Adaptive Differentiation of NBA1/MERIT40 of Three Species of Hippophae L.——Discussion on the Application of Next-generation Sequencing Technology in Hybrid Identification

doi:10.7525/j.issn.1673-5102.2020.05.002

Abstract

Abstract: With the development of high-throughput sequencing technology, the study of molecular mechanisms of adaptive evolution in the "Omics" level has become a hotspot of evolutionary research. In this study, transcriptome sequencing was carried out using materials of Hippophae rhamnoides ssp. sinensis, H.neurocarpa and H.goniocarpa that is a hybrid species from homoploid hybridization between the former two species, and the gene of subunit NBA1 of BRA1-A&BRISC complex was selected to deeply study on the basis of its positive selection(w>1). Bioinformatics analysis found that the coding region of NBA1 gene was 771 bp in three sea buckthorns in length, which was a nuclear localized hydrophilic protein that encoding a total of 256 amino acids. The amino acid sequence of NBA1 of H.rhamnoides ssp. sinensis and H.neurocarpa have different loci which is loci of 218 and 236. The site of 218 which close to ligand binding sites in H.rhamnoides ssp. sinensis is different from the VWA domain of H.neurocarpa and terrestrial plants, and it has been mutated from conserved leucine to methionine. This resulted in a significant change in the protein tertiary structure of H.rhamnoides ssp. sinensis and H.neurocarpa, and makes the protein binding sites have significant difference in spatial structure. Above all, we speculated that the NBA1 subunits differ in binding to another subunit. Mainly led to the difference in the BRCA1-A complex repair DNA damage repair function that caused by UV radiation, and it may be related to the adaptation of H.rhamnoides ssp. sinensis and H.neurocarpa to different elevations. In addition, Sanger sequencing has verified the accuracy of the next generation sequencing results, and has proved that is a homozygous gene of single copy in two parental species H.rhamnoides ssp. sinensis and H.neurocarpa, and exists in codominant allele way in H.goniocarpa. Further analysis found that the next generation sequencing data is not suitable for identifying hybrids at the level of individual, but it can reflect the parental source of the hybrid randomly to some extent if we parallel sequencing in multiple individuals within the populations. This study provides a reference data for further revealing the molecular mechanism of adaptation of Hippophae L. to different altitudes, and proposes advice in choose transcriptome sequencing methods to identify hybrid species.

Key words: NBA1, Hippophae rhamnoides ssp. sinensis, H.neurocarpa, H.goniocarpa, adaptive differentiation, hybrid identification

CLC Number:

S793.6

SUN Kun, DING Xue-Yang, ZHANG Hui, LI Xue-Li, WANG Ying, WANG Juan, LIU Ben-Li. Adaptive Differentiation of NBA1/MERIT40 of Three Species of Hippophae L.——Discussion on the Application of Next-generation Sequencing Technology in Hybrid Identification[J]. Bulletin of Botanical Research, 2020, 40(5): 648-658.

