Codon bias analysis in chloroplast genomes of 3 avocado species in Persea
-
摘要: 【目的】 分析鳄梨属3种油梨叶绿体基因组密码子的使用偏好性，为油梨叶绿体基因工程中提高外源基因在载体内表达及油梨分子育种提供理论依据。【方法】 以在鳄梨属3种油梨（墨西哥种、危地马拉种和西印度群岛种）叶绿体基因组中筛选出的49条编码区（CDS）序列为研究对象，利用Excel 2010、Origin 2021、TBtools、CodonW 1.4.2、Chi-plot在线网站和CUSP软件对3种油梨叶绿体基因组密码子进行密码子组成分析、参数相关分析、中性绘图分析、ENC-plot分析、PR2-plot分析和最优密码子分析。【结果】 3种油梨叶绿体基因组密码子第1、第2和第3位上碱基GC含量的排序为GC1>GC2>GC3，表明GC在密码子不同位置上的分布不均匀。GC1分别与GC2、GC3、GC及ENC呈正相关，其中GC1与GC之间的相关系数最高（0.80）。GC2分别与GC3和ENC呈负相关。中性绘图分析结果显示，墨西哥种、危地马拉种和西印度群岛种3种油梨叶绿体基因组GC3与GC12间的回归系数分别为0.0956、0.0869和0.0872，相关系数分别为0.0050、0.0042和0.0043，表明密码子使用偏好性主要受自然选择的影响。ENC-plot分析结果显示，大多数基因偏离标准曲线散布在标准曲线下方，较少的基因分布在标准曲线上方或接近标准曲线，表明不同的基因受突变压力和自然选择影响不同。3种油梨叶绿体密码子偏好性受自然选择的影响程度较大。PR2-plot分析结果显示，密码子第3位上的碱基T的使用频率高于A，而G的使用频率高于C，说明密码子使用偏好性除受到突变压力影响外，也受自然选择等因素的影响。鳄梨属3种油梨均筛选出15个最优密码子，分别为UUU、UUA、UUG、CUU、AUU、GUU、UCU、CCU、CCC、ACU、ACC、GCU、UAA、UGU和AGA。【结论】 鳄梨属3种油梨叶绿体基因组密码子偏好性主要受到自然选择的影响，同时也受突变压力等多重因素的共同作用；并筛选出的15个最优密码子的第3位碱基大多以A/U结尾。Abstract: 【Objective】 To study the codon bias in chloroplast genome of 3 avocado species in Persea,which could provide theoretical basis for improving the expression of exogenous genes in genetic engineering of avocado and molecu‐lar breeding of avocado.【Method】The 49 coding region （CDS） sequences in chloroplast genomes of 3 avocado species in Persea（P.americana var.drymifolia,P.americana var.guatemalensis,P.americana var.americana） were selected as the study object.Using Excel 2010,Origin 2021,TBtools,CodonW 1.4.2,Chiplot online website and CUSP software,codon composition analysis,parameter correlation analysis,neutral mapping analysis,ENC-plot analysis,PR2-plot analysis and optimal codon analysis of chloroplast genomes codons of 3 avocado species were carried out. 【Result】 The se‐quence of GC content at the first,second and third bases of the chloroplast genome codons of 3 avocado species was GC1＞GC2＞GC3,indicating that the distribution of GC at different codon locations was uneven.GC1 was positively correlated with GC2,GC3,GC and ENC,and the correlation coefficient between GC1 and GC was the highest （0.80）.GC2 was negatively correlated with GC3 and ENC respectively.The results of neutral mapping analysis showed that the regression coefficients between the chloroplast genome GC3 and GC12 of P.americana var.drymifolia,P.americana var.guatemalensis and P.americana var.americana were 0.0956,0.0869 and 0.0872,and the correlation coefficients were 0.0050,0.0042 and 0.0043 respectively.It showed that codon bias was mainly influenced by natural selection.The results of ENC-plot analysis showed that most genes deviated from the standard curve and were scattered below the standard curve,while a few genes were distributed above or close to the standard curve,indicating that different genes were af‐fected differently by mutation pressure and natural selection.The chloroplast codon preference of 3 avocado species were greatly affected by natural selection.PR2-plot analysis results showed that the usage bias of base T at the third position of the codon was higher than that of A,while that of G was higher than that of C,indicating that the usage bias of the codon was affected not only by mutation pressure,but also by natural selection and other factors.A total of 15 optimal codons were screened from 3 avocado species in Persea:UUU,UUA,UUG,CUU,AUU,GUU,UCU,CCU,CCC,ACU,ACC,GCU,UAA,UGU and AGA. 【Conclusion】 The codon bias in the chloroplast genomes of 3 avocado species in Persea are mainly influenced by natural selection,but also influenced by multiple factors such as mutation pressure,and most of the third bases of the 15 optimal codons screened ended in A/U.
