J Syst Evol ›› 2015, Vol. 53 ›› Issue (5): 432-447.doi: 10.1111/jse.12176

• Research Articles • Previous Articles     Next Articles

Phylogenomics of polyploid Fothergilla (Hamamelidaceae) by RAD-tag based GBS—insights into species origin and effects of software pipelines

Zhe-Chen Qi1,4, Yi Yu1†, Xiang Liu1, Andrew Pais1, Thomas Ranney2*, Ross Whetten3*, and Qiu-Yun (Jenny) Xiang1*   

  1. 1Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
    2Department of Horticulture Sciences, North Carolina State University, Mills River, NC, USA
    3Department of Forestry & Environmental Resources, North Carolina State University, Raleigh, NC, USA
    4College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China Present Address: Guangzhou Baiyunshan Zhongyi Pharmaceutical Company Limited, Guangzhou 510530, China
  • Received:2015-08-07 Online:2015-08-24 Published:2015-09-22

Abstract: Fothergilla (Hamamelidaceae) consists of Fothergilla gardenii (4x) from the coastal plains of the southeastern USA, F. major (6x) from the piedmont and mountains of the same region, and a few allopatric diploid populations of unknown taxonomic status. The objective of this study was to explore the relationships of the polyploid species with the diploid plants. Genotyping by sequencing (GBS) was applied to generate genome-wide molecular markers for phylogenetic and genetic structure analyses of 36 accessions of Fothergilla. Sanger sequencing of three plastid and one nuclear regions provided data for comparison with GBS-based results. Phylogenetic outcomes were compared using data from different sequencing runs and different software workflows. The different data sets showed substantial differences in inferred phylogenies, but all supported a genetically distinct 6x F. major and two lineages of the diploid populations closely associated with the 4x F. gardenii. We hypothesize that the 4x F. gardenii originated through hybridization between the Gulf coastal 2x and an extinct (or undiscovered) 2x lineage, followed by backcrosses to the Atlantic coastal 2x before chromosome doubling, and the 6x F. major also originated from the “extinct” 2x lineage. Alternative scenarios are possible but are not as well supported. The origins and divergence of the polyploid species likely occurred during the Pleistocene cycles of glaciation, although fossil evidence indicates the genus might have existed for a much longer time with a wider past distribution. Our study demonstrates the power of combining GBS data with Sanger sequencing in reconstructing the evolutionary network of polyploid lineages.

Key words: Fothergilla, hybridization, illumina sequencing, phylogenomics, RAD-tag-based GBS, polyploidy

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[1] Yan Xiao-hua Cai Zhu-ping. Effects of S-07, PP333 and Triadimefon on Peroxidaseisoentyme of Rice Seedling[J]. Chin Bull Bot, 1995, 12(专辑3): 109 -112 .
[2] . [J]. Chin Bull Bot, 1994, 11(专辑): 13 .
[3] Xiaomin Yu;Xingguo Lan;Yuhua Li. The Ub/26S Proteasome Pathway and Self-incompatible Responses in Flowering Plants[J]. Chin Bull Bot, 2006, 23(2): 197 -206 .
[4] WANG Ling-Li LIU Wen-Zhe. Contents of Camptothecin in Camptotheca acuminata from Different Provenances[J]. Chin Bull Bot, 2005, 22(05): 584 -589 .
[5] Dai Yun-ling and Xu Chun-hui. Advances in Research on Protein Components of Oxygen-evolving Complex[J]. Chin Bull Bot, 1992, 9(03): 1 -16 .
[6] . Advances in Research on Photosynthesis of Submerged Macrophytes[J]. Chin Bull Bot, 2005, 22(增刊): 128 -138 .
[7] Shaobin Zhang;Guoqin Liu. Research Advances in Plant Actin Isoforms[J]. Chin Bull Bot, 2006, 23(3): 242 -248 .
[9] MA Li-Hui, WU Pu-Te, and WANG You-Ke. Spatial pattern of root systems of dense jujube plantation with jujube age in the semiarid loess hilly region of China[J]. Chin J Plan Ecolo, 2012, 36(4): 292 -301 .
[10] PAN Yu-De, Melillo J. M., Kicklighter D. W., XIAO Xiang-Ming, McGuire A. D.. Modeling Structural and Functional Responses of Terrestria Ecosystems in China to Changes in Climate and Atmospheric CO2[J]. Chin J Plan Ecolo, 2001, 25(2): 175 -189 .