References

[1] 陈学林,廉永善.沙棘属植物的分布格局及其成因[J].沙棘,2007,20(4):1-5.Chen X L,Lian Y S.Distributional patterns of genus Hippophae L.and their causes of formation[J].Hippophae,2007,20(4):1-5.
[2] Sun K,Ma R J,Chen X L,et al.Hybrid origin of the diploid species Hippophae goniocarpa evidenced by the internal transcribed spacers(ITS) of nuclear rDNA[J].Belgian Journal of Botany,2003,136(1):91-96.
[3] 廉永善,陈学林,于倬德,等.沙棘属植物起源的研究[J].沙棘,1997,10(2):1-7.Lian Y S,Chen X L,Yu Z D,et al.The study of origin of the genus Hippophae L.[J].Hippophae,1997,10(2):1-7.
[4] Bartish I V,Jeppsson N,Nybom H,et al.Phylogeny of Hippophae(Elaeagnaceae) Inferred from Parsimony Analysis of Chloroplast DNA and Morphology[J].Systematic Botany,2002,27(1):41-54.
[5] 孟丽华,杨慧玲,吴桂丽,等.基于叶绿体DNA trnL-F序列研究肋果沙棘的谱系地理学[J].植物分类学报,2008,46(1):32-40.Meng L H,Yang H L,Wu G L,et al.Phylogeography of Hippophae neurocarpa(Elaeagnaceae) inferred from the chloroplast DNA trnL-F sequence variation[J].Journal of Systematics and Evolution,2008,46(1):32-40.
[6] 蒋严妃,严容,苏雪,等.二倍体杂交种棱果沙棘双向杂交起源及其母本主要来源于中国沙棘的分子证据[J].植物研究,2014,34(1):32-36.Jiang Y F,Yan R,Su X,et al.Molecular evidence for bidirectional hybrid origin and Hippophae rhamnoides ssp.sinensis as the mainly maternal plant of the diploid hybrid H.goniocarpa(Elaeagnaceae)[J].Bulletin of Botanical Research,2014,34(1):32-36.
[7] 张辉.棱果沙棘的同倍体杂交起源:来自叶绿体基因组和核基因组的证据[D].兰州:西北师范大学,2005.Zhang H.Homoploid hybrid origin of Hippophae goniocarpa subsp.goniocarpa-Evidence from chloroplast genome and nuclear genome[D].Lanzhou:Northwest Normal University,2005.
[8] 何涛,吴学明,贾敬芬.青藏高原高山植物的形态和解剖结构及其对环境的适应性研究进展[J].生态学报,2007,27(6):2574-2583.He T,Wu X M,Jia J F.Research advances in morphology and anatomy of alpine plans growing in the Qinghai-Tibet Plateau and their adaptations to envirormients[J].Acta Ecologica Sinica,2007,27(6):2574-2583.
[9] 陈学林,马瑞君,孙坤,等.中国沙棘属种质资源及其生境类型的研究[J].西北植物学报,2003,23(3):451-455.Chen X L,Ma R J,Sun K,et al.Germplasm resource and habitat types of Seabuckthorn in China[J].Acta Botanica Boreali Occidentalia Sinica,2003,23(3):451-455.
[10] Miki Y,Swensen J,Shattuck-Eidens D,et al.A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1[J].Science,1994,266(5182):66-71.
[11] Savage K I,Harkin D P.BRCA1,a ‘complex’ protein involved in the maintenance of genomic stability[J].The FEBS Journal,2015,282(4):630-646.
[12] Wang B,Matsuoka S,Ballif B A,et al.Abraxas and RAP80 Form a BRCA1 Protein Complex Required for the DNA Damage Response[J].Science,2007,316(5828):1194-1198.
[13] Kim H,Huang J,Chen J J.CCDC98 is a BRCA1-BRCT domain binding protein involved in the DNA damage response[J].Nature Structural & Molecular Biology,2007,14(8):710-715.
[14] Shao G,Lilli D R,Patterson-Fortin J,et al.The Rap80-BRCC36 de-ubiquitinating enzyme complex antagonizes RNF8-Ubc13-dependent ubiquitination events at DNA double strand breaks[J].Proceedings of the National Academy of Sciences of the United States of America,2009,106(9):3166-3171.
[15] Dong Y,Hakimi M A,Chen X W,et al.Regulation of BRCC,a Holoenzyme Complex Containing BRCA1 and BRCA2,by a Signalosome-like Subunit and Its Role in DNA Repair[J].Molecular Cell,2003,12(5):1087-1099.
[16] Gu C,Castellino A,Chan J Y,et al.BRE:a modulator of TNF-α action[J].The Faseb Journal,1998,12(12):1101-1108.
[17] Feng L,Huang J,Chen J J.MERIT40 facilitates BRCA1 localization and DNA damage repair[J].Genes & Development,2009,23(6):719-728.
[18] Wang B,Hurov K,Hofmann K,et al.NBA1,a new player in the Brca1 A complex,is required for DNA damage resistance and checkpoint control[J].Genes & Development,2009,23(6):729-739.
[19] Her J,Lee N S,Kim Y,et al.Factors forming the BRCA1-A complex orchestrate BRCA1 recruitment to the sites of DNA damage[J].Acta Biochimica et Biophysica Sinica,2016,48(7):658-664.
[20] Zheng H,Gupta V,Patterson-Fortin J,et al.A BRISC-SHMT Complex Deubiquitinates IFNAR1 and Regulates Interferon Responses[J].Cell Reports,2013,5(1):180-193.
[21] Yan K W,Li L J,Wang X S,et al.The deubiquitinating enzyme complex BRISC is required for proper mitotic spindle assembly in mammalian cells[J].The Journal of Cell Biology,2015,210(2):209-224.
[22] Kim H,Chen J J.New Players in the BRCA1-mediated DNA Damage Responsive Pathway[J].Molecules & Cells,2008,25(4):457-461.
[23] Scully R,Livingston D M.In search of the tumour-suppressor functions of BRCA1 and BRCA2[J].Nature,2000,408(6811):429-432.
[24] Shao G Z,Patterson-Fortin J,Messick T E,et al.MERIT40 controls BRCA1-Rap80 complex integrity and recruitment to DNA double-strand breaks[J].Genes & Development,2009,23(6):740-754.
