Comparative Transcriptome Analysis of Five Species of Lilium

doi:10.7525/j.issn.1673-5102.2021.04.017

Abstract

Abstract:

Lilium are perennial herbaceous plants with important ornamental value and some species are edible and medicinal. In the present study， the transcriptome of four species of Lilium（L. pumilum， L. davidii， L. lancifolium and L. brownii var. viridulum） was sequenced respectively， and the genes which involved in flower development were analyzed. Combined with the previous transcriptome data of L. brownii， the orthologous genes were selected by comparative transcriptome analysis. Positive selections were screened and their environmental adaptability were analyzed respectively. 44 565， 51 413， 41 638 and 44 716 unigenes were obtained from L. pumilum， L. davidii， L. lancifolium and L. brownii var. viridulum respectively by assembly. In order to understand the function of unigene， the unigenes were compared and annotated in the public database. 13 genes related to the development of flower were identified. A total of 8 247 orthologous genes were obtained in five species， and Ka， Ks and Ka/Ks values were calculated. 33 pairs of homologous genes were strongly positive selected in five species. Subsequently， GO and KEGG enrichment analysis and gene function annotation were carried out， and it was found that these genes were mainly related to plant defense and biosynthesis.

Key words: Lilium, transcriptome, flower development gene, orthologous gene, positive gene

CLC Number:

S644.1

Xue-Yan ZHAO, Si-Feng LI, Guo-Qing BAI, Wei-Min LI. Comparative Transcriptome Analysis of Five Species of Lilium[J]. Bulletin of Botanical Research, 2021, 41(4): 614-625.

