虎耳草目木本分支叶绿体系统发育基因组学研究

	虎耳草目木本分支叶绿体系统发育基因组学研究
	王淑颖
导师	纪运恒
关键词	蕈树科 Altingiaceae, Hamamelidaceae, Cercidiphyllaceae, Daphniphyllaceae, Phylogenomics 金缕梅科连香树科虎皮楠科系统发育
摘要	摘要虎耳草目（Saxifragales）早期分化经历了快速辐射，系统发育关系长期难以解决。其中，最具争议的是木本分支（woody clade）的系统发育关系，即蕈树科（Altingiaceae）、连香树科（Cercidiphyllaceae）、虎皮楠科（Daphniphyllaceae）和金缕梅科（Hamamelidaceae）的系统发育关系。为了进一步解析木本分支的系统发育关系，本研究：（1）分析了木本分支56个物种的叶绿体基因组，涵盖金缕梅科15属41种、蕈树科单属8种、虎皮楠科单属5种、连香树科单属2种；（2）以芍药科8个物种为外类群，基于木本分支和芍药科78个共有叶绿体蛋白编码基因，用最大似然法和贝叶斯法进行系统发育分析；（3）基于最大似然树的拓扑结构估算了木本分支的分化时间；（4）结合形态学和核转录组系统发育研究讨论了木本分支的系统发育关系。主要研究结果如下： 1.比较基因组分析本研究中虎耳草目木本分支的叶绿体基因组均为一个大单拷贝区（LSC）、一个小单拷贝区（SSC）和两个反向重复区（IR）组成的闭合环状四分体，结构高度保守。叶绿体基因组长度为158,149 bp–160,861 bp，GC含量为37.7% – 38.2%。每个叶绿体基因组包含单拷贝基因115个，其中，蛋白编码基因81个，tRNA30个，rRNA 4个，无基因缺失和明显的结构重排。在所有物种的叶绿体蛋白编码基因中，仅发现山铜材（Chunia bucklandiodes）的ycf15基因为假基因。四个科叶绿体基因组的交界区相似，反向重复区没有出现明显的扩张或收缩。非编码区的序列差异是木本分支叶绿体基因组大小存在差异的主要原因。 2.系统发育分析基于木本分支56个物种、芍药科8个物种（外类群）的78个共有叶绿体蛋白编码基因进行系统发育分析，最大似然树和贝叶斯树的拓扑结构基本一致。木本分支4个科互为单系，科间的系统发育关系为（蕈树科，（金缕梅科，（连香树科，虎皮楠科））），获得了较高的支持（PP≥1.00，BS≥80%），但该关系与核转录组的系统发育关系不一致。本研究认为古杂交可能导致了木本分支的核质冲突，但该推论需要验证。金缕梅科的4个亚科互为单系，亚科间的系统发育关系为（马蹄荷亚科Exbucklandioideae，（壳菜果亚科Mytilarioideae，（双花木亚科Disanthoideae，金缕梅亚科Hamamelidoideae）））。金缕梅亚科中，本研究采样的5个族互为单系，（檵木族Loropetaleae，蜡瓣花族Corylopsideae）和（秀柱花族Eustigmateae，（金缕梅族Hamamelideae，银刷树族Fothergilleae））是姐妹群。然而，基于核转录组的系统发育研究显示银刷树族为并系群。本研究对银刷树族取样不全，无法推论两个族真实的系统发育关系，后续研究应对金缕梅亚科全面取样，以探讨该亚科的族间关系。银刷树族中，蚊母树属（Distylium）、假蚊母属（Distyliopsis）、银缕梅属（Shaniodendron）和水丝梨属（Sycopsis）并不互为单系，结合形态和细胞学证据，本研究认为四个属的分类界定不合理，不完全谱系分选和杂交是否对其产生影响则需进一步的分析。 3.分化时间估算基于最大似然树的拓扑结构，以连香树科（55.8 Ma，干群）、蕈树科（89.3 Ma，干群）和金缕梅亚科（83.5 Ma，冠群）的化石年龄分别标定时间节点，估算分化时间。结果显示，木本分支的冠群在晚白垩世（Upper Cretaceous）早期（92.76–89.13 Ma）分化；金缕梅科、蕈树科、虎皮楠科和连香树科的冠群分别在晚白垩世中期（88.46–84.07 Ma）、始新世（Eocene）–中新世（Miocene）（50.81–9.53 Ma）、渐新世（Oligocene）–中新世中期（30.65–8.08 Ma）和中新世末期–更新世（Pleistocene）（6.82–0.09 Ma）分化。木本分支各属的冠群均在中新世（23.03–5.3 Ma）强烈分化。化石和分子证据表明木本分支四个科的谱系古老而现存物种年轻，本研究认为该现象与木本分支频繁的物种灭绝有关。蜡瓣花属的进化历史表明木本分支的物种分化和灭绝可能与全球气候变化有关。; Abstract Saxifragales is a clade whose deep-level relationships have been difficult to resolve due to a rapid, ancient radiation. Which most controversial inside Saxifragales is the relationships of woody clade, that is, the phylogenetic relationships of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae. To further resolve the phylogenetic relationships of woody clade, (1) complete plastomes of 56 species were analyzed, including 41 species of 15 genera of Hamamelidaceae, 8 species of single genus of Altingiaceae, 5 species of single genus of Daphniphyllaceae, and 2 species of single genus of Cercidiphyllaceae; (2) phylogenetic