Mining and analysis of the self-incompatibility <i>S</i> gene in <i>Aconitum pendulum</i> N. Busch based on RNA-seq

Li Xue-Li; Geng Tian-Tian; Wang Ying; Qian Ting; Zhang Yu-Jie; Zhao Fan; Sun Kun; Zhang Hui

doi:10.11913/PSJ.2095-0837.2021.20172

Plant Science Journal > 2021 > 39(2): 172-182. > DOI: 10.11913/PSJ.2095-0837.2021.20172 CSTR: 32231.14.PSJ.2095-0837.2021.20172

Li Xue-Li, Geng Tian-Tian, Wang Ying, Qian Ting, Zhang Yu-Jie, Zhao Fan, Sun Kun, Zhang Hui. Mining and analysis of the self-incompatibility S gene in Aconitum pendulum N. Busch based on RNA-seq[J]. Plant Science Journal, 2021, 39(2): 172-182. DOI: 10.11913/PSJ.2095-0837.2021.20172

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Mining and analysis of the self-incompatibility S gene in Aconitum pendulum N. Busch based on RNA-seq

College of Life Science, Northwest Normal University, Lanzhou 730070, China

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This work was supported by grants from the Open Fund Project of the State Key Laboratory of Chromosome Engineering, Institute of Genetic Development, Chinese Academy of Sciences (PCCE-KF-2019-06) and National Natural Science Foundation of China (31660060, 31060033)

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Received Date: September 02, 2020
Revised Date: November 10, 2020
Available Online: October 31, 2022
Published Date: April 27, 2021

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Abstract

Abstract

Two Aconitum pendulum N. Busch cultivars (‘WSYB1’ and ‘WSYY1’) were used as materials for transcriptome sequencing (RNA-seq) using bioinformatics to identify possible style and pollen S genes and analyze their sequence characteristics. Results identified two style S genes (ApSRNase) specifically or highly expressed in the style and two pollen S genes (ApSLF) specifically expressed in pollen. Similar to the sequenced plant Aquilegia coerulea James, this study showed that there was a S-RNase-based self-incompatibility system controlled by S-RNase and SLF in A. pendulum, but no Papaveraceae-type self-incompatibility system controlled by sS and pS.
- Aconitum pendulum,
- RNA-seq,
- Self-incompatibility,
- S-RNase,
- SLF

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References (35)

