SUN T L, LI S S, et al. The Acer truncatum genome provides insights into nervonic acid biosynthesis[J]. Plant J, 2020, 104(3):662-678.DOI:10.1111/tpj.14954.
https://doi.org/10.1111/tpj.14954
https://onlinelibrary.wiley.com/toc/1365313x/104/3
Cited in this article [3]
[3]
刘便强, 仲乙, 沈光海. 青楷槭化学成分及抗氧化活性的研究[J]. 吉林医药学院学报, 2021, 42(5):328-332.
LIU B Q, ZHONG Y, LIU B Q, SHEN G H. Chemical constituents and antioxidant activity of Acer tegmentosum[J]. J Jilin Med Univ, 2021, 42(5):328-332.DOI:10.13845/j.cnki.issn1673-2995.2021.05.003.
https://doi.org/10.13845/j.cnki.issn1673-2995.2021.05.003
Cited in this article [1]
[4]
白雪, 李小英, 邱宗海. 添加生物炭与菌肥的复合基质对元宝枫幼苗生长的影响[J]. 西南林业大学学报(自然科学), 2020, 40(4):14-22.
BAI X, LI X Y, QIU Z H. Effects of adding compound substrates with biochar and bacterial fertilizer on the growth of Acer truncatum seedlings[J]. J Southwest For Univ (Nat Sci), 2020, 40(4):14-22.
Cited in this article [1]
[5]
吕传青. 中华槭与鸡爪槭远缘杂交初探及杂种子代鉴定[D]. 泰安: 山东农业大学, 2015.
LV C Q. Preliminary study on distant hybridization of Acer sinense Pax × Acer palmatum Thunb and hybrids identification[D]. Tai’an: Shandong Agricultural University, 2015.
Cited in this article [1]
[6]
王雅倩, 张尚昆, 李冬兵. 木醋液对元宝枫幼苗生长发育的影响[J]. 中国农学通报, 2021, 37(25):41-46.
WANG Y Q, ZHANG S K, LI D B. Effects of wood vinegar on the growth and development of Acer truncatum seedlings[J]. Chin Agric Sci Bull, 2021, 37(25):41-46.
Cited in this article [1]
[7]
马秋月, 李倩中, 李淑顺, 等. 元宝枫组织培养及快速繁殖技术研究[J]. 南京林业大学学报(自然科学版), 2021, 45(2):220-224.
MA Q Y, LI Q Z, LI S S, et al. Study on tissue culture and rapid propagation of Acer truncatum Bunge[J]. J Nanjing For Univ (Nat Sci Ed), 2021, 45(2):220-224.
Cited in this article [2]
[8]
林立, 林乐静, 祝志勇, 等. 93份槭树种质资源的SSR指纹图谱构建与遗传多样性分析[J]. 分子植物育种, 2021,1-17.
LIN L, LIN L J, ZHU Z Y, et al. Construction of SSR fingerprint and genetic diversity analysis of 93 maple germplasm resources[J]. Molecular Plant Breeding, 2021,1-17.
Cited in this article [1]
[9]
李佳霖, 高玉福, 翁卓, 等. 5种观赏槭树叶片形态特征及秋季变色规律[J]. 延边大学农学学报, 2021, 43(2):19-24.
LI J L, GAO Y F, WENG Z, et al. Leaf morphology and color change of five ornamental maples in Yanji City[J]. Agric Sci J Yanbian Univ, 2021, 43(2):19-24.DOI:10.13478/j.cnki.jasyu.2021.02.004.
https://doi.org/10.13478/j.cnki.jasyu.2021.02.004
Cited in this article [1]
[10]
金亮, 徐伟韦, 李小白, 等. DNA流式细胞术在植物遗传及育种中的应用[J]. 中国细胞生物学学报, 2016, 38(2):225-234.
JIN L, XU W W, LI X B, et al. Application of DNA flow cytometry to plant genetics and breeding[J]. Chin J Cell Biol, 2016, 38(2):225-234.
Cited in this article [4]
[11]
田新民, 周香艳, 弓娜. 流式细胞术在植物学研究中的应用:检测植物核DNA含量和倍性水平[J]. 中国农学通报, 2011, 27(9):21-27.
TIAN X M, ZHOU X Y, GONG N. Applications of flow cytometry in plant research: analysis of nuclear DNA content and ploidy level in plant cells[J]. Chin Agric Sci Bull, 2011, 27(9):21-27.