trees based on maximum likelihood and Bayesian analysis were reconstructed using a matrix of 78 common chloroplast protein coding genes of 56 species of woody clade and 8 species of Paeoniaceae as outgroup; (3) divergence time was estimated based on topology of maximum likelihood tree; (4) phylogenetic relationships of woody clade were dicussed in conjunction with morphology and phylogeny of nuclear transcriptome. Primary results are as follow: 1.Comparative analysis of plastomes The plastomes of woody clade analyzed in this study all consist of a large single copy region (LSC), a small single copy region (SSC), and two reverse repeat regions (IR), which are highly conservative. The size and GC content of plastomes vary from 158,149 bp to 160,861 bp and 37.7% to 38.2% respectively. Each plastome contains 115 single copy genes, including 81 protein coding genes, 30 transport RNAs and 4 ribosomal RNAs, without gene deletion and rearrangement. Only ycf15 gene of Chunia bucklandiodes was found as a pseudogene. The boundaries of plastomes are similar, there is no obvious contraction or expansion in reverse repeat regions. The main reason for the variety of plastome size of woody clade is the variety of non-coding regions. 2.Phylogenetic analysis The topology of maximum likelihood tree and Bayesian tree based on 78 common chloroplast protein coding genes of 56 species of woody clade and 8 species of Paeoniaceae as outgroup is congruent. Altingiaceae, Hamamelidaceae, Cercidiphyllaceae, and Daphniphyllaceae are monophyletic entities. The phylogenetic relationships of woody clade are as follow: (Altingiaceae, (Hamamelidaceae, (Cercidiphyllaceae, Daphniphyllaceae))), which is well supported by Bayesian analysis (PP≥1.00) and maximum likelihood analysis (BS≥80%). However, the phylogenetic relationships are incongruent with phylogenetic relationships based on nuclear transcriptomes. Hybridization played essential role in cytonuclear discordance of woody clade, but the inference needs to be verified. All subfamilies of Hamamelidaceae are monophyletic entities. The phylogenetic relationships of subfamilies are as follow: (Exbucklandioideae, (Mytilarioideae, (Disanthoideae, Hamamelidoideae))). Inside Hamamelidoideae, each tribe sampled in this study is monophyletic. (Loropetaleae, Corylopsideae) is sister to (Eus
语种	中文
	2022-06
学位授予单位	中国科学院大学
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75101
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	王淑颖. 虎耳草目木本分支叶绿体系统发育基因组学研究[D]. 中国科学院大学,2022.

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