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Su N, Hodel RG, Wang X, Wang JR, Xie SY, Gui CX, Zhang L, Chang ZY, Zhao L, Potter D, Wen J. Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses. PLANT DIVERSITY 2023; 45:397-408. [PMID: 37601549 PMCID: PMC10435964 DOI: 10.1016/j.pld.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 08/22/2023]
Abstract
Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome data recovered a well-resolved phylogeny. The species were divided into three main clades corresponding to their inflorescence types, - the racemose group, the solitary-flower group and the corymbose group - with the latter two sister to one another. Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago. The diversification of the three major clades began between the Paleocene and Miocene, suggesting that paleoclimatic events were an important driving force for Prunus diversification. Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences, and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis, respectively. We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies. Prunus has undergone extensive hybridization events, although it is difficult to identify conclusively specific instances of hybridization when using SNP data, especially deep in the phylogeny. Our study provides well-resolved nuclear and plastid phylogenies of Prunus, reveals substantial cytonuclear discord at shallow scales, and sheds new light on inflorescence evolution in this economically important lineage.
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Affiliation(s)
- Na Su
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Richard G.J. Hodel
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Xi Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Jun-Ru Wang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Si-Yu Xie
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Chao-Xia Gui
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Ling Zhang
- College of Life Sciences, Tarim University, Alaer 843300, China
| | - Zhao-Yang Chang
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
- Herbarium of Northwest A&F University, Yangling 712100, China
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California, Davis, CA 95616, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
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Wu JQ, Wang Y, Sun P, Sun ZS, Shen JS. The complete chloroplast genome of Prunus phaeosticta (Hance) Maxim. (Rosaceae) and its phylogenetic implications. Mitochondrial DNA B Resour 2023; 8:136-140. [PMID: 36685644 PMCID: PMC9848267 DOI: 10.1080/23802359.2022.2163841] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The complete chloroplast (cp) genome of Prunus phaeosticta (Hance) Maxim. has been characterized by reference-based assembly using Illumina paired-end data. The circular complete cp genome is 158,752 bp in length, comprising a large single-copy (LSC) region of 87,085 bp, a small single-copy (SSC) region of 18,923 bp, and a pair of inverted repeats (IRs) of 26,372 bp.A total of 129 functional genes were identified, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. The phylogenetic analysis showed that P. phaeosticta displayed a kinship to Prunus zippeliana.
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Affiliation(s)
- Jia-Qi Wu
- Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Yi Wang
- Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Ping Sun
- Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China
| | - Zhong-Shuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Jian-Sheng Shen
- Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China,CONTACT Jian-Sheng Shen Flower, Forestry and Fruit Institute, Jinhua Academy of Agricultural Sciences, Jinhua, China
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3
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Zhang J, Wang Y, Chen T, Chen Q, Wang L, Liu ZS, Wang H, Xie R, He W, Li M, Liu CL, Yang SF, Li MY, Lin YX, Zhang YT, Zhang Y, Luo Y, Tang HR, Gao LZ, Wang XR. Evolution of Rosaceae Plastomes Highlights Unique Cerasus Diversification and Independent Origins of Fruiting Cherry. FRONTIERS IN PLANT SCIENCE 2021; 12:736053. [PMID: 34868119 PMCID: PMC8639594 DOI: 10.3389/fpls.2021.736053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Rosaceae comprises numerous types of economically important fruits, ornamentals, and timber. The lack of plastome characteristics has blocked our understanding of the evolution of plastome and plastid genes of Rosaceae crops. Using comparative genomics and phylogenomics, we analyzed 121 Rosaceae plastomes of 54 taxa from 13 genera, predominantly including Cerasus (true cherry) and its relatives. To our knowledge, we generated the first comprehensive map of genomic variation across Rosaceae plastomes. Contraction/expansion of inverted repeat regions and sequence losses of the two single-copy regions underlie large genomic variations in size among Rosaceae plastomes. Plastid protein-coding genes were characterized with a high proportion (over 50%) of synonymous variants and insertion-deletions with multiple triplets. Five photosynthesis-related genes were specially selected in perennial woody trees. Comparative genomic analyses implied divergent evolutionary patterns between pomaceous and drupaceous trees. Across all examined plastomes, unique and divergent evolution was detected in Cerasus plastomes. Phylogenomic analyses and molecular dating highlighted the relatively distant phylogenetic relationship between Cerasus and relatives (Microcerasus, Amygdalus, Prunus, and Armeniaca), which strongly supported treating the monophyletic true cherry group as a separate genus excluding dwarf cherry. High genetic differentiation and distinct phylogenetic relationships implied independent origins and domestication between fruiting cherries, particularly between Prunus pseudocerasus (Cerasus pseudocerasus) and P. avium (C. avium). Well-resolved maternal phylogeny suggested that cultivated P. pseudocerasus originated from Longmenshan Fault zone, the eastern edge of Himalaya-Hengduan Mountains, where it was subjected to frequent genomic introgression between its presumed wild ancestors and relatives.
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Affiliation(s)
- Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Tao Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Lei Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Zhen-shan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Rui Xie
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Ming Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Cong-li Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Shao-feng Yang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Meng-yao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Yuan-xiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yun-ting Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
| | - Hao-ru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
| | - Li-zhi Gao
- Institute of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-rong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, China
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, China
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Li C, Cai C, Tao Y, Sun Z, Jiang M, Chen L, Li J. Variation and Evolution of the Whole Chloroplast Genomes of Fragaria spp. (Rosaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:754209. [PMID: 34721483 PMCID: PMC8551639 DOI: 10.3389/fpls.2021.754209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/21/2021] [Indexed: 06/02/2023]
Abstract
Species identification is vital for protecting species diversity and selecting high-quality germplasm resources. Wild Fragaria spp. comprise rich and excellent germplasm resources; however, the variation and evolution of the whole chloroplast (cp) genomes in the genus Fragaria have been ignored. In the present study, 27 complete chloroplast genomes of 11 wild Fragaria species were sequenced using the Illumina platform. Then, the variation among complete cp genomes of Fragaria was analyzed, and phylogenetic relationships were reconstructed from those genome sequences. There was an overall high similarity of sequences, with some divergence. According to analysis with mVISTA, non-coding regions were more variable than coding regions. Inverted repeats (IRs) were observed to contract or expand to different degrees, which resulted in different sizes of cp genomes. Additionally, five variable loci, trnS-trnG, trnR-atpA, trnC-petN, rbcL-accD, and psbE-petL, were identified that could be used to develop DNA barcoding for identification of Fragaria species. Phylogenetic analyses based on the whole cp genomes supported clustering all species into two groups (A and B). Group A species were mainly distributed in western China, while group B contained several species from Europe and Americas. These results support allopolyploid origins of the octoploid species F. chiloensis and F. virginiana and the tetraploid species F. moupinensis and F. tibetica. The complete cp genomes of these Fragaria spp. provide valuable information for selecting high-quality Fragaria germplasm resources in the future.
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Affiliation(s)
- Chenxin Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Chaonan Cai
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Yutian Tao
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Zhongshuai Sun
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Ming Jiang
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
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Du Z, Lu K, Zhang K, He Y, Wang H, Chai G, Shi J, Duan Y. The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time. BMC Genomics 2021; 22:645. [PMID: 34493218 PMCID: PMC8425060 DOI: 10.1186/s12864-021-07968-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/25/2021] [Indexed: 11/21/2022] Open
Abstract
Background Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg. Amygdalus. Results The results showed that subg. Amygdalus species exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137–26,467 bp, a large single-copy region that ranged from 85,757–86,608 bp, and a small single-copy region that ranged from 19,020–19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg. Amygdalus complete cp genomes was highly conserved, and the 12 subg. Amygdalus species had an rps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg. Amygdalus species. All 12 subg. Amygdalus species clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg. Amygdalus species diverged approximately 15.65 Mya. Conclusion Our results provide data on the genomic structure of subg. Amygdalus and elucidates their phylogenetic relationships and divergence time. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07968-6.
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Affiliation(s)
- Zhongyu Du
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China.,School of Ecology and environment, Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China
| | - Ke Lu
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Kai Zhang
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Yiming He
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Haitao Wang
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Guaiqiang Chai
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Jianguo Shi
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China
| | - Yizhong Duan
- College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China.
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The Status of Prunus padus L. (Bird Cherry) in Forest Communities throughout Europe and Asia. FORESTS 2020. [DOI: 10.3390/f11050497] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Prunus padus L. (bird cherry) belongs to the Racemosa group in subgenus Padus in the genus Prunus L. It is a hardy invasive species, which makes it valuable for securing slopes, and for eco-design. It is a good solitary park tree with early flowering of white flowers in racemes, which have a pleasant smell. However, it may be attacked by cherry-oat aphid, and the small ermine moth, which may weave giant webs over the whole tree, which demonstrates the important role of P. padus in the food web of forest ecosystems. The species is in balance with these pests, other herbivores and diseases throughout Europe and Asia. Another threat is the competition against the invasive P. serotina, but it seems that P. padus is not strongly threatened, though they compete for the same habitats. Moreover, human interference of forest community ecology is probably the greatest threat. The tree is not only winter hardy; it can also survive hot summers and tolerate a wide variety of soil types. It may form dense thickets due to the regeneration of branches bent to the ground and basal shoots, and may be invasive. These characteristics are important in determining the ecological niche of P. padus, which involves the position of the species within an ecosystem, comprising both its habitat requirements and the functional role. It is also important that P. padus has effective dispersal of pollen and seeds. This, together with the previously noted characteristics and the fact that the tree can cope well with climate change, define it as a not threatened species. However, the ssp. borealis is threatened and national level monitoring is required. Prunus padus has been exploited by farmers and rural population, but is less used today. However, it is still used for making syrup, jam and liquor. Moreover, the wood is valuable for wood carving and making cabinets. All tissues are valuable as sources of powerful natural antioxidants. However, the interest in the P. padus fruit and other tissues is overshadowed by the interest in other wild species of edible and human health-related berries. Moreover, the tree is used in horticulture as an ornamental in gardens and parks, values that deserve a new focus.
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Sokoloff DD, Ignatov MS, Remizowa MV, Nuraliev MS, Blagoderov V, Garbout A, Perkovsky EE. Staminate flower of Prunus s. l. (Rosaceae) from Eocene Rovno amber (Ukraine). JOURNAL OF PLANT RESEARCH 2018; 131:925-943. [PMID: 30032395 DOI: 10.1007/s10265-018-1057-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
The late Eocene ambers provide plethora of animal and plant fossils including well-preserved angiosperm flowers from the Baltic amber. The Rovno amber from NW Ukraine resembles in many aspects the Baltic amber; however, only fossilized animals and some bryophytes have yet been studied from the Rovno amber. We provide the first detailed description of an angiosperm flower from Rovno amber. The flower is staminate with conspicuous hypanthium, double pentamerous perianth and whorled androecium of 24 stamens much longer than the petals. Sepals are sparsely pubescent and petals are densely hirsute outside. The fossil shares important features with extant members of Prunus subgen. Padus s. l. (incl. Laurocerasus, Pygeum and Maddenia), especially with its evergreen paleotropical species. It is described here as a new species Prunus hirsutipetala D.D.Sokoloff, Remizowa et Nuraliev. Our study provides the first convincing record of fossil flowers of Rosaceae from Eocene of Europe and the earliest fossil flower of Prunus outside North America. Our record of a plant resembling extant tropical species supports palaeoentomological evidences for warm winters in northwestern Ukraine during the late Eocene, as well as suggesting a more significant role of tropical insects in Rovno amber than inferred from Baltic amber.
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Affiliation(s)
- Dmitry D Sokoloff
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234, Moscow, Russia.
| | - Michael S Ignatov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234, Moscow, Russia
- Tsitsin Main Botanical Garden of the Russian Academy of Sciences, Botanicheskaya 4, 127276, Moscow, Russia
| | - Margarita V Remizowa
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234, Moscow, Russia
| | - Maxim S Nuraliev
- Faculty of Biology, M.V. Lomonosov Moscow State University, 1, 12, Leninskie Gory, 119234, Moscow, Russia
- Joint Russian-Vietnamese Tropical Scientific and Technological Center, Cau Giay, Hanoi, Vietnam
| | | | - Amin Garbout
- Core Research Labs, Natural History Museum, Cromwell Road, London, UK
| | - Evgeny E Perkovsky
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, vul.B. Khmelnitskogo, 15, Kiev, 01030, Ukraine
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Zhao L, Jiang XW, Zuo YJ, Liu XL, Chin SW, Haberle R, Potter D, Chang ZY, Wen J. Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data. PLoS One 2016; 11:e0157123. [PMID: 27294529 PMCID: PMC4905661 DOI: 10.1371/journal.pone.0157123] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 05/25/2016] [Indexed: 01/01/2023] Open
Abstract
Prunus is an economically important genus well-known for cherries, plums, almonds, and peaches. The genus can be divided into three major groups based on inflorescence structure and ploidy levels: (1) the diploid solitary-flower group (subg. Prunus, Amygdalus and Emplectocladus); (2) the diploid corymbose group (subg. Cerasus); and (3) the polyploid racemose group (subg. Padus, subg. Laurocerasus, and the Maddenia group). The plastid phylogeny suggests three major clades within Prunus: Prunus-Amygdalus-Emplectocladus, Cerasus, and Laurocerasus-Padus-Maddenia, while nuclear ITS trees resolve Laurocerasus-Padus-Maddenia as a paraphyletic group. In this study, we employed sequences of the nuclear loci At103, ITS and s6pdh to explore the origins and evolution of the racemose group. Two copies of the At103 gene were identified in Prunus. One copy is found in Prunus species with solitary and corymbose inflorescences as well as those with racemose inflorescences, while the second copy (II) is present only in taxa with racemose inflorescences. The copy I sequences suggest that all racemose species form a paraphyletic group composed of four clades, each of which is definable by morphology and geography. The tree from the combined At103 and ITS sequences and the tree based on the single gene s6pdh had similar general topologies to the tree based on the copy I sequences of At103, with the combined At103-ITS tree showing stronger support in most clades. The nuclear At103, ITS and s6pdh data in conjunction with the plastid data are consistent with the hypothesis that multiple independent allopolyploidy events contributed to the origins of the racemose group. A widespread species or lineage may have served as the maternal parent for multiple hybridizations involving several paternal lineages. This hypothesis of the complex evolutionary history of the racemose group in Prunus reflects a major step forward in our understanding of diversification of the genus and has important implications for the interpretation of its phylogeny, evolution, and classification.
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Affiliation(s)
- Liang Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xi-Wang Jiang
- College of Life Sciences, Jianghan University, Wuhan, Hubei, 430056, China
| | - Yun-juan Zuo
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences / Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Songjiang, Shanghai, 201602, China
| | - Xiao-Lin Liu
- School of Applied Chemistry and Biological Engineering, Weifang Engineering Vocational College, Qingzhou, Shandong, 262500, China
| | - Siew-Wai Chin
- Department of Plant Sciences, MS2, University of California Davis, Davis, California, 95616, United States of America
| | - Rosemarie Haberle
- Department of Biology, Pacific Lutheran University, Tacoma, Washington, 98447, United States of America
| | - Daniel Potter
- Department of Plant Sciences, MS2, University of California Davis, Davis, California, 95616, United States of America
| | - Zhao-Yang Chang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, 20013–7012, United States of America
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9
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Diversification of almonds, peaches, plums and cherries – Molecular systematics and biogeographic history of Prunus (Rosaceae). Mol Phylogenet Evol 2014; 76:34-48. [DOI: 10.1016/j.ympev.2014.02.024] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 12/15/2013] [Accepted: 02/27/2014] [Indexed: 11/20/2022]
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