-
Keywords:
- Persea /
- chloroplast genome /
- codon usage bias /
- optimal codon
-
-
赖瑞联,陈瑾,冯新,覃振师,陈义挺,沈朝贵,田奇琳,吴如健.2022.橄榄叶绿体基因组密码子偏好性特征[J].福建农林大学学报(自然科学版),51(4):502-509.[Lai RL,Chen J,Feng X,Qin Z S,Chen Y T,Shen C G,Tian QL,Wu R J.2022.Codon usage preference of chloroplast genome of Canarium album[J].Journal of Fujian Agricul-ture and Forestry University(Natural Science Edition),51(4):502-509.]doi: 10.13323/j.cnki.j.fafu(nat.sci.).2022.04.008. 李亚麒,严炜,娄予强,黄家雄,胡发广,付兴飞,李亚男,程金焕.2023.高产小粒咖啡叶绿体基因组密码子偏好性分析[J].南方农业学报,54(8):2330-2339.[Li Y Q,Yan W,Lou Y Q,Huang J X,Hu F G,Fu X F,Li Y N,Cheng JH.2023.Codon usage bias in the chloroplast genome of high production Coffea arabica L[.J].Journal of Southern Agriculture,54(8):2330-2339.]doi: 10.3969/j.issn.2095-1191.2023.08.014. 唐玉娟,赵英,黄国弟,付海天,宋恩亮,李日旺,金刚.2021.芒果叶绿体基因组密码子使用偏好性分析[J].热带作物学报,42(8):2143-2150.[Tang Y J,Zhao Y,Huang G D,Fu H T,Song E L,Li R W,Jin G.2021.Analysis on codon usage bias of chloroplast genes from mango[J].Chi-nese Journal of Tropical Crops,42(8):2143-2150.]doi: 10.3969/j.issn.1000-2561.2021.08.004. 王杰敏,马东来,韩晓伟,严玉平,郑玉光,孙会改.2023.24份忍冬属材料叶绿体基因组密码子使用偏好性分析[J].植物资源与环境学报,32(3):12-23.[Wang J M,Ma D L,Han X W,Yan Y P,Zheng Y G,Sun H G.2023.Analysis on codon usage bias of chloroplast genomes of 24 Lonicera materials[J].Journal of Plant Resources and Environment,32(3):12-23.]doi: 10.3969/j.issn.1674-7895.2023.03.02. 王淘,陈烨,李竹,李瑞民.2023.枳叶绿体基因组密码子偏好性分析[J].基因组学与应用生物学,42(10):1050-1057.[Wang T,Chen Y,Li Z,Li R M.2023.Analysis of codon usage bias in the chloroplast genome of Citrus trifoliata[J].Genomics and Applied Biology,42(10):1050-1057.]doi: 10.13417/j.gab.042.001050. 肖明昆,严炜,熊贤坤,沈绍斌,宋记明,易怀锋,张林辉.2022.云南樟叶绿体基因组密码子偏好性分析[J].中南林业科技大学学报,42(6):127-134.[Xiao M K,Yan W,Xiong X K,Shen S B,Song J M,Yi H F,Zhang L H.2022.Analysis of codon usage bias in the chloroplast genome of Cinnamomum glanduliferum[J].Journal of Cen-tral South University of Forestry&Technology,42(6):127-134.]doi: 10.14067/j.cnki.1673-923x.2022.06.014. 辛雅萱,董章宏,瞿绍宏,刘成,叶鹏,辛培尧.2020.杜梨叶绿体基因组密码子偏好性分析[J].河北农业大学学报,43(6):51-59.[Xin Y X,Dong Z H,Qu S H,Liu C,Ye P,Xin P Y.2020.Analysis on codon usage bias of chloroplast genome in Pyrus betulifolia Bge[.J].Journal of Hebei Agri-cultural University,43(6):51-59.]doi: 10.13320/j.cnki.jauh.2020.0112. 杨祥燕,蔡元保,谭秦亮,覃旭,黄显雅,吴密.2022.菠萝叶绿体基因组密码子偏好性分析[J].热带作物学报,43(3):439-446.[Yang X Y,Cai Y B,Tan Q L,Qin X,Huang XY,Wu M.2022.Analysis of codon usage bias in the chlo-roplast genome of Ananas comosus[J].Chinese Journal of Tropical Crops,43(3):439-446.]doi: 10.3969/j.issn.1000-2561.2022.03.001. 赵森,邓力华,陈芬.2020.秋茄叶绿体基因组密码子使用偏好性分析[J].森林与环境学报,40(5):534-541.[Zhao S,Deng L H,Chen F.2020.Codon usage bias of chloro-plast genome in Kandelia obovata[J].Journal of Forestry and Environment,40(5):534-541.]doi: 10.13324/j.cnki.jfcf.2020.05.011. 朱艳,韩长志.2024.普通核桃与深纹核桃中叶绿体基因组密码子使用特征对比[J].江苏农业学报,40(8):1507-1520.[Zhu Y,Han C Z.2024.Comparison of codon usage characteristics of chloroplast genomes in Juglans regia and Juglans sigillata[J].Jiangsu Journal of Agricultural Sciences,40(8):1507-1520.]doi: 10.3969/j.issn.1000-4440.2024.08.015. Amado D A V,Detoni A M,de Carvalho S L C,Torquato A S,Martin C A,Tiuman T S,Aguiar C M,Cottica S M.2019.Tocopherol and fatty acids content and proximal compo-sition of four avocado cultivars (Persea Americana Mill)[J].Acta Alimentaria,48(1):47-55.doi: 10.1556/066.2019.48.1.6.