[25] Block-Schmidt A S,Dukowic-Schulze S,Wanieck K,et al.BRCC36A is epistatic to BRCA1 in DNA crosslink repair and homologous recombination in Arabidopsis thaliana[J].Nucleic Acids Research,2011,39(1):146-154.
[26] Hu X,Kim J A,Castillo A,et al.NBA1/MERIT40 and BRE Interaction Is Required for the Integrity of Two Distinct Deubiquitinating Enzyme BRCC36-containing Complexes[J].Journal of Biological Chemistry,2011,286(13):11734-11745.
[27] Solyom S,Patterson-Fortin J,Pylkäs K,et al.Mutation screening of the MERIT40 gene encoding a novel BRCA1 and RAP80 interacting protein in breast cancer families[J].Breast Cancer Research and Treatment,2010,120(1):165-168.
[28] Riedinger C,Boehringer J,Trempe J F,et al.Structure of Rpn10 and Its Interactions with Polyubiquitin Chains and the Proteasome Subunit Rpn12[J].Journal of Biological Chemistry,2010,285(44):33992-34003.
[29] Rabl J,Bunker R D,Schenk A D,et al.Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation[J].Molecular Cell,2019,75(3):483-497.
[30] Lu C F,Jian L C,Kuang T Y.Freezing hardiness in alpine plants[J].Chinese Bulletin of Botany,1998,15(3):17-22.
[31] 王玉国.自然杂交与物种形成[J].生物多样性,2017,25(6):565-576.Wang Y G.Natural hybridization and speciation[J].Biodiversity Science,2017,25(6):565-576.
[32] 刘念,王庆彪,陈婕,等.麻黄属rbcL基因的适应性进化检测与结构模建[J].科学通报,2010,55(14):1341-1346.Liu N,Wang Q B,Chen J,et al.Adaptive evolution and structure modeling of rbcL gene in Ephedra[J].Chinese Science Bulletin,2010,55(2):2341-2346.
[33] Li W H,Wu C I,Luo C C.A new method for estimating synonymous and nonsynonymous rates of nucleotide sub-stitution considering the relative likelihood of nucleotideand codon changes[J].Molecular Biology and Evolution,1985,2(2):150-174.
[34] McCarthy C.Chromas 2.1.Griffith University:Australia.2012.Software available at:http://www.technelysium.com.au/wp/.
[35] Johnson M,Zaretskaya I,Raytselis Y,et al.NCBI BLAST:a better web interface[J].Nucleic acids research,2008,36(Web Server Issue):W5-W9.
[36] Burland T G.DNASTAR's Lasergene sequence analysis software[M].//Bioinformatics methods and protocols.Totowa,NJ:Humana Press,2000:71-91.
[37] Morya V K,Yadav S,Kim E K,et al.In silico characterization of alkaline proteases from different species of Aspergillus[J].Applied biochemistry and biotechnology,2012,166(1):243-257.
[38] Wichers H J,de Beijer T,Savelkoul H F J,et al.The major peanut allergen Arah 1 and its cleaved-off N-terminal peptide; possible implications for peanut allergen detection[J].Journal of agricultural and food chemistry,2004,52(15):4903-4907.
[39] Rost B,Yachdav G,Liu J.The predictprotein server[J].Nucleic acids research,2004,32(S_2):W321-W326.
[40] Yachdav G,Kloppmann E,Kajan L,et al.Predict Protein-an open resource for online prediction of protein structural and functional features[J].Nucleic acids research,2014,42(W1):W337-W343.
[41] Lee J,Freddolino P L,Zhang Y.Ab initio protein structure prediction[M].//Rigden J D.From protein structure to function with bioinformatics.Dordrecht:Springer,2017:3-35.
[42] De Lano W L.Pymol:An open-source molecular graphics tool[J].CCP4 Newsletter on protein crystallography,2002,40:82-92.
[43] Braun R C,Pedretti K T,Casavant T L,et al.Parallelization of local BLAST service on workstation clusters[J].Future Generation Computer Systems,2001,17(6):745-754.
[44] Chenna R,Sugawara H,Koike T,et al.Multiple sequence alignment with the Clustal series of programs[J].Nucleic acids research,2003,31(13):3497-3500.
[45] Abascal F,Zardoya R,Posada D.ProtTest:selection of best-fit models of protein evolution[J].Bioinformatics,2005,21(9):2104-2105.
[46] Kumar S,Tamura K,Nei M.MEGA:molecular evolutionary genetics analysis software for microcomputers[J].Bioinformatics,1994,10(2):189-191.
[47] 王超.萎缩芽孢杆菌(Bacillus atrophaeus)与铀、铬相互作用机理研究[D].绵阳:西南科技大学,2015.Wang C.Study on Interaction Mechanism between Bacillus atrophaeus and Uranium,Chromium[D].Mianyang:Southwest University of Science and Technology,2015.
[48] Bolton K.L,Tyrer J,Song H L,et al.Common variants at 19p13 are associated with susceptibility to ovarian cancer[J].Nature Genetics,2010,42(10):880-884.
[49] Kim J.S,Saint-André C,Lim H S,et al.Crystal Structure of the Rad3/XPD Regulatory Domain of Ssl1/p44[J].Journal of Biological Chemistry,2015,290(13):8321-8330.
[50] Stevens P F.(2001 onwards).Angiosperm Phylogeny Website.Version 14,July 2017[and more or less continuously updated since].
[51] Metzker M L.Sequencing technologies-the next generation[J].Nature reviews genetics,2010,11(1):31-46.