31 results on '"Zhao-Yang Chang"'
Search Results
2. On the Species Delimitation of the Maddenia Group of Prunus (Rosaceae): Evidence From Plastome and Nuclear Sequences and Morphology
- Author
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Na Su, Bin-bin Liu, Jun-ru Wang, Ru-chang Tong, Chen Ren, Zhao-yang Chang, Liang Zhao, Daniel Potter, and Jun Wen
- Subjects
Maddenia ,Prunus ,Rosaceae ,barcoding ,chloroplast genome ,single-copy nuclear genes ,Plant culture ,SB1-1110 - Abstract
The recognition, identification, and differentiation of closely related plant species present significant and notorious challenges to taxonomists. The Maddenia group of Prunus, which comprises four to seven species, is an example of a group in which species delimitation and phylogenetic reconstruction have been difficult, due to the lack of clear morphological distinctions, limited sampling, and low informativeness of molecular evidence. Thus, the precise number of species in the group and the relationships among them remain unclear. Here, we used genome skimming to generate the DNA sequence data for 22 samples, including 17 Maddenia individuals and five outgroups in Amygdaloideae of Rosaceae, from which we assembled the plastome and 446 single-copy nuclear (SCN) genes for each sample. The phylogenetic relationships of the Maddenia group were then reconstructed using both concatenated and coalescent-based methods. We also identified eight highly variable regions and detected simple sequence repeats (SSRs) and repeat sequences in the Maddenia species plastomes. The phylogenetic analysis based on the complete plastomes strongly supported three main subclades in the Maddenia group of Prunus, while five subclades were recognized based on the nuclear tree. The phylogenetic network analysis detected six hybridization events. Integrating the nuclear and morphological evidence, we proposed to recognize five species within the Maddenia group, i.e., Prunus fujianensis, P. himalayana, P. gongshanensis, P. hypoleuca, and P. hypoxantha. Within this group, the first three species are well-supported, while the gene flow occurring throughout the Maddenia group seems to be especially frequent between P. hypoleuca and P. hypoxantha, eroding the barrier between them. The phylogenetic trees based on eight concatenated hypervariable regions had a similar topology with the complete plastomes, showing their potential as molecular markers and effective barcodes for further phylogeographic studies on Maddenia.
- Published
- 2021
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3. Comparative Chloroplast Genomics and Phylogenetic Analysis of Zygophyllum (Zygophyllaceae) of China
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Ling Zhang, Shu Wang, Chun Su, AJ Harris, Liang Zhao, Na Su, Jun-Ru Wang, Lei Duan, and Zhao-Yang Chang
- Subjects
chloroplast genome ,comparative analysis ,phylogeny ,Zygophyllum ,Zygophyllaceae ,Plant culture ,SB1-1110 - Abstract
The genus Zygophyllum comprises over 150 species within the plant family Zygophyllaceae. These species predominantly grow in arid and semiarid areas, and about 20 occur in northwestern China. In this study, we sampled 24 individuals of Zygophyllum representing 15 species and sequenced their complete chloroplast (cp) genomes. For comparison, we also sequenced cp genomes of two species of Peganum from China representing the closely allied family, Nitrariaceae. The 24 cp genomes of Zygophyllum were smaller and ranged in size from 104,221 to 106,286 bp, each containing a large single-copy (LSC) region (79,245–80,439 bp), a small single-copy (SSC) region (16,285–17,146 bp), and a pair of inverted repeat (IR) regions (3,792–4,466 bp). These cp genomes contained 111–112 genes each, including 74–75 protein-coding genes (PCGs), four ribosomal RNA genes, and 33 transfer RNA genes, and all cp genomes showed similar gene order, content, and structure. The cp genomes of Zygophyllum appeared to lose some genes such as ndh genes and rRNA genes, of which four rRNA genes were in the SSC region, not in the IR regions. However, the SC and IR regions had greater similarity within Zygophyllum than between the genus and Peganum. We detected nine highly variable intergenic spacers: matK-trnQ, psaC-rps15, psbZ-trnG, rps7-trnL, rps15-trnN, trnE-trnT, trnL-rpl32, trnQ-psbK, and trnS-trnG. Additionally, we identified 156 simple sequence repeat (cpSSR) markers shared among the genomes of the 24 Zygophyllum samples and seven cpSSRs that were unique to the species of Zygophyllum. These markers may be useful in future studies on genetic diversity and relationships of Zygophyllum and closely related taxa. Using the sequenced cp genomes, we reconstructed a phylogeny that strongly supported the division of Chinese Zygophyllum into herbaceous and shrubby clades. We utilized our phylogenetic results along with prior morphological studies to address several remaining taxonomic questions within Zygophyllum. Specifically, we found that Zygophyllum kaschgaricum is included within Zygophyllum xanthoxylon supporting the present treatment of the former genus Sarcozygium as a subgenus within Zygophyllum. Our results provide a foundation for future research on the genetic resources of Zygophyllum.
