透過您的圖書館登入
IP:44.213.80.203
  • 學位論文

解序無根藤、厚殼桂及新樟之葉綠體基因體:探討半寄生植物之葉綠體基因體演化

Complete Plastome Sequences of Cassytha filiformis, Cryptocarya chinensis, and Neocinnamomum delavayi: Insights into the Plastome Evolution in Hemiparasitic Plants

指導教授 : 王亞男
共同指導教授 : 趙淑妙(Shu-Miaw Chaw)

摘要


無根藤 (Cassytha filiformis),又名無根草,其葉部退化,莖部呈黃褐色,彎曲似藤蔓狀。外型與菟絲子屬 (Cuscuta) 酷似,但在分類上,無根藤被歸類為樟科 (Lauraceae) 植物,而菟絲子為旋花科 (Convolvulaceae) 植物。無根藤屬 (Cassytha) 為樟科內的特殊一群,是樟科內唯一的半寄生植物。因為根系已退化,無根藤必須藉由莖部的特化吸器 (Haustorium),從宿主的組織吸取生活所需的營養鹽類和水分。但因無根藤仍可進行光合作用,不同於全寄生植物完全喪失光合作用的能力,無根藤被歸類為半寄生植物。由於無根藤半寄生營養型態,迥異於光自營性的樟科植物,因此比較無根藤與其他樟科物種的葉綠體基因體,將有助於我們了解半寄生植物葉綠體基因體的演化。 本研究解序無根藤、新樟 (Neocinnamomum delavayi)、及厚殼桂(Cryptocarya chinensis) 的完整葉綠體基因體,加上現有的樟屬 (Cinnamomum)、楨楠屬 (Machilus)、及三蕊楠屬 (Endiandra) 之葉綠體基因體,共取樣六屬樟科植物,進行葉綠體基因體的比較分析。親緣演化樹分析支持無根藤為樟科內的一群,且與樟屬+楨楠屬+新樟屬的單系群成為姊妹群。本研究發現樟科植物葉綠體基因體的大重複序列片段 (Large inverted repeats, IRs),至少經歷三次獨立演化,且兩大重複序列片段 (IRA & IRB) 分別丟失部分序列,導致無根藤缺失了一對大重複序列片段。此外,無根藤亦丟失了11個NDH及rpl23基因。上述的大重複序列片段與基因丟失事件造成無根藤葉綠體基因體減縮 (Plastome reduction),因此其基因體長度僅有114,622 bp,遠小於其他樟科物種的151,000–158,507 bp。 同源基因區間 (Intergenic) 和內含子 (Intronic sequence) 的長度分析上,無根藤沒有顯著的減縮,表示無根藤沒有演化朝向葉綠體基因體緊縮 (Plastome compaction) 的趨勢。另外,無根藤基因體含有眾多小重複序列片段 (Repeat),其密度為其他樟科物種的幾十倍。而在核苷酸取代率 (Nucleotide substitution rate) 上,無根藤的同義 (Synonymous) 和非同義 (Non-synonymous) 的核苷酸取代率,皆呈現基因體全面性 (Genome-wide) 提高的現象。 綜合以上發現,包含:基因體減縮、基因丟失、大量的小重複序列片段、和基因體全面性的提高核苷酸取代率,無根藤葉綠體基因體的演化特徵,與已知的半寄生植物之葉綠體基因體演化趨勢,不謀而合。本研究成果,以無根藤為材料,印證半寄生型態與葉綠體基因體的演化息息相關。

並列摘要


Cassytha, commonly known as the laurel dodder, has reduced leaves, swirling stems, and a vine-like appearance with a yellow to orange color. Its appearance is similar to a remote parasitic genus Cuscuta, the dodder. However, Cassytha is included in Lauraceae, in which it is the only parasitic genus. Different from its photoautotrophic relatives in Lauraceae, Cassytha has a dysfunctional root system. Therefore, Cassytha has to utilize specialized organs, called haustoria, to capture water and nutrients from a diverse range of hosts. Cassytha is categorized as an obligate hemiparasitic plant because it possesses several characteristics of parasitism without completely loss of its photosynthetic ability. As the only hemiparasitic genus within Lauraceae, Cassytha is ideal for evaluating the evolution of plastid genomes (plastomes) in hemiparasitic plants. This study, I determined three complete plastome sequences: Cassytha filiformis and its two photoautotrophic relatives, Cryptocarya chinensis and Neocinnamomum delavayi. Other available plastomes of Lauraceae species (i.e., Cinnamomum, Endiandra and Machilus spp.) were also included for comparative analyses. Further, plastid phylogenomic analyses suggest that Cassytha is sister to the clades comprising Neocinnamomum and Cinnamomeae. Based on the comparison of plastome structures, this study proposes that the large inverted repeats (IRs) have independently evolved at least three times during the evolution of Lauraceae. In Cas. filiformis, losses of IRs, 11 NDH, and rpl23 genes account for the plastome reduction, resulting in a relatively small size (114,622 bp) compared to that of other Lauraceae species (151,000‒158,507 bp). However, the intergenic and intronic regions of Cas. filiformis do not shrink significantly, indicating that its plastome likely has not evolved towards compaction. In addition, the plastome of Cas. filiformis contains abundant repeats, with its density of repeats exceeding that of its photoautotrophic relatives by an order of magnitude. Moreover, Cas. filiformis has an accelerated synonymous and nonsynonymous substitution rates, irrespective of the different functions genes. This suggests that a plastome-wide elevation of substitution rates has taken place in Cas. filiformis. Collectively, the findings demonstrating that the plastome of Cas. filiformis has reduced size, abundant repeats, and accelerated substitution rates are in all agreement with the general features observed in other hemiparasitic plastomes. This reflects that the ineffective capability of conducting photosynthesis does have profound impact on the plastome evolution in hemiparasitic plants.

參考文獻


Abubacker, M. N., Prince, M., & Hariharan, Y. (2005). Histochemical and biochemical studies of parasite-host interaction of Cassytha filiformis Linn. and Zizyphus jujuba Lamk. Current science, 89:2156–2159.
Barkman, T., McNeal, J., Lim, S. H., Coat, G., Croom, H., Young, N., & dePamphilis, C. (2007). Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants. BMC Evolutionary Biology, 7:248.
Barrett, C. F., & Davis, J. I. (2012). The plastid genome of the mycoheterotrophic Corallorhiza striata (Orchidaceae) is in the relatively early stages of degradation. American Journal of Botany, 99:1513–1523.
Barrett, C. F., Freudenstein, J. V., Li, J., Mayfield-Jones, D. R., Perez, L., Pires, J. C., & Santos, C. (2014). Investigating the path of plastid genome degradation in an early-transitional clade of heterotrophic orchids, and implications for heterotrophic angiosperms. Molecular Biology and Evolution, 252.
Bergsten, J. (2005). A review of long‐branch attraction. Cladistics, 21:163–193.

延伸閱讀