References

[1]	Takayama S, Isogai A. Self-Incompatibility in plants[J]. Annu Rev of Plant Biol, 2005, 56(1):467-489.
[2]	Lewis D. Incompatibility in plants[J]. J Cell Biochem, 2006, 99(2):373-81.
[3]	姜立杰, 曹家树. 芸薹属植物自交不亲和性的分子机制[J]. 植物学通报, 2001, 18(4):411-417. Jiang LJ, Cao JS. The molecular mechanism of self-incompatibility in Brassica[J]. Chinese Bulletin of Botany, 2001, 18(4):411-417.
[4]	刘素玲, 赵国建, 吴欣, 张百行, 高岭巍, 等. 植物自交不亲和机制研究进展[J]. 中国农业科技导报, 2016, 18(4):31-37. Liu SL, Zhao GJ, Wu X, Zhang BH, Gao LW, et al. Research progress on plant self-incompatibility mechanism[J]. Journal of Agricultural Science and Technology, 2016, 18(4):31-37.
[5]	Lawrence MJ, Afzal M, Kenrick J. The genetical control of self-incompatibility in Papaver rhoeas[J]. Heredity, 1978, 40(2):239-253.
[6]	Igic B, Kohn JR. Evolutionary relationships among self-incompatibility RNases[J]. Proc Natl Acad Sci USA, 2001, 98(23):13167-13171.
[7]	张一婧, 薛勇彪. 基于S-核酸酶的自交不亲和性的分子机制[J]. 植物学通报, 2007, 24(3):372-388. Zhang YJ, Xue YB. Molecular mechanism of self-incompatibility based on S-RNase[J]. Chinese Bulletin of Botany, 2007(3):372-388.
[8]	Xue YB, Carpenter R, Dickinson HG, Coen ES. Origin of allelic diversity in Antirrhinum S locus RNases[J]. Plant Cell, 1996, 8(5):805-814.
[9]	Kao T, Tsukamoto T. The molecular and genetic bases of S-RNase-based self-incompatibility[J]. Plant Cell, 2004, 16(s1):S72-S83.
[10]	Lai Z, Ma WS, Han B, Liang LZ, Zhang YS, et al. An F-box gene linked to the self-incompatibility (S) locus of Antirrhinum is expressed specifically in pollen and tapetum[J]. Plant Mol Biol, 2002, 50(1):29-42.
[11]	张辉. 金鱼草自交不亲和S-位点的结构与进化[D]. 北京:中国科学院大学, 2014.
[12]	Zhang Y, Zhang H, Zhao F, Song ZD, Guo YZ, et al. A molecular evolutionary framework of self-Incompatibility in the angiosperms[J]. SSRN Electronic Journal, 2020.DOI: 10.2139/ssrn.3596584.
[13]	Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome[J]. Nat Biotechnol, 2011, 29(7):644-652.
[14]	Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome[J]. Genome Biol, 2009, 10(3):R25.
[15]	Li B, Dewey CN. RSEM:accurate transcript quantification from RNA-seq data with or without a reference genome[J]. BMC Bioinformatics, 2011, 12(1):323-323.
[16]	Wheeler MJ, de Graaf BHJ, Hadjiosif N, Perry RM, Poulter NS, et al. Identification of the pollen self-incompatibility determinant in Papaver rhoeas[J]. Nature, 2009, 459(7249):992-995.
[17]	Foote HC, Ride JP, Franklin-Tong VE, Walker EA, Lawrence MJ, et al. Cloning and expression of a distinctive class of self-incompatibility (S) gene from Papaver rhoeas L.[J]. Proc Natl Acad Sci USA, 1994, 91(6):2265-2269.
[18]	Walker EA, Ride JP, Kurup S, Franklin-Tong VE, Lawrence MJ, Franklin FCH. Molecular analysis of two functional homologues of the S₃ allele of the Papaver rhoeas self-incompatibility gene isolated from different populations[J]. Plant Mol Biol, 1996, 30(5):983-994.
[19]	Kurup S, Ride JP, Jordan N, Fletcher G, Franklin-Tong VE, et al. Identification and cloning of related self-incompatibility S-genes in Papaver rhoeas and Papaver nudicaule[J]. Sex Plant Reprod, 1998, 11(4):192-198.
[20]	Paape T, Miyake T, Takebayashi N, Wolf D, Kohn JR, et al. Evolutionary genetics of an S-like polymorphism in Papaveraceae with putative function in self-incompatibility[J]. PLoS One, 2011, 6(8):e23635.
[21]	Zhang JH, Madden TL. PowerBLAST:a new network BLAST application for interactive or automated sequence analysis and annotation[J]. Genome Res, 1997, 7(6):649-656.
[22]	许克恒, 张云彤, 张莹, 王彬, 王法微, 李海燕. 植物F-box基因家族的研究进展[J]. 生物技术通报, 2018, 34(1):26-32. Xu KH, Zhang YT, Zhang Y, Wang B, Wang FW, Li HY. Research advances on the F-box gene family in plants[J]. Biotechnology Bulletin, 2018, 34(1):26-32.
[23]	Eddy SR. A probabilistic model of local sequence alignment that simplifies statistical significance estimation[J]. PLoS Comput Biol, 2008, 4(5):e1000069.
[24]	Edgar RC. MUSCLE:multiple sequence alignment with high accuracy and high throughput[J]. Nucleic Acids Res, 2004, 32(5):1792-1797.
[25]	Kumar S, Stecher G, Tamura K. MEGA7:Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Mo Biol Evol, 2016, 33(7):1870-1874.
[26]	Stamatakis A. RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies[J]. Bioinformatics, 2014, 30(9):1312-1313.
[27]	陈娜娜, 刘金义, 蔡斌, 王刚, 王敏, 程宗明. 苹果SnRK2基因家族的鉴定和生物信息学分析[J]. 中国农学通报, 2013, 29(13):120-127. Chen NN, Liu JY, Cai B, Wang G, Wang M, Cheng ZM. Identification and bioinformatics analysis of theSnRK2 gene family in apple (Malus×domestica Borkh.)[J]. Chinese Agricultural Science Bulletin, 2013(13):120-127.
[28]	Meinken J, Asch DK, Neizer-Ashun KA, Chang GH, Cooper JR CR, Xiang JM. FunSecKB2:真菌蛋白亚细胞定位的知识库[J]. 计算分子生物学, 2015, 4(10):1-11. Meinken J, Asch DK, Neizer-Ashun KA, Chang GH, Cooper JR CR, Xiang JM. FunSecKB2:a fungal protein subcellular location knowledgebase[J]. Computational Molecular Biology, 2015, 4(10):1-11.
[29]	王月志, 戴美松, 蔡丹英, 施泽彬. 基于高通量测序的梨果实常用内参基因表达稳定性分析[J]. 分子植物育种, 2019, 17(3):746-753. Wang YZ, Dai MS, Cai DY, Shi ZB. Expression stability analysis of common internal reference genes in pear fruit based on high-throughput sequencing[J]. Molecular Plant Breeding, 2019, 17(3):746-753.
[30]	Aguiar B, Vieira J, Cunha AE, Vieira CP. No evidence for Fabaceae Gametophytic self-incompatibility being determined by Rosaceae, Solanaceae, and Plantaginaceae S-RNase lineage genes[J]. BMC Plant Biol, 2015, 15(1):129.
[31]	余镇藩, 马鑫鑫, 曾斌, 王建友, 阿布都卡尤木·阿依麦提. 植物配子体自交不亲和SBP1基因研究进展[J]. 分子植物育种, 2019, 17(16):5285-5290. Yu ZF, Ma XX, Zeng B, Wang JY, Abdkym·Aymt. Research progress onSBP1 gene of plant gametophytic self-incompatibility[J]. Molecular Plant Breeding, 2019, 17(16):5285-5290.
[32]	Kubo KI, Entani T, Takara A, Wang N, Fields AM, et al. Collaborative non-self recognition system in S-RNase-based self-Incompatibility[J]. Science, 2010, 330(6005):796-799.
[33]	Goldraij A, Kondo K, Lee CB, Hancock CN, Sivaguru M, et al. Compartmentalization of S-RNase and HT-B degradation in self-incompatible Nicotiana[J]. Nature, 2006, 439(7078):805-810.
[34]	李富婷, 唐飞, 高冬丽, 段思凡, 李云海, 等. 配子体型自交不亲和调控机制的研究进展[J]. 云南师范大学学报(自然科学版), 2019, 39(6):65-70. Li FT, Tang F, Gao DL, Duan SF, Li YH, et al. Research progress on the regulation mechanism of gametophytic self-incompatibility[J]. Journal of Yunnan Normal University (Natural Science Edition), 2019, 39(6):65-70.
[35]	Newbigin E, Paape T, Kohn JR. RNase-based self-Incompatibility:puzzled by pollen S[J]. Plant Cell, 2008, 20(9):2286-2292.

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Mining and analysis of the self-incompatibility S gene in Aconitum pendulum N. Busch based on RNA-seq

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Mining and analysis of the self-incompatibility S gene in Aconitum pendulum N. Busch based on RNA-seq

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