- Published
- 2021
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4. Why More Leaflets? The Role of Natural Selection in Shaping the Spatial Pattern of Leaf-Shape Variation in Oxytropis diversifolia (Fabaceae) and Two Close Relatives
- Author
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Hui Wang, Pei-Liang Liu, Jian Li, Han Yang, Qin Li, and Zhao-Yang Chang
- Subjects
leaf shape ,cline ,natural selection ,gene flow ,Oxytropis ,Plant culture ,SB1-1110 - Abstract
Leaf shape exhibits tremendous diversity in angiosperms. It has long been argued that leaf shape can affect major physiological and ecological properties of plants and thus is likely to be adaptive, but the evolutionary evidence is still scarce. Oxytropis diversifolia (Fabaceae) is polymorphic for leaf shape (1 leaflet, 1–3 leaflets, and 3 leaflets) and exhibits clinal variation in steppes of Nei Mongol, China. With two close relatives predominantly fixed for one phenotype as comparison (Oxytropis neimonggolica with 1 leaflet and Oxytropis leptophylla with 5–13 leaflets), we used a comprehensive cline-fitting approach to assess the role of natural selection in shaping the spatial pattern of leaf-shape variation in this system. For 551 individuals sampled from 22 populations, we quantified leaf-morphological differentiation, evaluated patterns of neutral genetic variation using five chloroplast DNA intergenic regions and 11 nuclear microsatellite loci, and performed microhabitat and macroclimatic-association analyses. We found that 1-leaflet proportions in O. diversifolia populations significantly increased from west to east, and three phenotypes also differed in leaflet-blade size. However, compared with the other two species, populations of O. diversifolia showed little neutral genetic differentiation, and no population structure was detected at either marker. We further revealed that the leaf-shape cline could largely be explained by three macroclimatic variables, with leaflet number decreasing and leaflet-blade size increasing with annual precipitation and showing the reverse trends with temperature seasonality and isothermality. Our results suggest that spatially varying abiotic environmental factors contribute to shape the leaf-shape cline in O. diversifolia, while the interspecific pattern may be due to both local adaptation and historical events.
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- 2021
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5. The complete chloroplast genome of Sesbania cannabina (Fabaceae) from China
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Chun Su, Hong-Feng Chen, Zhao-Yang Chang, and Lei Duan
- Subjects
sesbania cannabina ,fabaceae ,chloroplast genome ,Genetics ,QH426-470 - Abstract
Sesbania cannabina (Retz.) Poir. (Fabaceae) is an annual herb, widely distributed in the tropical and subtropical regions. In this study, the complete chloroplast (cp) genome of S. cannabina was reported and phylogenetic analysis was conducted with Fabaceae species based on the cp genome sequences. The cp genome of S. cannabina is 156,894 bp in length, consisting of a pair of inverted repeats (IR, 25,465 bp), a small single-copy (SSC, 18,837bp) and a large single-copy (LSC, 87128 bp) region. It encodes 126 genes including 81 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The Maximum Likelihood tree shows S. cannabina which is nested in Hologalegina clade of the subfamily Papilionoideae (Fabaceae).
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- 2020
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6. Efficient Identification of Pulsatilla (Ranunculaceae) Using DNA Barcodes and Micro-Morphological Characters
- Author
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Qiu-jie Li, Xi Wang, Jun-ru Wang, Na Su, Ling Zhang, Yue-ping Ma, Zhao-yang Chang, Liang Zhao, and Daniel Potter
- Subjects
barcoding markers ,ITS ,pulsatilla ,ranunculaceae ,species identification ,Plant culture ,SB1-1110 - Abstract
Pulsatilla (Ranunculaceae) comprises about 40 species, many of which have horticultural and/or medicinal importance. However, the recognition and identification of wild Pulsatilla species is difficult due to the presence of complex morphological characters. DNA barcoding is a powerful molecular tool capable of rapidly and accurately distinguishing between species. Here, we assessed the effectiveness of four commonly used DNA barcoding loci—rbcL (R), trnH-psbA ( T ), matK (M), and ITS (I)—to identify species of Pulsatilla from a comprehensive sampling group. Among the four barcoding single loci, the nuclear ITS marker showed the highest interspecific distances and the highest rate of correct identification. Among the eleven combinations, the chloroplast multi-locus R+T and R+M+T combinations were found to have the best species discrimination rate, followed by R+M. Overall, we propose that the R+M+T combination and the ITS marker on its own are, respectively, the best multi- and single-locus barcodes for discriminating among species of Pulsatilla. The phylogenetic analysis was able to distinguish species of Pulsatilla to the subgenus level, but the analysis also showed relatively low species resolution. This may be caused by incomplete lineage sorting and/or hybridization events in the evolutionary history of the genus, or by the resolution limit of the candidate barcodes. We also investigated the leaf epidermis of eight representative species using scanning electronic microscopy. The resulting micro-morphological characters were valuable for identification of related species. Using additional genome fragments, or even whole chloroplast genomes combined with micro-morphological data may permit even higher resolution of species in Pulsatilla.
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- 2019
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7. The complete chloroplast genome sequence of Oxytropis bicolor Bunge (Fabaceae)
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Chun Su, Pei-Liang Liu, Zhao-Yang Chang, and Jun Wen
- Subjects
chloroplast genome ,oxytropis ,intron loss ,fabaceae ,Genetics ,QH426-470 - Abstract
The first complete chloroplast genome of Oxytropis bicolor Bunge is reported and characterized in this study. The whole chloroplast genome was 122,461 base pairs in length with 110 genes, including 76 protein-coding genes, 30 tRNAs, and 4 rRNAs. In addition, the atpF intron was absent. Maximum-likelihood (ML) phylogenetic analysis indicated that O. bicolor and species of Astragalus were closely related, which is congruent with previous studies.
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- 2019
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8. Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic - Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences.
- Author
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Pei-Liang Liu, Jun Wen, Lei Duan, Emine Arslan, Kuddisi Ertuğrul, and Zhao-Yang Chang
- Subjects
Medicine ,Science - Abstract
The legume family (Fabaceae) exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae) showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences. Both nuclear and plastid data support two major lineages in Hedysarum: the Hedysarum s.s. clade and the Sartoria clade. In the nuclear tree, Hedysarum is biphyletic with the Hedysarum s.s. clade sister to the Corethrodendron + Eversmannia + Greuteria + Onobrychis clade (the CEGO clade), whereas the Sartoria clade is sister to the genus Taverniera DC. In the plastid tree, Hedysarum is monophyletic and sister to Taverniera. The incongruent position of the Hedysarum s.s. clade between the nuclear and plastid trees may be best explained by a chloroplast capture hypothesis via introgression. The Hedysarum sect. Stracheya clade is resolved as sister to the H. sect. Hedysarum clade in both nuclear and plastid trees, and our analyses support merging Stracheya into Hedysarum. Based on our new evidence from multiple sequences, Hedysarum is not monophyletic, and its generic delimitation needs to be reconsidered.
