Plastome phylogenomics of Saussurea (Asteraceae: Cardueae)
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RESEARCH ARTICLE
Open Access
Plastome phylogenomics of Saussurea (Asteraceae: Cardueae) Xu Zhang1,2,3†, Tao Deng3†, Michael J. Moore4, Yunheng Ji3, Nan Lin1,2,3, Huajie Zhang1,2, Aiping Meng1, Hengchang Wang1*, Yanxia Sun1* and Hang Sun3*
Abstract Background: Saussurea DC. is one of the largest and most morphologically heterogeneous genera in Asteraceae. The relationships within Saussurea have been poorly resolved, probably due an early, rapid radiation. To examine plastome evolution and resolve backbone relationships within Saussurea, we sequenced the complete plastomes of 17 species representing all four subgenera. Results: All Saussurea plastomes shared the gene content and structure of most Asteraceae plastomes. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection. Phylogenomic analyses of 20 Saussurea plastomes that alternatively included nucleotide or amino acid sequences of all protein-coding genes, vs. the nucleotide sequence of the entire plastome, supported the monophyly of Saussurea and identified three clades within it. Three of the four traditional subgenera were recovered as paraphyletic. Seven plastome regions were identified as containing the highest nucleotide variability. Conclusions: Our analyses reveal both the structural conservatism and power of the plastome for resolving relationships in congeneric taxa. It is very likely that differences in topology among data sets is due primarily to differences in numbers of parsimony-informative characters. Our study demonstrates that the current taxonomy of Saussurea is likely based at least partly on convergent morphological character states. Greater taxon sampling will be necessary to explore character evolution and biogeography in the genus. Our results here provide helpful insight into which loci will provide the most phylogenetic signal in Saussurea and Cardueae. Keywords: Saussurea, Rapid radiations, Plastome, Genome, Phylogenomic analysis, Purifying selection
Background Saussurea DC. is one of the largest genera in the family Asteraceae [1, 2]. It comprises approximately 300 species that are distributed in Asia, Europe and North America, with the highest diversity in the Himalayas and central Asia [3, 4]. Saussurea exhibits extreme morphological diversity and exists in habitats ranging from steppes to moist forests to cold and dry alpine meadows above 5000 m [3, 5]. * Correspondence: [email protected]; [email protected]; [email protected] † Xu Zhang and Tao Deng contributed equally to this work. 1 CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China 3 Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China Full list of author information is available at the end of the article
Several phylogenetic studies have been conducted on Saussurea but the circumscription and infrageneric
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