References

1	李金鹏，郑春雨，刘井莉.百合属植物的研究进展［J］.北方园艺，2013，（7）：197-200.
1	Li J P，Zheng C Y，Liu J L.Research progress on Lilium plants［J］.Northern Horticulture，2013，（7）：197-200.
2	胡悦，杜运鹏，田翠杰，等.百合属植物化学成分及其生物活性的研究进展［J］.食品科学，2018，39（15）：323-332.
2	Hu Y，Du Y P，Tian C J，et al.A review of chemical components and their bioactivities from the genus Lilium［J］.Food Science，2018，39（15）：323-332.
3	杨柳慧，汪王，刘艳秋，等.细叶百合LpWRKY20基因的克隆和表达分析［J］.西北林学院学报，2019，34（3）：104-110.
3	Yang L H，Wang W，Liu Y Q，et al.Cloning and expression analysis of LpWRKY20 gene from Lilium pumilum［J］.Journal of Northwest Forestry University，2019，34（3）：104-110.
4	中华人民共和国药典委员会.中国药典［M］.北京：中国医药科技出版社，2015：132.
4	Chinese Pharmacopeia Committee.Phamacopoeia of the People’s Republic of China［M］.Beijing：China Medical Science and Technology Press，2015：132.
5	张卫，王嘉伦，张志杰，等.经典名方药用百合本草考证［J］.中国中药杂志，2019，44（22）：5007-5011.
5	Zhang W，Wang J L，Zhang Z J，et al.Herbal textual research on triditional Chinese medicine “Baihe”（Lilii Bulbus）［J］.China Journal of Chinese Materia Medica，2019，44（22）：5007-5011.
6	周佳民，宋荣，曹亮，等.不同百合（品）种生长发育特性、光合特性的比较分析及综合评价［J］.中国中药杂志，2019，44（21）：4581-4587.
6	Zhou J M，Song R，Cao L，et al.Comparative analysis and comprehensive evaluation for growth and photosynthetic characteristics of different lily species and varieties［J］.China Journal of Chinese Materia Medica，2019，44（21）：4581-4587.
7	苏菁华.渥丹与川百合组培快繁体系的研究［D］.武汉：华中农业大学，2014.
7	Su J H.Researches on tissue culture and rapid propagation of Lilium concolor and Lilium davidii［D］.Wuhan：Huazhong agricultural university，2014.
8	Ai B，Gao Y，Zhang X L，et al.Comparative transcriptome resources of eleven primulina species，a group of “stone plants” from a biodiversity hot spot［J］.Molecular ecology resources，2015，15（3）：619-632.
9	刘合霞，李博.牛耳朵与黄花牛耳朵比较转录组学分析［J］.分子植物育种，2019，17（6）：1853-1863.
9	Liu H X，Li B.Comparative transcriptome analysis of Primulina eburnea and Primulina lutea［J］.Molecular Plant Breeding，2019，17（6）：1853-1863.
10	赵建花.地黄属五种植物的比较转录组研究［D］.西安：西北大学，2017.
10	Zhao J H.Comparative transcriptome analysis on five species of Rehmannia［D］.Xi’an：Northwest University，2017.
11	Guo W H，Jeong J，Kim Z，al Wet.Genetic diversity of Liliumtsingtauense in China and Korea revealed by ISSR markers and morphological characters［J］.Biochemical Systematics and Ecology，2011，39（4-6）：352-360.
12	梅芳，李晓玲，张德春.神农架自然保护区宜昌百合染色体核型分析［J］.安徽农业科学，2011，39（20）：12111-12112，12115.
12	Mei F，Li X L，Zhang D C.Karyotype analysis of Lilium leucanthum（Baker） Baker in Shennongjia national nature reserve［J］.Journal of Anhui Agricultural Sciences，2011，39（20）：12111-12112，12115.
13	Du Y P，He H B，Wang Z X，et al.Molecular phylogeny and genetic variation in the genus Lilium native to China based on the internal transcribed spacer sequences of nuclear ribosomal DNA［J］.Journal of Plant Research，2014，127（2）：249-263.
14	Li L，Stoeckert C J JR，Roos D S.OrthoMCL：identification of ortholog groups for eukaryotic genomes［J］.Genome Research，2003，13（9）：2178-2189.
15	Young M D，Wakefield M J，Smyth G K，et al.Gene ontology analysis for RNA-seq：accounting for selection bias［J］.Genome Biology，2010，11（2）：R14.
16	Yang Z H.PAML 4：phylogenetic analysis by maximum likelihood［J］.Molecular Biology and Evolution，2007，24（8）：1586-1591.
17	Kanehisa M，Araki M，Goto S，et al.KEGG for linking genomes to life and the environment［J］.Nucleic Acids Research，2008，36（Database issue）：D480-D484.
18	Grabherr M G，Haas B J，Yassour M，et al.Full-length transcriptome assembly from RNA-Seq data without a reference genome［J］.Nature Biotechnology，2011，29（7）：644-652.