Andargie M,Congyi Z.2022.Genome-wide analysis of codon usage in sesame(Sesamum indicum L.)[J].Heliyon,8(1):e08687.doi: 10.1016/j.heliyon.2021.e08687.
Chakraborty S,Yengkhom S,Uddin A.2020.Analysis of codon usage bias of chloroplast genes in Oryza species[J].Planta,252(4):67.doi: 10.1007/s00425-020-03470-7.
Chen J,Ma W Q,Hu X W,Zhou K B.2023.Synonymous codon usage bias in the chloroplast genomes of 13 oil-tea camellia samples from south China[J].Forests,14(4):794.doi: 10.3390/f14040794.
Dobrogojski J,Adamiec M,Luciński R.2020.The chloroplast genome:A review[J].Acta Physiologiae Plantarum,42(6):98.doi: 10.1007/s11738-020-03089-x.
Duarte P F,Chaves M A,Borges C D,Mendonca C R B.2016.Avocado:Characteristics,health benefits and uses[J].Cien-cia Rural,46(4):747-754.doi: 10.1590/0103-8478cr20141516.
Ge Y,Dong X S,Wu B,Wang N,Chen H H,Zuo M H,Xu ZN,Tan L,Zhan R L.2019.Evolutionary analysis of six chloroplast genomes from three Persea americana ecologi-cal races:Insights into sequence divergences and phyloge-netic relationships[J].PLoS One,14(9):e0221827.doi: 10.1371/journal.pone.0221827.
Geng X S,Huang N,Zhu Y L,Qin L,Hui L.2022.Codon usage bias analysis of the chloroplast genome of cassava[J].South African Journal of Botany,151:970-975.doi: 10.1016/j.sajb.2022.11.022.
Green B R.2011.Chloroplast genomes of photosynthetic eukaryotes[J].The Plant Journal,66(1):34-44.doi: 10.1111/j.1365-313X.2011.04541.
Hernandez I,Uarrota V,Fuentealba C,Paredes D,Defilippi BG,Campos-Vargas R,Nunez G,Carrera E,Meneses C,Hertog M,Pedreschi R.2022.Transcriptome and hormone analyses reveals differences in physiological age of‘Hass’avocado fruit[J].Postharvest Biology and Technology,185:111806.doi: 10.1016/j.postharvbio.2021.111806.
Juarez-Escobar J,Guerrero-Analco J A,Zamora-Briseño J A,Elizalde-Contreras J M,Bautista-Valle M V,BojórquezVelázquez E,Loyola-Vargas V M,Mata-Rosas M,RuízMay E.2021.Tissue-specific proteome characterization of avocado seed during postharvest shelf life[J].Journal of Proteomics,235:104112.doi: 10.1016/j.jprot.2021.104112.
Li J Y,Yang C,Tian Y Y,Liu J X.2022.Regulation of chloro-plast development and function at adverse temperatures in plants[J].Plant and Cell Physiology,63(5):580-591.doi: 10.1093/pcp/pcac022.
Li Y Q,Hu X,Xiao M K,Huang J X,Lou Y Q,Hu F G,Fu XF,Li Y N,He H Y,Cheng J H.2023.An analysis of codon utilization patterns in the chloroplast genomes of three spe-cies of Coffea[J].BMC Genomic Data,24(1):42.doi: 10.1186/s12863-023-01143-4.