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- 2017
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9. Multiple Events of Allopolyploidy in the Evolution of the Racemose Lineages in Prunus (Rosaceae) Based on Integrated Evidence from Nuclear and Plastid Data.
- Author
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Liang Zhao, Xi-Wang Jiang, Yun-Juan Zuo, Xiao-Lin Liu, Siew-Wai Chin, Rosemarie Haberle, Daniel Potter, Zhao-Yang Chang, and Jun Wen
- Subjects
Medicine ,Science - 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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- 2016
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10. A New Species of Astragalus (Leguminosae) from Northwestern Xinjiang, China
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Xiao-Lin, Liu, Xiao-Na, Yue, Zhao-Yang, Chang, Lang-Ran, Xu, and BioStor
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- 2011
11. Tension zone trapped by exogenous cline: Analysis of a narrow hybrid zone between two parapatric
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Hui, Wang, Xin-Nuo, Li, Song-Hua, Mo, Min, Wang, Pei-Liang, Liu, Qin, Li, and Zhao-Yang, Chang
- Abstract
Hybrid zones have been widely highlighted for their interest in understanding evolutionary processes. It is generally accepted that hybrid zones can be maintained in a balance between dispersal and selection. However, the selective forces can either be endogenous (i.e., genetic incompatibilities between parental taxa) or exogenous (i.e., parental taxa are adapted to different environments). In this study, we evaluated these alternatives and determined the maintenance of a narrow hybrid zone between parapatric distributed
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- 2022
12. Floral morphogenesis of the Maddenia and Pygeum groups of Prunus (Rosaceae), with an emphasis on the perianth
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Zhao-Yang Chang, Xiao-hui Zhang, Xi Wang, Liang Zhao, Jun-ru Wang, Louis P. Ronse De Craene, Siyu Xie, and Jun Wen
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Prunus ,Rosaceae ,Botany ,Morphogenesis ,Petal ,Plant Science ,Biology ,Perianth ,Pygeum ,biology.organism_classification ,Ecology, Evolution, Behavior and Systematics - Published
- 2021
13. Comparative study of floral developments and its systematic importance in the genus Astragalus L. and Oxytropis DC. (Fabaceae, Leguminosae: Papilionoideae)
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Shabir A. Rather, Liang Zhao, Jun-ru Wang, Ying Wei, and Zhao-Yang Chang
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0106 biological sciences ,0301 basic medicine ,biology ,Stamen ,Cell Biology ,Plant Science ,Fabaceae ,biology.organism_classification ,01 natural sciences ,Biochemistry ,Oxytropis ,03 medical and health sciences ,Astragalus ,030104 developmental biology ,Raceme ,Inflorescence ,Botany ,Genetics ,Animal Science and Zoology ,Petal ,Primordium ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
The initiation pattern of the floral organs of the Astragalus species displays uniqueness at the initial stages of ontogeny. However, its most common way is unidirectional initiation, which occurs from the abaxial to the adaxial sides. The overlapping of organs and the emergence of common primordia shortens the time of development and is of an evolutionary advantage to the genus. Astragalus species are constantly evolving, and they are bestowed with unique floral ontogeny that offers various advantages to these plants to survive and adapt to changing environmental conditions. The morphological features of the floral organ production of four Astragalus species were identical in the early and middle stages of development. During the middle and the late stages, some unique features such as rolled petals, sticky keel tips, diadelphous androecium were observed. Semi-circular receptacular nectaries were found in Astragalus henryi. Comparison of the inflorescence development between A. henryi and A. membranaceus revealed that A. membranaceus formed one terminal inflorescence, which developed into a raceme while A. henryi formed a variety of terminal inflorescences, branched by racemes to form panicles. Development of common primordia and organ overlap was also observed in both Oxytropis ochrocephala and Astragalus species. However, the most significant difference was observed in the keel petals of O. ochrocephala, which developed a beak at the later stages of development. The study unravels interesting relationships between four species of Astragalus and one species of Oxytropis. Study of floral ontogeny through series of sections using various microscopic techniques provided insights into the understudied floral traits of the genera. Such studies also need to be corroborated with other empirical evidence and analyses.
- Published
- 2021
14. Why More Leaflets? The Role of Natural Selection in Shaping the Spatial Pattern of Leaf-Shape Variation in Oxytropis diversifolia (Fabaceae) and Two Close Relatives
- Author
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Qin Li, Han Yang, Pei-Liang Liu, Zhao-Yang Chang, Hui Wang, and Jian Li
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Natural selection ,Leaflet (botany) ,biology ,food and beverages ,Plant culture ,natural selection ,Plant Science ,Cline (biology) ,Interspecific competition ,biology.organism_classification ,leaf shape ,Oxytropis ,SB1-1110 ,Gene flow ,Evolutionary biology ,Genetic variation ,gene flow ,cline ,Local adaptation - Abstract
Leaf shape exhibits tremendous diversity in angiosperms. It has long been argued that leaf shape can affect major physiological and ecological properties of plants and thus is likely to be adaptive, but the evolutionary evidence is still scarce. Oxytropis diversifolia (Fabaceae) is polymorphic for leaf shape (1 leaflet, 1–3 leaflets, and 3 leaflets) and exhibits clinal variation in steppes of Nei Mongol, China. With two close relatives predominantly fixed for one phenotype as comparison (Oxytropis neimonggolica with 1 leaflet and Oxytropis leptophylla with 5–13 leaflets), we used a comprehensive cline-fitting approach to assess the role of natural selection in shaping the spatial pattern of leaf-shape variation in this system. For 551 individuals sampled from 22 populations, we quantified leaf-morphological differentiation, evaluated patterns of neutral genetic variation using five chloroplast DNA intergenic regions and 11 nuclear microsatellite loci, and performed microhabitat and macroclimatic-association analyses. We found that 1-leaflet proportions in O. diversifolia populations significantly increased from west to east, and three phenotypes also differed in leaflet-blade size. However, compared with the other two species, populations of O. diversifolia showed little neutral genetic differentiation, and no population structure was detected at either marker. We further revealed that the leaf-shape cline could largely be explained by three macroclimatic variables, with leaflet number decreasing and leaflet-blade size increasing with annual precipitation and showing the reverse trends with temperature seasonality and isothermality. Our results suggest that spatially varying abiotic environmental factors contribute to shape the leaf-shape cline in O. diversifolia, while the interspecific pattern may be due to both local adaptation and historical events.