19	Prasad K，Vijayraghavan U.Double-stranded RNA interference of a rice PI/GLO paralog，OsMADS2，uncovers its second-whorl-specific function in floral organ patterning［J］.Genetics，2003，165（4）：2301-2305.
20	Tzeng T Y，Chen H Y，Yang C H.Ectopic expression of carpel-specific MADS box genes from lily and lisianthus causes similar homeotic conversion of sepal and petal in Arabidopsis［J］.Plant Physiology，2002，130（4）：1827-1836.
21	杨梁，王爱然，唐金富，等.百合花发育的分子生物学研究进展［J］.华北农学报，2006，21（S1）：81-85.
21	Yang L，Wang A R，Tang J F，et al.Research progress of molecular biology about flower development in Lily［J］.Acta Agriculturae Boreali-Sinica，2006，21（S1）：81-85.
22	Jeon J S，Lee S，Jung K H，et al.Production of transgenic rice plants showing reduced heading date and plant height by ectopic expression of rice MADS-box genes［J］.Molecular Breeding，2000，6（6）：581-592.
23	Ohmori S，Kimizu M，Sugita M，et al.MOSAIC FLORAL ORGANS1，an AGL6-like MADS box gene，regulates floral organ identity and meristem fate in rice［J］.The Plant Cell，2009，21（10）：3008-3025.
24	Wang S，Huang H J，Han R，et al.Negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in Betula platyphylla × B.pendula［J］.Plant Science，2019，289：110280.
25	Nagasawa N，Miyoshi M，Sano Y，et al.SUPERWOMAN1 and DROOPING LEAF genes control floral organ identity in rice［J］.Development，2003，130（4）：705-718.
26	Lee S，Jeon J S，An K，et al.Alteration of floral organ identity in rice through ectopic expression of OsMADS16［J］.Planta，2003，217（6）：904-911.
27	Wang S，Huang H J，Han R，et al.BpAP1 directly regulates BpDEF to promote male in?orescence formation in Betula platyphylla × B.pendula［J］.Tree Physiology，2019，39（6）：1046-1060.
28	Adamczyk B J，Fernandez D E.MIKC* MADS domain heterodimers are required for pollen maturation and tube growth in Arabidopsis［J］.Plant Physiology，2009，149（4）：1713-1723.
29	Bemer M，Hvan Mourik，Mui?o J M，et al.FRUITFULL controls SAUR10 expression and regulates Arabidopsis growth and architecture［J］.Journal of Experimental Botany，2017，68（13）：3391-3403.
30	Sch?nrock N，Bouveret R，Leroy O，et al.Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway［J］.Genes & development，2006，20（12）：1667-1678.
31	Soyk S，Lemmon Z H，Oved M，et al.Bypassing negative epistasis on yield in tomato imposed by a domestication gene［J］.Cell，2017，169（6）：1142-1155.e12.
32	Nara T，Saka T，Sawado T，et al.Isolation of a LIM15/DMC1 homolog from the basidiomycete Coprinus cinereus and its expression in relation to meiotic chromosome pairing［J］.Molecular and General Genetics，1999，262（4）：781-789.
33	Mori T，Kuroiwa H，Higashiyama T，et al.Identification of higher plant GlsA，a putative morphogenesis factor of gametic cells［J］.Biochemical and Biophysical Research Communications，2003，306（2）：564-569.
34	孟祥鹏.拟南芥抗病基因RIN4和RPM1的克隆及在大豆中的功能验证［D］.长春：吉林农业大学，2018.
34	Meng X P.Cloning of arabidopsis resistance gene RIN4 and RPM1 and functional verification in soybean［D］.Changchun：Jilin Agricultural University，2018.
35	王玉，杨雪，杨蕊菁，等.调控苯丙烷类生物合成的MYB类转录因子研究进展［J］.安徽农业大学学报，2019，46（5）：859-864.
35	Wang Y，Yang X，Yang R J，et al.Advances in research of MYB transcription factors in regulating phenylpropane biosynthesis［J］.Journal of Anhui Agricultural University，2019，46（5）：859-864.
36	Zhao L，Zhang N，Ma P F，et al.Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae［J］.PLoS One，2013，8（5）：e64642.
37	Zhang J，Xie P H，Lascoux M，et al.Rapidly evolving genes and stress adaptation of two desert poplars，Populus euphratica and P.pruinosa［J］.PLoS One，2013，8（6）：e66370.