Ma L,He Y Z,Yu J Y,Gu C H,Liao X Z,Wu Z Q.2020.The complete chloroplast genome sequence of Cuphea hyssopi-folia[J].Mitochondrial DNA Part B,5(2):1415-1416.doi: 10.1080/23802359.2020.1735966.
Parvathy S T,Udayasuriyan V,Bhadana V.2022.Codon usage bias[J].Molecular Biology Reports,49(1):539-565.doi: 10.1007/s11033-021-06749-4.
Rao A,Chen Z P,Wu D B,Wang Y Y,Hou N.2024.Codon usage bias in the chloroplast genomes of Cymbidium spe-cies in Guizhou,China[J].South African Journal of Botany,164:429-437.doi: 10.1016/j.sajb.2023.12.009.
Raubeson L A,Peery R,Chumley T W,Dziubek C,Fourcade HM,Boore J L,Jansen R K.2007.Comparative chloroplast genomics:Analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus[J].BMC Genomics,8:174.doi: 10.1186/1471-2164-8-174.
Sheng J J,She X,Liu X Y,Wang J,Hu Z L.2021.Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species[J].PeerJ,9:e12173.doi: 10.7717/peerj.12173.
Song Y F,Yang Q H,Yi X G,Zhu Z Q,Wang X R,Li M.2022.Comparative analysis of codon usage patterns in chloro-plast genomes of cherries[J].Forests,13(11):1891.doi: 10.3390/f13111891.
Su X X,Zhao J,Wang Z Y.2020.The complete chloroplast genome of Hordeum brevisubulatum[J].Mitochondrial DNA Part B,5(3):2988-2989.doi: 10.1080/23802359.2020.1797552.
Wang J S,Wang A B,Zang X P,Tan L,Xu B Y,Chen H H,Jin Z Q,Ma W H.2019.Physicochemical,functional and emulsion properties of edible protein from avocado (Per-sea americana Mill.) oil processing by-products[J].Food Chemistry,288:146-153.doi: 10.1016/j.foodchem.2019.02.098.
Wang L J,Roossinck M J.2006.Comparative analysis of expressed sequences reveals a conserved pattern of opti-mal codon usage in plants[J].Plant Molecular Biology,61(4-5):699-710.doi: 10.1007/s11103-006-0041-8.
Wang L Y,Xing H X,Yuan Y C,Wang X L,Saeed M,Tao J C,Feng W,Zhang G H,Song X L,Sun X Z.2018.Genomewide analysis of codon usage bias in four sequenced cotton species[J].PLoS One,13(3):e0194372.doi: 10.1371/journal.pone.0194372.
Wang W B,Yu H,Wang J H,Lei W J,Gao J H,Qiu X P,Wang J S.2017.The complete chloroplast genome sequences of the medicinal plant Forsythia suspensa(Oleaceae)[J].International Journal of Molecular Sciences,18(11):2288.doi: 10.3390/ijms18112288.
Wang Z J,Cai Q W,Wang Y,Li M H,Wang C C,Wang Z X,Jiao C Y,Xu C C,Wang H Y,Zhang Z L.2022.Compara-tive analysis of codon bias in the chloroplast genomes of Theaceae species[J].Frontiers in Genetics,13:824610.doi: 10.3389/fgene.2022.824610.
Wang Z J,Xu B,Li B B,Zhou Q Q,Wang G Y,Jiang X Z,Wang C C,Xu Z D.2020.Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbia-ceae species[J].PeerJ,8:e8251.doi: 10.7717/peerj.8251.
Wright F.1990.The‘effective number of codons’used in a gene[J].Gene,87(1):23-29.doi: 10.1016/0378-1119(90)90491-9.
Zeng Y J,Shen L W,Chen S Q,Qu S,Hou N.2023.Codon usage profiling of chloroplast genome in Juglandaceae[J].Forests,14(2):378.doi: 10.1016/0378-1119(90)90491-9.
Zhang P P,Xu W B,Lu X,Wang L.2021.Analysis of codon usage bias of chloroplast genomes in Gynostemma species[J].Physiology and Molecular Biology of Plants,27(12):2727-2737.doi: 10.1007/s12298-021-01105-z.
Zhou M,Long W,Li X.2008.Analysis of synonymous codon usage in chloroplast genome of Populus alba[J].Journal of Forestry Research,19(4):293-297.doi: 10.1007/s11676-008-0052-1.
计量
- 文章访问数: 1
- HTML全文浏览量: 0
- PDF下载量: 0
下载: