基于祖先性状演化和叶绿体基因组的马先蒿形态特征分析

doi:10.11733/j.issn.1007-0435.2024.07.005

草地学报 ›› 2024, Vol. 32 ›› Issue (7): 2039-2053.DOI: 10.11733/j.issn.1007-0435.2024.07.005

基于祖先性状演化和叶绿体基因组的马先蒿形态特征分析

王涛, 徐成体, 唐楚煜, 曹正飞, 肖梦君, 何敏, 李秀璋, 李玉玲

青海大学畜牧兽医科学院, 三江源区高寒草地生态教育部重点实验室, 青海西宁 810016

收稿日期:2023-12-12 修回日期:2024-03-01 出版日期:2024-07-15 发布日期:2024-08-03
通讯作者: 李玉玲，E-mail:yulingli2000@163.com
作者简介:王涛(1995-)，男，汉族，安徽淮北人，博士研究生，主要从事草学研究，E-mail：13085500761@163.com
基金资助:
国家自然科学基金(32360349)资助

Morphological Analysis of Pedicularis Based on Ancestral Character Evolution and Chloroplast Genome

WANG Tao, XU Cheng-ti, TANG Chu-yu, CAO Zheng-fei, XIAO Meng-jun, HE Min, LI Xiu-zhang, LI Yu-ling

Key Laboratory of the Alpine Grassland Ecology in the Three Rivers Region, Ministry of Education, Qinghai University, Xining, Qinghai Province 810016, China

Received:2023-12-12 Revised:2024-03-01 Online:2024-07-15 Published:2024-08-03

摘要/Abstract

摘要： 为了探究马先蒿属(Pedicularis)植物的关键形态特征，为其辨别与鉴定提供参考。本研究采用祖先性状演化推测Pedicularis最保守的形态特征，并基于10种马先蒿属植物完整叶绿体基因组，探讨马先蒿属植物形态的变异原因。结果表明基于花序类型性状演化分析和系统发育分析支持马先蒿属隶属于列当科(Orobanchaceae)的分类地位。叶绿体基因组变异分析找到Pi值较高的7个变异基因和6个变异区域，且多分布在大单拷贝区(LSC)和小单拷贝区(SSC)区。反向重复区(IRs)的rps19和ycf1基因跨越了区域边界造成IRs基因丢失。因此，总状花序是马先蒿属最为保守的形态特征，可作为其分类依据。而IRs的扩张导致IRs基因丢失的同时提高LSC和SSC的多样性，导致二者为高变异区，可能是马先蒿属植物形态变异的原因之一。这些结果将促进马先蒿属植物系统分类和种间进化的研究。

关键词: 马先蒿属, 叶绿体基因组, 系统发育, 祖先形态

Abstract: To explore the key morphological characteristics of Pedicularis plants and to provide reference for their identification,the most conserved morphological characteristics of Pedicularis were speculated by the evolution of ancestral traits,and the reasons for the morphological variation of Pedicularis were discussed based on the complete chloroplast genomes of 10 species of Pedicularis in this study. The results showed that the evolution analysis and phylogenetic analysis based on inflorescence type traits supported the taxonomic status of Pedicularis belonging to Orobanchaceae. The chloroplast genome variation analysis found 7 variable genes and 6 variable regions with high Pi values,and most of them were distributed in the LSC and SSC. The rps19 and ycf1 genes in the IRs crossed the region boundary and caused the loss of IRs genes. Therefore,raceme is the most conserved morphological feature of Pedicularis,which can be used as the basis for its classification. The expansion of IRs leads to the loss of IRs genes and the diversity of LSC and SSC,which leads to the high variation area of LSC and SSC,which may be one of the reasons for the morphological variation of Pedicularis. These results will promote the study of systematic classification and interspecific evolution of Pedicularis.

Key words: Pedicularis, Chloroplast genome, Phylogeny, Ancestral morphology

中图分类号:

Q732

王涛, 徐成体, 唐楚煜, 曹正飞, 肖梦君, 何敏, 李秀璋, 李玉玲. 基于祖先性状演化和叶绿体基因组的马先蒿形态特征分析[J]. 草地学报, 2024, 32(7): 2039-2053.

WANG Tao, XU Cheng-ti, TANG Chu-yu, CAO Zheng-fei, XIAO Meng-jun, HE Min, LI Xiu-zhang, LI Yu-ling. Morphological Analysis of Pedicularis Based on Ancestral Character Evolution and Chloroplast Genome[J]. Acta Agrestia Sinica, 2024, 32(7): 2039-2053.

参考文献

[1] LIU M L，YUM W B，WANG H. Rapid identification of plant species and iflora：application of DNA barcoding in a large temperate genus Pedicularis(Orobanchaceae)[J]. Plant Diversity and Resources，2013(35)：707-714
[2] YATOO M I，DIMRI U，GOPALAKRISHAN A，et al. Antidiabetic and oxidative stress ameliorative potential of ethanolic extract of Pedicularis longiflora Rudolph[J]. International Journal of Pharmacology，2016(12)：177-187
[3] PETRU M. Year-to-year oscillations in demography of the strictly biennial Pedicularis sylvatica and effects of experimental disturbances[J]. Plant Ecology and Diversity，2005(181)：289-298
[4] JIN W T，SCHUITEMAN A，CHASE M W，et al. Phylogenetics of subtribe Orchidinae S.L.(Orchidaceae;Orchidoideae)based on seven markers(plastid matK，psaB，rbcL，trnL-F，trnH-psba，and nuclear nrITS，Xdh)：implications for generic delimitation[J]. BMC Plant Biology，2017(17)：e222
[5] 郝新艳，赵淑文，刘嘉伟，等. 杂花苜蓿叶绿体基因组特征及系统发育分析[J]. 草地学报，2023，31(6)：1665-1672
[6] YANG F S，WANG X Q. Extensive length variation in the cpDNA trnT-trnF region of hemiparasitic Pedicularis and its phylogenetic implications[J]. Plant Systematics and Evolution，2007(264)：251-264
[7] YU W B，LIU M L，WANG H，et al. Towards a comprehensive phylogeny of the large temperate genus Pedicularis(Orobanchaceae)，with an emphasis on species from the Himalaya-Hengduan Mountains[J]. BMC Plant Biology，2015，(15)：176-199
[8] 卢政阳，于凤扬，肖月娥，等. 北陵鸢尾叶绿体基因组及其特征分析[J]. 草地学报，2023，31(6)：1656-1664
[9] ZHU A，GUO W，GUPTA S，et al. Evolutionary dynamics of the plastid inverted repeat：the effects of expan-sion，contraction，and loss on substitution rates[J]. New Phytologist，2016(209)：1747-1756
[10] MOWER J P，VICKREY T L. Structural diversity among plastid genomes of land plants. In Advances in Botanical Research[M]. London：Longman Group Ltd，2018:263-292
[11] ZHANG R，XU B，LI J，et al. Transit from autotrophism to heterotrophism:sequence variation and evolution of chloroplast genomes in Orobanchaceae species[J]. Front in Genetics，2020(11)：e542017
[12] WICKE S，NAUMANN J. Molecular evolution of plastid genomes in parasitic flowering plants[J]. Genome Biology and Evolution，2018(85)：315-347
[13] SHIN H W，LEE N S. Understanding plastome evolution in hemiparasitic Santalales:complete chloroplast genomes of three species，Dendrotrophe varians，Helixanthera parasitica，and Macrosolen cochinchinensis[J]. Plos One，2018(13)：e0200293
[14] LI M X，HE X R，TAO R，et al. Phytochemistry and pharmacology of the genus Pedicularis used in traditional chinese medicine[J]. American Journal of Chinese Medicine，2014(42)：1071-1098
[15] 马妍. 两种同域马先蒿近缘种的花冠表型对比及选择作用研究[D]. 兰州：西北师范大学，2019：44-47
[16] UCUNCU O，BALTACI C，ILTER S M. Chemical composition，antimicrobial and antioxidant aactivities of essential oil from Pedicularis condensata BIEB[J]. Journal of Information Science and Engineering，2016(3)：105-109
[17] LI X，FENG T，RANDLE C，et al. Phylogenetic relationships in Orobanchaceae inferred from low-copy nuclear genes:consolidation of major clades and identification of a novel position of the non-photosynthetic Orobanche clade sister to all other parasitic Orobanchaceae[J]. Frontiers in Plant Science，2019(902)：1-14
[18] 刘蕊. 榆属系统发育基因组学及形态演化研究[D]. 郑州：河南农业大学，2023：53-55
[19] 黄祥，何梦瑶，王子煊，等. 紫叶风箱果叶绿体基因组特征及绣线菊亚科系统发育分析[J]. 草业学报，2024，33(3)：161-173
[20] KATOH K，STANDLEY D M. MAFFT multiple sequence alignment software version 7:improvements in performance and usability[J]. Molecular Biology and Evolution，2013，30(4)：772-780
[21] FRAZER K A，PACHTER L，POLIAKOV A，et al. VISTA:computational tools for comparative genomics[J]. Nucleic Acids Research，2004，32(2)：273-279
[22] DARLING A C，MAU B，BLATTNER F R，et al. Mauve:multiple alignment of conserved genomic sequence with rearrangements[J]. Genome Research，2004，14(7)：1394-1403
[23] MANUEL M. Computational Tools for Genomic Studies in Plants[J]. Current Genomics，2016，11(6)：509-514
[24] LOBRY J R. Asymmetric substitution patterns in the two DNA strands of bacteria[J]. Molecular Biology and Evolution，1996(13)：660-665
[25] WASSIM A，THEIN M，LARUE R W，et al. Diagnosis of histoplasmosis using the mvista histoplasma galactomannan antigen qualitative lateral flow-based immunoassay;a multicenter study[J]. Open Forum Infectious Diseases，2021(8)：e454
[26] AMIRYOUSEFI A，HYVONEN P P. IRscope:an online program to visualize the junction sites of chloroplast genomes[J]. Bioinformatics，2018(34)：3033-3031
[27] YU W B，HUANG P H，REE R H，et al. DNA barcoding of Pedicularis L.(Orobanchaceae):Evaluating four universal barcode loci in a large and hemiparasitic genus[J]. Journal of Systematics and Evolution，2011(49)：425-437
[28] RICHARD H R. Phylogeny and the evolution of floral diversity in Pedicularis(Orobanchaceae)[J]. International Journal of Plant Sciences，2005(166)：595-613 29］MA X F，SZMIDT A E，WANG X R. Genetic structure and evolutionary history of a diploid hybrid pine Pinus densata inferred from the nucleotide variation at seven gene loci[J]. Molecular Biology and Evolution，2006，(28)：807-816
[30] LI X，FENG T，RANDLE C，et al. Phylogenetic relationships in Orobanchaceae inferred from low-copy nuclear genes: consolidation of major clades and identification of a novel position of the non-photosynthetic Orobanche clade sister to all other parasitic Orobanchaceae[J]. Frontiers in Plant Science，2019(902)：1-14
[31] L I X，YANG J B，WANG H，et al. Plastid NDH pseudogenization and gene loss in a recently derived lineage from the largest hemiparasitic plant genus Pedicularis (Orobanchaceae)[J]. Plant and Cell Physiology，2021(62)：971-984
[32] WANG P，HUANG Q. Interspecific and intraspecific variation in corolla tube length in Pedicularis species achieved by both cell anisotropy and division[J]. Journal of Systematics and Evolution，2017(55)：208-214
[33] YU W B，WANG H，LIU M L,et al. Phylogenetic approaches resolve taxonomical confusion in Pedicularis (Orobanchaceae): reinstatement of Pedicularis delavayi and discovering a new species Pedicularis milliana[J]. Plos One，2018(13):e0200372
[34] SAIKIA M，WANG X，MAO Y，et al. Codon optimality controls differential mRNA translation during amino acid starvation[J]. RNA，2016(11)：1719-1727
[35] PAUL P，MALAKAR A K，CHAKRABORTY S. Compositional bias coupled with selection and mutation pressure drives codon usage in Brassica campestris genes[J]. Food Science and Biotechnology，2018(27)：725-733
[36] JIA D. Survey and analysis of simple sequence repeats(SSRs)in three genomes of Candida species[J]. Gene，2016(584)：129-135
[37] QI W，LIN F，LIU Y，et al. High-throughput development of simple sequence repeat markers for genetic diversity research in Crambe abyssinica[J]. BMC Plant Biology，2016(16)：139-150
[38] PENNISI E. DNA barcodes jump-start search for new species[J]. Science，2019(364)：920-921
[39] ZHANG R，WANG J，HAN K，et al. Complete chloroplast genome sequence of Pedicularis cheilanthifolia，an alpine plant in China[J]. Conservation Genetics Resources，2017(9)：619-621
[40] CHASE M W，CHRISTENHUSZ M J，FAY M F，et al. An update of the angiosperm phylogeny group classification for the orders and families of flowering plants:APG IV[J]. Botanical Journal of the Linnean Society，2016(181)：1-20
[41] ZENG S，ZHOU T，HAN K，et al. The complete chloroplast genome sequences of six Rehmannia species[J]. Genes, 2017(8):103-118
[42] TKACH N，REE R H，KUSS P，et al. High mountain origin，phylogenetics，evolution，and niche conservatism of arctic lineages in the hemiparasitic genus Pedicularis(Orobanchaceae)[J]. Molecular Phylogenetics and Evolution，2014(76)：75-92
[43] XU X D，GUAN J Y，ZHANG Z Y，et al. Novel tRNA gene rearrangements in the mitochondrial genomes of praying mantises (Mantodea:Mantidae):translocation，duplication and pseudogenization[J]. International Journal of Biological Macromolecules，2021(185)：403-411
[44] ZHOU L，CHEN T，QIU X，et al. Evolutionary differences in gene loss and pseudogenization among mycoheterotrophic orchids in the tribe Vanilleae(subfamily Vanilloideae)[J]. Frontiers in Plant Science，2023(14)：1160446-1160460
[45] SCOBEYEVA V A，ARTYUSHIN I V，KRINITSINA A A，et al. Gene loss，pseudogenization in plastomes of genus Allium (Amaryllidaceae)，and putative selection for adaptation to environmental conditions[J]. Frontiers in Genetics，2021(12)：674783-674799
[46] TOMOTAKA M，ANOOP J，PABLO B C，et al. Pseudogenization of the chloroplast threonine(TRNT-GGU) gene in the sunflower family(Asteraceae)[J]. Scientific Reports，2021(11)：21122-21140
[47] LI X，YANG J B，WANG H，et al. Plastid NDH pseudogenization and gene loss in a recently derived lineage from the largest hemiparasitic plant genus Pedicularis(Orobanchaceae)[J]. Plant and Cell Physiology，2021(62)：971-984
[48] SWETA T，MIGUEL A N，ENRIQUE M. A methodology to study pseudogenized lincRNAs[J]. Methods in Molecular Biology，2021，23(24)：49-63
[49] CAMPBEL W H，GOWRI G. Codon usage in higher plants，green algae，and cyanobacteria[J]. Plant Physiology，1990(92)：1-11
[50] SHEN J，LI X，LI M，et al. Characterization，comparative phylogenetic，and gene transfer analyses of organelle genomes of Rhododendron×pulchrum[J]. Frontiers in Plant Science，2022(13)：e969765
[51] ZHANG X，DENG T，MOORE M J，et al. Plastome phylogenomics of Saussurea(Asteraceae:Cardueae)[J]. BMC Plant Biology，2019，1(19)：e290

基于祖先性状演化和叶绿体基因组的马先蒿形态特征分析

Morphological Analysis of Pedicularis Based on Ancestral Character Evolution and Chloroplast Genome

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