- Published
- 2021
15. New species discovered from old collections, the case of Hedysarum wangii sp. nov. (Fabaceae, Hedysareae)
- Author
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Xue-Lin Chen, Yuan Lu, Ming Yue, Zhao-Yang Chang, and Pei-Liang Liu
- Subjects
Herbarium ,biology ,Phylogenetic tree ,Phylogenetics ,Botany ,Hedysarum ,Species diversity ,Taxonomy (biology) ,Plant Science ,Fabaceae ,biology.organism_classification ,Eudicots ,Ecology, Evolution, Behavior and Systematics - Abstract
Hedysarum wangii sp. nov. (Fabaceae) is described and illustrated based on historical collections, field observations and molecular phylogenetic analysis. The new species is similar to H. minjanense and H. lehmannianum, but can be diagnosed by details of its leaves, flowers and fruit. Phylogenetic trees based on nuclear ETS, ITS and plastid psbA-trnH, trnL-F, trnS-G and petN-psbM sequences indicated that H. wangii is a member of sect. Stracheya, and is closely related to H. minjanense. A key to species in sect. Stracheya is provided. Initiated by a specimen collected in the year 1937, the discovery of H. wangii highlights the importance of historical herbarium collections in our understanding of species diversity.
- Published
- 2019
16. Floral organogenesis of Prunus laurocerasus and P. serotina and its significance for the systematics of the genus and androecium diversity in Rosaceae
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Liang Zhao, Xi Wang, Qiu-jie Li, Zhao-Yang Chang, Jun-ru Wang, Jing-zhi Gong, Xiao-hui Zhang, Yueping Ma, and Jun Wen
- Subjects
0106 biological sciences ,Systematics ,Ecology ,Rosaceae ,Stamen ,Plant Science ,Prunus laurocerasus ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Prunus ,Taxon ,Genus ,Botany ,Clade ,Ecology, Evolution, Behavior and Systematics ,010606 plant biology & botany - Abstract
Phylogenetic studies have shown that most clades in Prunus are well-supported by the flower structure, but most taxa in the racemose group have not yet been re-evaluated and could contribute to the understanding of the systematic relationships of the subgenera. We examined the inflorescence and flower development in Prunus laurocerasus L. (subgenus Laurocerasus) and P. serotina Ehrh. (subgenus Padus I) using scanning electron microscopy. Our results indicate that they share several floral development characters but differ in the following aspects: (i) all of their flowers are fully developed and each flower is enclosed by a bract and two bracteoles, which later stop development (vs. the terminal flower degenerates and only a single bract subtends each flower); (ii) the style protrudes from the floral bud (vs. the style is crooked and below the anthers); (iii) the outer integument initiates close to the inner one (vs. in the middle of the ovule); and (iv) an obturator appears after initiation of the two integuments (vs. simultaneously with the inner integument). Although our results are preliminary, differences in floral developmental characters support the different origins of Prunus subgenera Laurocerasus and Padus as based on molecular phylogenetic studies.
- Published
- 2019
17. Phylogeny and spatio‐temporal diversification ofPrunussubgenusLaurocerasussectionMesopygeum(Rosaceae) in the Malesian region
- Author
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Pei-Liang Liu, Liang Zhao, Zhao-Yang Chang, Jun Wen, Daniel Potter, Yuan Xu, and Gabriel Johnson
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0106 biological sciences ,0301 basic medicine ,Biogeography ,Subclade ,Plant Science ,Late Miocene ,Neogene ,Wallace Line ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Paleontology ,Monophyly ,030104 developmental biology ,Taxon ,Geography ,Subgenus ,Ecology, Evolution, Behavior and Systematics - Abstract
The goals of this study were to reconstruct the phylogeny of Prunus subgenus Laurocerasus section Mesopygeum and to provide a preliminary assessment of its spatio‐temporal diversification in the Malesian region. We inferred the phylogeny using nuclear ITS and ETS and plastid psbA‐trnH, rps16, rpl16, and trnC‐petN sequences. Our analyses support the monophyly of sect. Mesopygeum. Within sect. Mesopygeum, we identified four main subclades: (i) Prunus lancilimba from continental Asia; (ii) Prunus ruthii from Malay Peninsula; (iii) a subclade comprising species from areas centered on the Sunda shelf and also a few species from continental Asia and Wallacea; and (iv) a subclade composed of species from areas of the Sahul shelf, with a small number of taxa also from areas of the Sunda shelf, continental Asia, and the Philippines. We estimated that sect. Mesopygeum originated in continental Asia at c. 44.71 Mya (95% HPD: 31.66–46.90). Nine dispersals between major geographic areas were inferred. From continental Asia, three and two dispersals were inferred to the Sunda shelf and the Sahul shelf in the mid‐Oligocene, respectively. Two dispersals were inferred from the Sahul shelf region to the Sunda shelf in late Oligecene and early Miocene, respectively. There were also two dispersals inferred from the Sunda shelf region, one to the Philippines and one to Wallacea, in the middle and late Miocene, respectively. The diversification in sect. Mesopygeum was likely driven by active geologic events and orogenies in the Neogene in the Malesian region.
