Citation: | Yuan X L, Yang Y X, Mao M H, et al. Prediction and Analysis of Genome Size of Orophea yunnanensis[J]. Journal of Southwest Forestry University, 2025, 45(3): 1–6. DOI: 10.11929/j.swfu.202407030 |
Flow cytometry and K-mer survey methods were utilized to estimate the genome size of Orophea yunnanensis, and analyzed the genome and its characteristics, and Zea mays DNA was used as standards in this study. The results showed that, the genome size of O. yunnanensis was estimated to be approximately 866.53 Mb or 801.96 Mb by flow cytometry; 125.97 Gb original data was obtained through high-throughout sequencing, and approximately high-quality 123.33 Gb clean data was acquired after processing, and this illustrated the sequencing data was good; the genome size of O. yunnanensis was about 782.9 Mb(K-mer=19), the heterozygous rate was about 0.86 %; when K-mer=21, the genome size was estimated to be 782.20 Mb, and the heterozygous rate was about 0.90 %; these suggested the genome of O. yunnanensis was highly heterozygotic genome; the top three species Chieniodendron hainanense, Alphonsea hainanensis and Stelechocarpus burahol were found to be the same family as O. yunnanensis compared using NT database.
[1] |
Johnston J S, Pepper A E, Hall A E, et al. Evolution of genome size in Brassicaceae [J]. Annals of Botany, 2005, 95(1): 229−235. DOI: 10.1093/aob/mci016
|
[2] |
Garcia S, Garnatje T, Hidalgo O, et al. First genome size estimations for some eudicot families and Genera [J]. Collectanea Botanica, 2010, 29: 7−16. DOI: 10.3989/collectbot.2010.v29.001
|
[3] |
Kim J H, Roh J Y, Kwon D H, et al. Estimation of the genome sizes of the chigger mites Leptotrombidium pallidum and Leptotrombidium scutellare based on quantitative PCR and k-mer analysis [J]. Parasites & Vectors, 2014, 7: 279.
|
[4] |
Goel N, Zaidi S, Khare S K. Whole genome sequencing and functional analysis of a novel biofilm-eradicating strain Nocardiopsis lucentensis EMB25 [J]. World Journal of Microbiology & Biotechnology, 2023, 39(11): 292.
|
[5] |
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
|
[6] |
杜文文, 王祥宁, 段青, 等. 34种秋海棠基因组大小比较与分析 [J]. 植物遗传资源学报, 2018, 19(2): 370−376.
|
[7] |
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.
|
[8] |
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. A. Mey.)植物基因组大小测定 [J]. 植物遗传资源学报, 2021, 22(2): 561−570.
|
[9] |
刘涛, 刘玉萍, 富贵, 等. 基于流式细胞法和K−mer分析法检测沙鞭基因组大小 [J]. 草业学报, 2022, 31(12): 133−145. DOI: 10.11686/cyxb2021491
|
[10] |
任喆, 陈丽, 彭华. 云南澄广花应该作为极小种群植物加强保护 [J]. 生物多样性, 2016, 24(3): 358−359. DOI: 10.17520/biods.2016064
|
[11] |
Lan W J, Wang J, Guo Y Q, et al. Oropheayunnol, an unusual 22, 23-epoxy apotirucallane triterpenoid from Orophea Yunnanensis [J]. Natural Product Communications, 2012, 7(4): 495−496.
|
[12] |
Liu Z W, Peng H. Notes on the key role of stenochoric endemic plants in the floristic regionalization of Yunnan [J]. Plant Diversity, 2016, 38(6): 289−294. DOI: 10.1016/j.pld.2016.11.011
|
[13] |
王连润, 陶磅, 万红, 等. 云南4种野生猕猴桃基因组大小测定与比较 [J]. 中国南方果树, 2022, 51(4): 100−103.
|
[14] |
Dolezel J, Bartos J. Plant DNA flow cytometry and estimation of nuclear genome size [J]. Annals of Botany, 2005, 95(1): 99−110. DOI: 10.1093/aob/mci005
|
[15] |
Dolezel J, Greilhuber J, Suda J. Estimation of nuclear DNA content in plants using flow cytometry [J]. Nature Protocols, 2007, 2(9): 2233−2244. DOI: 10.1038/nprot.2007.310
|
[16] |
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.
|
[17] |
刘亚洲, 贾海凤, 刘叶, 等. 基于流式细胞术和基因组Survey测定牛膝基因组大小[J/OL]. 分子植物育种, 2022 (2022−04−29). https://kns.cnki.net/kcms/detail/46.1068.S.20220428.1549.023.html.
|
[18] |
Cock P J A, Fields C J, Goto N, et al. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants [J]. Nucleic Acids Research, 2010, 38(6): 1767−1771. DOI: 10.1093/nar/gkp1137
|
[19] |
Marçais G, Kingsford C. A fast, lock-free approach for efficient parallel counting of occurrences of K−mers [J]. Bioinformatics, 2011, 27(6): 764−770. DOI: 10.1093/bioinformatics/btr011
|
[20] |
Chen W B, Hasegawa D K, Arumuganathan K, et al. Estimation of the whitefly Bemisia tabaci genome size based on K−mer and flow cytometric analyses [J]. Insects, 2015, 6(3): 704−715. DOI: 10.3390/insects6030704
|
[21] |
Altschul S F, Gish W, Miller W, et al. Basic local alignment search tool [J]. Journal of Molecular Biology, 1990, 215(3): 403−410. DOI: 10.1016/S0022-2836(05)80360-2
|
[22] |
Soltis D E, Soltis P S, Bennett M D, et al. Evolution of genome size in the angiosperms [J]. American Journal of Botany, 2003, 90(11): 1596−1603. DOI: 10.3732/ajb.90.11.1596
|
[23] |
Greilhuber J, Borsch T, Müller K, et al. Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size [J]. Plant Biology, 2006, 8(6): 770−777. DOI: 10.1055/s-2006-924101
|
[24] |
Pellicer J, FAY fls M F, LEITCH fls I J. The largest eukaryotic genome of them all? [J]. Botanical Journal of the Linnean Society, 2010, 164(1): 10−15. DOI: 10.1111/j.1095-8339.2010.01072.x
|
[25] |
Kang M, Tao J J, Wang J, et al. Adaptive and nonadaptive genome size evolution in Karst endemic flora of China [J]. New Phytologist, 2014, 202(4): 1371−1381. DOI: 10.1111/nph.12726
|
[26] |
Bennett M D, Leitch I J. Nuclear DNA amounts in angiosperms: progress, problems and prospects [J]. Annals of Botany, 2005, 95(1): 45−90. DOI: 10.1093/aob/mci003
|
[27] |
Park S T, Kim J. Trends in next-generation sequencing and a new era for whole genome sequencing [J]. International Neurourology Journal, 2016, 20(S2): 76−83. DOI: 10.5213/inj.1632742.371
|
[28] |
Temsch E M, Koutecký P, Urfus T, et al. Reference standards for flow cytometric estimation of absolute nuclear DNA content in plants [J]. Cytometry Part A, 2022, 101(9): 710−724. DOI: 10.1002/cyto.a.24495
|
[29] |
Praça-Fontes M M, Carvalho C R, Clarindo W R, et al. Revisiting the DNA C-values of the genome size-standards used in plant flow cytometry to choose the “best primary standards” [J]. Plant Cell Reports, 2011, 30(7): 1183−1191. DOI: 10.1007/s00299-011-1026-x
|
[30] |
欧汉彪, 韦铄星, 王智慧, 等. 香合欢全基因组Survey分析[J/OL]. 分子植物育种, 2022 (2022−03−08). https://kns.cnki.net/kcms/detail/46.1068.s.20220303.2055.049.html.
|
[31] |
Kozlowski G, Fragnière Y, Clément B, et al. Genome size in the Arenaria ciliata species complex (Caryophyllaceae), with special focus on northern Europe and the Arctic [J]. Plants, 2024, 13(5): 635. DOI: 10.3390/plants13050635
|