[1]	Zhanmin ZHENG, Yubing SHANG, Guangbo ZHOU, Di XIAO, Yi LIU, Xiangling YOU. Genetic Transformation and Function Analysis of PsnHB13 and PsnHB15 of Populus simonii × Populus nigra [J]. Bulletin of Botanical Research, 2023, 43(3): 340-350.
[2]	Dongmei HUANG, Ying CHEN, Lu BAI, Di’an NI, Yiyang XU, Zhiguo ZHANG, Qiaoping QIN. Transcriptome Analysis of Hemerocallis fulva Leaves Respond to Low Temperature Stress [J]. Bulletin of Botanical Research, 2022, 42(3): 424-436.
[3]	Jingya Yu, Mingze Xia, Hao Xu, Faqi Zhang. Comparative Transcriptome Analysis of Three Artemisia Species in Qinghai Tibet Plateau [J]. Bulletin of Botanical Research, 2022, 42(2): 200-210.
[4]	Yun TENG, Zong-Bo QIU, Wen-Li WANG, Xue-Ru ZHANG. Transcriptome Analysis in Vascular Cambium and Xylem of Paulownia tomentosa [J]. Bulletin of Botanical Research, 2021, 41(3): 354-361.
[5]	Chen-Chen ZHOU, Yi-Liang LI, Zhe WANG, Fen-Cheng ZHAO, Sui-Ying ZHONG, Chang-Ming LIN, Zhi-Qiang TAN, Fu-Ming LI, Hui-Shan WU, Wen-Bing GUO, Fang-Yan LIAO, Jian-Ge WANG. Screening and Expression Analysis of Different Genes for Oleoresin Production in the Specific Period of Pinus elliottii×P.caribaea by RNA-Seq Technology [J]. Bulletin of Botanical Research, 2021, 41(3): 419-428.
[6]	Lin LU, Shang-Yu YANG, Wei-Dong LIU, Li-Ming LU. To Explore the Transcription Factor in Response to Low Temperature Stress in Nicotiana alata by Transcriptome Sequencing [J]. Bulletin of Botanical Research, 2021, 41(1): 119-129.
[7]	Li-Qiang ZHAO, Chun-Miao SHAN, Sheng-Xiang ZHANG, Yuan-Yuan SHI, Ke-Long MA, Jia-Wen WU. Identification of Key Enzyme Genes Involved in Anthocyanin Synthesis pathway in Clinopodium gracile by Transcriptome Analysis [J]. Bulletin of Botanical Research, 2020, 40(6): 886-896.
[8]	LIU Dan, ZENG Qin-Meng, LIU Bin, LI Yu, CHEN Shi-Pin. Transcriptome Analysis and Gene Functional Annotation in Phoebe bournei [J]. Bulletin of Botanical Research, 2020, 40(4): 613-622.
[9]	ZHANG Yu, XIA Ming-Ze, ZHANG Fa-Qi. Transcriptome Analysis for Medicinal Plant Anisodus tanguticus [J]. Bulletin of Botanical Research, 2020, 40(3): 458-467.
[10]	ZHU Li-Li, DU Qing-Xin, HE Feng, QING Jun, DU Hong-Yan. Sequencing Analysis of Transcriptome of Male Floral Bud at Two Development Stages in Eucommia ulmoides [J]. Bulletin of Botanical Research, 2020, 40(2): 284-292.
[11]	LIU Xiong-Fang, LI Tai-Qiang, ZHANG Xu, LI Zheng-Hong, WAN You-Ming, AN Jing, LIU Xiu-Xian, MA Hong. Characteristic Analysis of Microsatellites in the Transcriptome of Phyllanthus emblica,an Important Edible and Medicinal Plant [J]. Bulletin of Botanical Research, 2019, 39(2): 294-302.
[12]	YE Xing-Zhuang, LIU Dan, LUO Jia-Jia, FAN Hui-Hua, ZHANG Guo-Fang, LIU Bao, CHEN Shi-Pin. Transcriptome Analysis for Rare and Endangered Plants of Semiliquidambar cathayensis [J]. Bulletin of Botanical Research, 2019, 39(2): 276-286.
[13]	WANG Da-Wei, ZHOU Fan, SHEN Bing-Qi, WANG Lian-Chun. Characteristics of Microsatellite in Camellia saluenensis by High-throughput Sequencing [J]. Bulletin of Botanical Research, 2019, 39(1): 148-155.
[14]	LI Yan, GENGJI Zhuo-Ma, JIA Liu-Kun, WANG Zhi-Hua, CHEN Shi-Long, GAO Qing-Bo. Analysis of SSR Information in Transcriptome Sequences of Saxifraga sinomontana [J]. Bulletin of Botanical Research, 2018, 38(6): 939-947.
[15]	WANG Rong, CHENG Meng-Lin, LIU Hui-Na, ZHAO Da-Qiu, TAO Jun. Effects of Melatonin on Flavonoids Content and Related Gene Expression Levels of Gardenia under Dark Conditions [J]. Bulletin of Botanical Research, 2018, 38(4): 559-567.