Cited in this article [3]
[12]
PELLICER J, HIDALGO O, DODSWORTH S, et al. Genome size diversity and its impact on the evolution of land plants[J]. Genes, 2018, 9(2):88.DOI:10.3390/genes9020088.
https://doi.org/10.3390/genes9020088
https://www.mdpi.com/2073-4425/9/2/88
Cited in this article [3]
[13]
FERRARINI M, MORETTO M, WARD J A, et al. An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome[J]. BMC Genomics, 2013, 14:670.DOI:10.1186/1471-2164-14-670.
https://doi.org/10.1186/1471-2164-14-670
https://doi.org/10.1186/1471-2164-14-670
Cited in this article [1]
[14]
马秋月, 李淑顺, 马骧, 等. 基于流式细胞技术的两种槭属植物基因组大小测定[J]. 南京林业大学学报(自然科学版), 2018, 42(5):201-205.
MA Q Y, LI S S, MA X, et al. Estimation of genome size of two Acer Linn.by flow cytometry[J]. J Nanjing For Univ (Nat Sci Ed), 2018, 42(5):201-205.
Cited in this article [5]
[15]
LEVINE R F, BUNN P A Jr, HAZZARD K C, et al. Flow cytometric analysis of megakaryocyte ploidy comparison with Feulgen microdensitometry and discovery that 8N is the predominant ploidy class in Guinea pig and monkey marrow[J]. Blood, 1980, 56(2):210-217.DOI:10.1182/blood.V56.2.210.210.
https://doi.org/10.1182/blood.V56.2.210.210
https://www.ncbi.nlm.nih.gov/pubmed/6772262
Cited in this article [2]
[16]
GUAN R, ZHAO Y P, ZHANG H, et al. Draft genome of the living fossil Ginkgo biloba[J]. Giga Science, 2016, 5(1):49.DOI:10.1186/s13742-016-0154-1.
https://doi.org/10.1186/s13742-016-0154-1
https://academic.oup.com/gigascience/article-lookup/doi/10.1186/s13742-016-0154-1
Cited in this article [2]
[17]
陈双双, 齐香玉, 冯景, 等. 基于流式细胞术和基因组Survey的绣球基因组大小及特征分析[J]. 江苏农业科学, 2021(12):39-44.
CHEN S S, QI X Y, FENG J, et al. Analysis of genome size and characteristics of Hydrangea macrophylla based on flow cytometry and genome survey sequencing[J]. Jiangsu Agric Sci, 2021(12):39-44.
Cited in this article [5]
[18]
徐廷志. 槭属的系统演化与地理分布[J]. 云南植物研究, 1998(4):383-393.
XU T Z. The systematic evolution and distribution of the genus Acer[J]. Acta Bot Yunnanica, 1998(4):383-393.
Cited in this article [1]
[19]
DAI X G, HU Q J, CAI Q L, et al. The willow genome and divergent evolution from poplar after the common genome duplication[J]. Cell Res, 2014, 24(10):1274-1277.DOI:10.1038/cr.2014.83.
https://doi.org/10.1038/cr.2014.83
https://www.ncbi.nlm.nih.gov/pubmed/24980958
Cited in this article [1]
[20]
CHEN J H, HAO Z D, GUANG X M, et al. Liriodendron genome sheds light on angiosperm phylogeny and species-pair differentiation[J]. Nat Plants, 2019, 5(1):18-25.DOI:10.1038/s41477-018-0323-6.
https://doi.org/10.1038/s41477-018-0323-6
https://doi.org/10.1038/s41477-018-0323-6
Cited in this article [1]
[21]
DOLEZEL J, BARTOS J. Plant DNA flow cytometry and estimation of nuclear genome size[J]. Ann Bot, 2005, 95(1):99-110.DOI:10.1093/aob/mci005.
https://doi.org/10.1093/aob/mci005
https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mci005
Cited in this article [1]
[22]
LI S F, ZHANG G J, YUAN Y C, et al. Three homologous genes encoding functional Δ8-sphingolipid desaturase in Populus tomentosa[J]. Genes Genom, 2014, 36(3):293-301.DOI:10.1007/s13258-013-0167-4.
https://doi.org/10.1007/s13258-013-0167-4
http://link.springer.com/10.1007/s13258-013-0167-4
Cited in this article [1]
[23]
MARÇAIS G, KINGSFORD C. A fast,lock-free approach for efficient parallel counting of occurrences of K-mers[J]. Bioinforma-tics, 2011, 27(6):764-770.DOI:10.1093/bioinformatics/btr011.
https://doi.org/10.1093/bioinformatics/btr011
Cited in this article [1]
[24]
魏高明, 方炎明. 栎属植物流式细胞术实验体系的建立与优化[J]. 南京林业大学学报(自然科学版), 2015, 39(1):167-172.
WEI G M, FANG Y M. Establishment and optimization of an experiment system for flow cytometry in Quercus[J]. J Nanjing For Univ (Nat Sci Ed), 2015, 39(1):167-172.
Cited in this article [3]
[25]
张云燕, 安宇, 林峰, 等. 基于流式细胞术和K-mer分析的银缕梅属(Parrotia C.)植物基因组大小测定[J]. 植物遗传资源学报, 2021, 22(2):561-570.
ZHANG Y Y, AN Y, LIN F, et al. Estimation of genome size of Parrotia C.A.Mey.by flow cytometry and K-mer analysis[J]. J Plant Genet Resour, 2021, 22(2):561-570.DOI:10.13430/j.cnki.jpgr.20200705002.
https://doi.org/10.13430/j.cnki.jpgr.20200705002
Cited in this article [6]
[26]
王雪, 周佳熠, 孙会改, 等. 新疆沙冬青基因组调查测序与基因组大小预测[J]. 植物遗传资源学报, 2018, 19(1):143-149.
WANG X, ZHOU J Y, SUN H G, et al. Genomic survey sequencing and estimation of genome size of Ammopiptanthus mongolicus[J]. J Plant Genet Resour, 2018, 19(1):143-149.DOI:10.13430/j.cnki.jpgr.2018.01.016.
https://doi.org/10.13430/j.cnki.jpgr.2018.01.016
Cited in this article [2]
[27]
林瀚, 韩晓文, 兰思仁, 等. 基于流式细胞技术两种兰属植物基因组大小的测定[J]. 森林与环境学报, 2019, 39(6):616-620.
LIN H, HAN X W, LAN S R, et al. Estimation of genome size of two Cymbidium by flow cytometry[J]. J For Environ, 2019, 39(6):616-620.DOI:10.13324/j.cnki.jfcf.2019.06.008.
https://doi.org/10.13324/j.cnki.jfcf.2019.06.008
Cited in this article [1]
[28]
YAN L, WANG X, LIU H, et al. The genome of Dendrobium officinale illuminates the biology of the important traditional Chinese orchid herb[J]. Mol Plant, 2015, 8(6):922-934.DOI:10.1016/j.molp.2014.12.011.
https://doi.org/10.1016/j.molp.2014.12.011
https://linkinghub.elsevier.com/retrieve/pii/S1674205214000471
Cited in this article [3]
[29]
HUANG S W, LI R Q, ZHANG Z H, et al. The genome of the cucumber,Cucumis sativus L[J]. Nat Genet, 2009, 41(12):1275-1281.DOI:10.1038/ng.475.
https://doi.org/10.1038/ng.475
https://doi.org/10.1038/ng.475
Cited in this article [3]
[30]
张小燕, 刘志香, 廖保生, 等. 基于本草基因组学应用流式量测序技术检测人参基因组大小[J]. 世界科学技术-中医药现代化, 2017, 19(10):1724-1728.
ZHANG X Y, LIU Z X, LIAO B S, et al. Estimation of genome size of ginseng based on herbgeno-mics by flow cytometric analysis and high-throughput sequence[J]. Mod Tradit Chin Med Mater Med World Sci Technol, 2017, 19(10):1724-1728.DOI:10.11842/wst.2017.10.023.
https://doi.org/10.11842/wst.2017.10.023
Cited in this article [3]
[31]
GREILHUBER J, DOLEZEL J, LYSÁK M A, et al. The origin,evolution and proposed stabilization of the terms ‘genome size’ and ‘C-value’ to describe nuclear DNA contents[J]. Ann Bot, 2005, 95(1):255-260.DOI:10.1093/aob/mci019.
https://doi.org/10.1093/aob/mci019
https://academic.oup.com/aob/article-lookup/doi/10.1093/aob/mci019
Cited in this article [1]
[32]
SOLTIS D E, SOLTIS P S, BENNETT M D, et al. Evolution of genome size in the angiosperms[J]. Am J Bot, 2003, 90(11):1596-1603.DOI:10.3732/ajb.90.11.1596.
https://doi.org/10.3732/ajb.90.11.1596
https://www.ncbi.nlm.nih.gov/pubmed/21653334
Cited in this article [2] Abstract
Genome size varies extensively across the flowering plants, which has stimulated speculation regarding the ancestral genome size of these plants and trends in genome evolution. We investigated the evolution of C-values across the angiosperms using a molecular phylogenetic framework and C-values not previously available for crucial basal angiosperms, including Amborella, Illiciaceae, and Austrobaileya. Reconstructions of genome size across the angiosperms and extant gymnosperms indicate that the ancestral genome size for angiosperms is very small (1C ≤ 1.4 pg), in agreement with an earlier analysis of Leitch et al. (1998). Furthermore, a very small genome size (1C ≤ 1.4 pg) is ancestral not only for the angiosperms in general, but also for most major clades of flowering plants, including the monocots and the eudicots. The ancestral genome of core eudicots may also have been very small given that very low 1C-values appear to be ancestral for major clades of core eudicots, such as Caryophyllales, Saxifragales, and asterids. Very large genomes occur in clades that occupy derived positions within the monocots and Santalales.
[33]
OLSZEWSKAM J, OSIECKA R. The relationship between 2 C DNA content,systematic position,and the level of nuclear DNA endoreplication during differentiation of root parenchyma in some dicotyledonous shrubs and trees: comparison with herbaceous species[J]. Biochem Und Physiol Der Pflanzen, 1984, 179(8):641-657.DOI:10.1016/S0015-3796(84)80021-9.
https://doi.org/10.1016/S0015-3796(84)80021-9
https://linkinghub.elsevier.com/retrieve/pii/S0015379684800219
Cited in this article [2]
[34]
WENDEL J F, JACKSON S A, MEYERS B C, et al. Evolution of plant genome architecture[J]. Genome Biol, 2016, 17:37.DOI:10.1186/s13059-016-0908-1.
https://doi.org/10.1186/s13059-016-0908-1
https://www.ncbi.nlm.nih.gov/pubmed/26926526
Cited in this article [1] Abstract
We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.
[35]
PUTTICKM N, CLARK J, DONOGHUE P C J. Size is not everything:rates of genome size evolution,not C-value,correlate with speciation in angiosperms[J]. Proc Biol Sci, 2015, 282(1820):20152289.DOI:10.1098/rspb.2015.2289.
https://doi.org/10.1098/rspb.2015.2289
Cited in this article [1]
[36]
吴丽萍, 唐岩, 李颖岳, 等. 枣和酸枣基因组大小测定[J]. 北京林业大学学报, 2013, 35(3):77-83.
WU L P, TANG Y, LI Y Y, et al. Estimation of genome size of Ziziphus jujuba and Z. acdiojujuba[J]. J Beijing For Univ, 2013, 35(3):77-83.DOI:10.13332/j.1000-1522.2013.03.012.
https://doi.org/10.13332/j.1000-1522.2013.03.012
Cited in this article [1]
[37]
陈丙义, 李金凤, 霍恒志, 等. 6种野生草莓基因组大小估算[J]. 果树学报, 2015(1):51-56.
CHEN B Y, LI J F, HUO H Z, et al. Estimation of genome size in six wild strawberry species[J]. J Fruit Sci, 2015(1):51-56.
Cited in this article [1]
[38]
伍艳芳, 肖复明, 徐海宁, 等. 樟树全基因组调查[J]. 植物遗传资源学报, 2014, 15(1):149-152.
WU Y F, XIAO F M, XU H N, et al. Genome survey in Cinnamomum camphora L. Presl[J]. J Plant Genet Resour, 2014, 15(1):149-152.DOI:10.13430/j.cnki.jpgr.2014.01.020.
https://doi.org/10.13430/j.cnki.jpgr.2014.01.020
Cited in this article [1]
[39]
殷剑美, 王立, 蒋璐, 等. 芋[Colocasia esculenta(L.) Schott]的倍性水平及基因组特征解析[J]. 江苏农业学报, 2019, 35(6):1284-1291.
YIN J M, WANG L, JIANG L, et al. Analysis of ploidy level and genome characterization on taro[Colocasia esculenta(L.)Schott[J]. Jiangsu J Agric Sci, 2019, 35(6):1284-1291.
Cited in this article [1]
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