- Published
- 2018
18. Chloroplast genomes elucidate diversity, phylogeny, and taxonomy of Pulsatilla (Ranunculaceae)
- Author
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Daniel Potter, Zhao-Yang Chang, Xiao-hui Zhang, Qiu-jie Li, Ru-chang Tong, Ling Zhang, Na Su, Liang Zhao, and Jun-ru Wang
- Subjects
0106 biological sciences ,0301 basic medicine ,Evolution ,lcsh:Medicine ,Single-nucleotide polymorphism ,Ranunculaceae ,Biology ,01 natural sciences ,Genome ,Polymorphism, Single Nucleotide ,Chloroplast ,Article ,Evolution, Molecular ,03 medical and health sciences ,Phylogenetics ,Genetics ,Polymorphism ,Genome, Chloroplast ,lcsh:Science ,Phylogeny ,Genetic diversity ,Multidisciplinary ,Phylogenetic tree ,Whole Genome Sequencing ,Human Genome ,lcsh:R ,Molecular ,Single Nucleotide ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,Microsatellite ,Taxonomy (biology) ,lcsh:Q ,Pulsatilla ,Plant sciences ,Systems biology ,010606 plant biology & botany ,Microsatellite Repeats - Abstract
Pulsatilla (Ranunculaceae) consists of about 40 species, and many of them have horticultural and/or medicinal value. However, it is difficult to recognize and identify wild Pulsatilla species. Universal molecular markers have been used to identify these species, but insufficient phylogenetic signal was available. Here, we compared the complete chloroplast genomes of seven Pulsatilla species. The chloroplast genomes of Pulsatilla were very similar and their length ranges from 161,501 to 162,669 bp. Eight highly variable regions and potential sources of molecular markers such as simple sequence repeats, large repeat sequences, and single nucleotide polymorphisms were identified, which are valuable for studies of infra- and inter-specific genetic diversity. The SNP number differentiating any two Pulsatilla chloroplast genomes ranged from 112 to 1214, and provided sufficient data for species delimitation. Phylogenetic trees based on different data sets were consistent with one another, with the IR, SSC regions and the barcode combination rbcL + matK + trnH-psbA produced slightly different results. Phylogenetic relationships within Pulsatilla were certainly resolved using the complete cp genome sequences. Overall, this study provides plentiful chloroplast genomic resources, which will be helpful to identify members of this taxonomically challenging group in further investigation.
- Published
- 2020
19. Chloroplast phylogenomics and character evolution of eastern Asian Astragalus (Leguminosae): Tackling the phylogenetic structure of the largest genus of flowering plants in Asia
- Author
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Pei-Liang Liu, Chun Su, Jing Liu, Jun Wen, Lei Duan, and Zhao-Yang Chang
- Subjects
0106 biological sciences ,0301 basic medicine ,Character evolution ,Asia ,Chloroplasts ,Time Factors ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Monophyly ,Phylogenomics ,Botany ,Genetics ,Clade ,Genome, Chloroplast ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Phylogenetic tree ,Bayes Theorem ,Astragalus Plant ,biology.organism_classification ,Astragalus ,030104 developmental biology ,Taxon ,Subgenus - Abstract
Astragalus, as the largest genus of the flowering plants, is well-known for its high species richness and morphological diversity. Previous studies suggested that many of the subgenera of Astragalus are not monophyletic and the phylogenetic relationships within the genus are still poorly known. In this study, we sampled 117 accessions of Astragalus and its close relatives, covering 55 sections of the genus plus 30 outgroup taxa to recover the main clades of eastern Asian Astragalus based on sequences of the whole chloroplast genome and 65 chloroplast CDSs. Astragalus is supported to be monophyletic and it is sister to the Oxytropis + Coluteoid clade. Within Astragalus, we recovered ten clades, and the ten clades differ substantially from Bunge’s subgenera. The former segregate genus Astracantha is also monophyletic, but embedded within Astragalus s. str., supporting the merge of the spiny former genus Astracantha with Astragalus. We detected the atpF intron losses in the chloroplast genome of the Oxytropis + Coluteoid clade, i.e., the sister clade to Astragalus. Furthermore, we estimated the ancestral states of the trichome morphology and habit via the Bayesian Binary Method. The medifixed hair type is inferred to have developed at least five times and the annual habit originated at least six times. In addition, Astragalus is estimated to have originated in the mid Miocene (stem age, 16.09 Ma, 95% HPD: 12.46–20.50 Ma). The divergence times of the medifixed hair groups ranged from 4.03 to 0.87 Ma, mostly 2–1 Ma, which are correlated with the estimated phased uplifts of the Qinghai-Tibetan Plateau (QTP). We hypothesize that the uplifts of the QTP, which contributed to aridification in eastern Asia and the adjacent regions, may have accelerated the rapid speciation of Astragalus, especially the xerophilous groups (i.e. the medifixed hair groups).
- Published
- 2020
20. Floral morphology and morphogenesis in Camptotheca (Nyssaceae), and its systematic significance
- Author
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Zhao-Yang Chang, Xiao-hui Zhang, Louis P. Ronse De Craene, Yueping Ma, Liang Zhao, Qiu-jie Li, Xi Wang, and Jing-zhi Gong
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0106 biological sciences ,biology ,Camptotheca ,Reproduction ,Cornaceae ,Ovary (botany) ,Flowers ,Original Articles ,Plant Science ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Hypanthium ,Diplopanax ,Inflorescence ,Botany ,Microscopy, Electron, Scanning ,Nyssaceae ,Mastixia ,Nyssa ,010606 plant biology & botany - Abstract
Background and aims Camptotheca is endemic to China and there are limited data about the breeding system and morphogenesis of the flowers. Camptotheca is thought to be related to Nyssa and Davidia in Nyssaceae, which has sometimes been included in Cornaceae. However, molecular phylogenetic studies confirmed the inclusion of Camptotheca in Nyssaceae and its exclusion from Cornaceae. The aim of this study was to reveal developmental features of the inflorescence and flowers in Camptotheca to compare with related taxa in Cornales. Methods Inflorescences and flowers of Camptotheca acuminata at all developmental stages were collected and studied with a scanning electron microscope and stereo microscope. Key results Camptotheca has botryoids which are composed of several capitate floral units (FUs) that are initiated acropetally. On each FU, flowers are grouped in dyads that are initiated acropetally. All floral organs are initiated centripetally. Calyx lobes are restricted to five teeth. The hypanthium, with five toothed calyx lobes, is adnate to the ovary. The five petals are free and valvate. Ten stamens are inserted in two whorls around the central depression, in which the style is immersed. Three carpels are initiated independently but the ovary is syncarpous and unilocular. The ovule is unitegmic and heterotropous. Inflorescences are functionally andromonoecious varying with the position of the FUs on the inflorescence system. Flowers on the upper FU often have robust styles and fully developed ovules. Flowers on the lower FU have undeveloped styles and aborted ovules, and the flowers on the middle FU are transitional. Conclusions Camptotheca possesses several traits that unify it with Nyssa, Mastixia and Diplopanax. Inflorescence and floral characters support a close relationship with Nyssaceae and Mastixiaceae but a distant relationship with Cornus. Our results corroborate molecular inferences and support a separate family Nyssaceae.
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- 2018
21. [A landscape of transcriptome analysis of three sclerotia growth stages in Polyporus umbellatus]
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Xiao-Yu, Bian, Tian-Lin, Pei, Zong-Suo, Liang, and Zhao-Yang, Chang
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China ,Gene Expression Profiling ,Genes, Fungal ,Medicine, Chinese Traditional ,Transcriptome ,Polyporus - Abstract
Polyporus umbellatus,a traditional Chinese precious medicine as long been used for eliminating dampness,diuresis and have effect on cancer,getting more and more popularly in China recently. And the developmental metabolic process of the medicinal fungus,P. umbellatus,has been gotten more attention. This study is for the first time to explore the three sclerotial growth stages in P. umbellatus,named " white Polyporus"( initial phase), " grey Polyporus"( developmental phase) and " black Polyporus"( mature phase),by utilizing the de novo transcriptome assembly analysis technology. Finally,we obtained 88. 12 Gb sequence containing85 235 unigenes( ≥200 bp) assembled and 100% were annotated. We identified genes differentially expressed among the three stages of the sclerotia and screened out MFSgst,ERG4/ERG24,WD40,Rho A,CYP450,PKS,GSase and CHS1,which may contribute to the production of medicinal secondary metabolites and the defense mechanism against the environmental stress and biological invasion. We did the qRT-PCR trial to verify our results,which is in line with expectations. Our results are purposed to unearth the molecular mechanism of the accumulation of active constituents in different stages of Polyporus sclerotia which can be applied in the production and protection of Polyporus effectively.
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- 2019
22. A molecular phylogeny of Caraganeae (Leguminosae, Papilionoideae) reveals insights into new generic and infrageneric delimitations
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Zhao-Yang Chang, Pei-Liang Liu, Gabriel Johnson, Jun Wen, Xue Yang, and Lei Duan
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0106 biological sciences ,0301 basic medicine ,Fabales ,Plant Science ,Biology ,phylogeny ,Tribe (biology) ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Monophyly ,Genus ,lcsh:Botany ,Polyphyly ,Botany ,Plantae ,Clade ,Ecology, Evolution, Behavior and Systematics ,Chesniella ,Chloroplast capture ,Phylogenetic tree ,lcsh:QK1-989 ,Caragana ,chloroplast capture ,Chesneya ,030104 developmental biology ,generic delimitation ,Molecular phylogenetics ,Leguminosae ,Research Article - Abstract
Based on sequence data of nuclear ITS and plastid matK, trnL-F and psbA-trnH markers, the phylogeny of the subtribes Caraganinae and Chesneyinae in tribe Caraganeae was inferred. The results support the monophyly of each of the subtribes. Within subtribes Caraganinae, Calophaca and Halimodendron are herein transferred into Caragana to ensure its generic monophyly. The subtribe Chesneyinae is composed of four well-supported genera: Chesneya, Chesniella, Gueldenstaedtia and Tibetia. Based on phylogenetic, morphological, distributional and habitat type evidence, the genus Chesneya was divided into three monophyletic sections: Chesneya sect. Chesneya, Chesneya sect. Pulvinatae and Chesneya sect. Spinosae. Chesneya macrantha is herein transferred into Chesniella. Spongiocarpella is polyphyletic and its generic rank is not maintained. The position of Chesneya was incongruent in the nuclear ITS and the plastid trees. A paternal chloroplast capture event via introgression is hypothesized for the origin of Chesneya, which is postulated to have involved the common ancestor of Chesniella (♂) and that of the Gueldenstaedtia – Tibetia (GUT) clade (♀) as the parents.
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- 2016
23. Isolation and characterization of microsatellite loci from
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Hui, Wang, Han, Yang, Pei-Liang, Liu, Chun, Su, Liang, Xiao, and Zhao-Yang, Chang
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nuclear microsatellites ,Primer Notes ,next‐generation sequencing ,Fabaceae ,Oxytropis diversifolia ,Primer Note - Abstract
Premise of the Study Microsatellite primers were developed for a perennial legume from northern China, Oxytropis diversifolia (Fabaceae), to investigate population genetic structure of this taxon, as well as potential hybridization events with closely related taxa in this genus. Methods and Results One hundred and five primer pairs were designed from Illumina sequence data and screened for suitability. Fifteen of these primer pairs were polymorphic, and these primers amplified tri‐, tetra‐, and pentanucleotide repeats with 10–56 alleles per locus. Cross‐amplification tests in three other Oxytropis species from northern China (O. leptophylla, O. neimonggolica, and O. squammulosa) revealed that all of these loci can be amplified successfully and show polymorphism. Conclusions These primer pairs can be used to assess the genetic diversity and population structure in future studies of O. diversifolia, as well as studies of potential hybridization events with closely related taxa in this genus.
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- 2018
24. Phylogeny of Hedysarum and tribe Hedysareae (Leguminosae: Papilionoideae) inferred from sequence data of ITS, matK , trnL ‐ F and psbA ‐ trnH
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Kuddisi Ertuğrul, Xue Yang, Pei-Liang Liu, Lei Duan, Jun Wen, Emine Arslan, and Zhao-Yang Chang
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Hedysareae ,biology ,Zoology ,Plant Science ,biology.organism_classification ,Tribe (biology) ,Galegeae ,Intergenic region ,Data sequences ,Phylogenetics ,Botany ,Hedysarum ,Taxonomy (biology) ,Ecology, Evolution, Behavior and Systematics - Published
- 2015
25. A cladistic analysis of medical Astragalus penduliflorus Lam. complex (Leguminosae: Papilionoideae) in China and its taxonomic implications
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Lei Duan, Zhao-Yang Chang, and Xiao-Lin Liu
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0106 biological sciences ,Traditional medicine ,Astragalus penduliflorus ,Dendrogram ,UPGMA ,Soil Science ,02 engineering and technology ,Plant Science ,Biology ,01 natural sciences ,Cladistics ,020401 chemical engineering ,Plant morphology ,Genetic marker ,Botany ,Amplified fragment length polymorphism ,Taxonomy (biology) ,0204 chemical engineering ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
To test the taxonomy of medical Astragalus penduliflorus complex and specific status of A. petrovii, eleven accessions (covering four species) in China were sampled herein for an AFLP study. A total of 346 informative polymorphic bands from eight primers pairs were obtained, dendrogram was generated using UPGMA analysis. The results indicated A. membranaceus is more morphologically and generically diverse than A. mongholicus on the populational level. Both of them and the former species A. minhensis were degraded as three varieties of A. penduliflorus. In the light of morphological and cladistic evidence, a new combination, A. penduliflorus ssp. mongholicus var. petrovii was proposed based on former species A. petrovii.
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- 2016
26. Isolation and characterization of microsatellite loci fromOxytropis diversifolia(Fabaceae)
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Zhao-Yang Chang, Han Yang, Pei-Liang Liu, Hui Wang, Liang Xiao, and Chun Su
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0301 basic medicine ,Genetics ,education.field_of_study ,Genetic diversity ,Population ,Locus (genetics) ,Plant Science ,Fabaceae ,Biology ,biology.organism_classification ,DNA sequencing ,Oxytropis ,03 medical and health sciences ,030104 developmental biology ,Genetic structure ,Microsatellite ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Premise of the Study Microsatellite primers were developed for a perennial legume from northern China, Oxytropis diversifolia (Fabaceae), to investigate population genetic structure of this taxon, as well as potential hybridization events with closely related taxa in this genus. Methods and Results One hundred and five primer pairs were designed from Illumina sequence data and screened for suitability. Fifteen of these primer pairs were polymorphic, and these primers amplified tri-, tetra-, and pentanucleotide repeats with 10-56 alleles per locus. Cross-amplification tests in three other Oxytropis species from northern China (O. leptophylla, O. neimonggolica, and O. squammulosa) revealed that all of these loci can be amplified successfully and show polymorphism. Conclusions These primer pairs can be used to assess the genetic diversity and population structure in future studies of O. diversifolia, as well as studies of potential hybridization events with closely related taxa in this genus.
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- 2018
27. Recognition of a new species of Hedysarum (Fabaceae, Hedysareae) from China based on morphological and molecular evidence
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Zhao-Yang Chang, Ying Wei, Jun Wen, and Pei-Liang Liu
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Intergenic region ,biology ,Phylogenetics ,Botany ,Hedysarum ,Taxonomy (biology) ,Plant Science ,Fabaceae ,biology.organism_classification ,Eudicots ,Ecology, Evolution, Behavior and Systematics ,Calyx ,Loment - Abstract
A new species, Hedysarum cuonanum (Fabaceae, Hedysareae), is described from the eastern Himalaya in China. This new species is similar to H. xizangense , but differs by its lanceolate or narrowly elliptic leaflet blade, ovate or lanceolate bracteole about half the length of calyx tube, acute or obtuse standard apex, and mucronate keel apex. It also resembles H. longigynophorum , but can be distinguished by its leaflet blade with 13–19 secondary veins on each side, abaxial calyx tooth about 1.5 times as long as the adaxial teeth, standard as long as keel, and elliptic or ovate loment article. Phylogenetic analyses based on the nuclear ITS, ETS sequences, and the plastid psbA-trnH , trnC-petN , petN-psbM sequences showed that H. cuonanum is sister to H. xizangense , and the H. cuonanum + H. xizangense clade is then sister to H. longigynophorum.
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- 2017
28. Hedysarum L. (Fabaceae: Hedysareae) Is Not Monophyletic – Evidence from Phylogenetic Analyses Based on Five Nuclear and Five Plastid Sequences
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Lei Duan, Jun Wen, Pei-Liang Liu, Zhao-Yang Chang, Kuddisi Ertuğrul, Emine Arslan, and Selçuk Üniversitesi
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0106 biological sciences ,0301 basic medicine ,Introgression ,lcsh:Medicine ,Plant Science ,01 natural sciences ,Trees ,Database and Informatics Methods ,Monophyly ,Taverniera ,Hedysarum ,Plastids ,lcsh:Science ,Clade ,Phylogeny ,Data Management ,Multidisciplinary ,biology ,Phylogenetic tree ,Chloroplast capture ,DNA, Chloroplast ,Fabaceae ,Phylogenetic Analysis ,Plants ,Legumes ,Phylogenetics ,Sequence Analysis ,Research Article ,Computer and Information Sciences ,Multiple Alignment Calculation ,Evolutionary Processes ,DNA, Plant ,Bioinformatics ,Plant Cell Biology ,Research and Analysis Methods ,010603 evolutionary biology ,Evolution, Molecular ,03 medical and health sciences ,Computational Techniques ,Botany ,Evolutionary Systematics ,Sartoria ,Molecular Biology Techniques ,Molecular Biology ,Taxonomy ,Cell Nucleus ,Molecular Biology Assays and Analysis Techniques ,Evolutionary Biology ,lcsh:R ,Organisms ,Biology and Life Sciences ,Cell Biology ,biology.organism_classification ,Split-Decomposition Method ,030104 developmental biology ,lcsh:Q - Abstract
WOS: 000396167300037, PubMed: 28122062, The legume family (Fabaceae) exhibits a high level of species diversity and evolutionary success worldwide. Previous phylogenetic studies of the genus Hedysarum L. (Fabaceae: Hedysareae) showed that the nuclear and the plastid topologies might be incongruent, and the systematic position of the Hedysarum sect. Stracheya clade was uncertain. In this study, phylogenetic relationships of Hedysarum were investigated based on the nuclear ITS, ETS, PGDH, SQD1, TRPT and the plastid psbA-trnH, trnC-petN, trnL-trnF, trnS-trnG, petN-psbM sequences. Both nuclear and plastid data support two major lineages in Hedysarum: the Hedysarum s. s. clade and the Sartoria clade. In the nuclear tree, Hedysarum is biphyletic with the Hedysarum s. s. clade sister to the Corethrodendron + Eversmannia + Greuteria + Onobrychis clade (the CEGO clade), whereas the Sartoria clade is sister to the genus Taverniera DC. In the plastid tree, Hedysarum is monophyletic and sister to Taverniera. The incongruent position of the Hedysarum s. s. clade between the nuclear and plastid trees may be best explained by a chloroplast capture hypothesis via introgression. The Hedysarum sect. Stracheya clade is resolved as sister to the H. sect. Hedysarum clade in both nuclear and plastid trees, and our analyses support merging Stracheya into Hedysarum. Based on our new evidence from multiple sequences, Hedysarum is not monophyletic, and its generic delimitation needs to be reconsidered., National Natural Science Foundation of ChinaNational Natural Science Foundation of China [30270106, 30870155]; China Scholarship CouncilChina Scholarship Council [201406300108], This work was supported by the National Natural Science Foundation of China (www.nsfc.gov.cn, grant numbers 30270106, 30870155, to ZYC) and China Scholarship Council (www.csc.edu.cn, grant number 201406300108, to PLL). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
- Published
- 2017
29. Polyphyly of the Padus group of Prunus (Rosaceae) and the evolution of biogeographic disjunctions between eastern Asia and eastern North America
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Ze-Long Nie, Zhao-Yang Chang, Zong-Suo Liang, Jun Wen, Gabriel Johnson, and Xiao-Lin Liu
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Phylogenetic tree ,Asia, Eastern ,Biogeography ,Molecular Sequence Data ,Sequence Homology ,Plant Science ,Sequence Analysis, DNA ,Biology ,Biological Evolution ,Polymerase Chain Reaction ,Prunus ,Taxon ,Phylogenetics ,Polyphyly ,Botany ,DNA, Ribosomal Spacer ,North America ,Plastids ,Subgenus ,Phylogeny ,NdhF ,Plant Proteins - Abstract
Prunus subgenus Padus is a group with a wide distribution in temperate eastern Asia and eastern North America with one species extending to Europe and one to Central America. Phylogenetic relationships of subgenus Padus were reconstructed using sequences of nuclear ribosomal ITS, and plastid ndhF gene, and rps16 intron and rpl16 intron. Prunus subgenus Padus is shown to be polyphyletic. Taxa of subgenus Padus and subgenus Laurocerasus are highly intermixed in both the ITS and the plastid trees. The results support two disjunctions between eastern North America and Eurasia within the Padus group. One disjunction is between Prunus virginiana of eastern North America and P. padus of Eurasia, estimated to have diverged at 2.99 (95 % HPD 0.59–6.15)–4.1 (95 % HPD 0.63–8.59) mya. The other disjunction is between P. serotina and its Asian relatives. The second disjunction may have occurred earlier than the former one, but the age estimate is difficult due to the unresolved phylogenetic position of the P. serotina complex.
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- 2011
30. A New Species ofAstragalus(Leguminosae) from Northwestern Xinjiang, China
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Xiao-lin, Liu, primary, Xiao-na, Yue, additional, Zhao-yang, Chang, additional, and Lang-ran, Xu, additional
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- 2011
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31. Phylogeny of Hedysarum and tribe Hedysareae (Leguminosae: Papilionoideae) inferred from sequence data of ITS, matK, trnL-F and psbA-trnH.
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Lei Duan, Jun Wen, Xue Yang, Pei-Liang Liu, Arslan, Emine, Ertuğrul, Kuddisi, and Zhao-Yang Chang
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HEDYSARUM ,LEGUMES ,POPULATION genetics ,BIOGEOGRAPHY ,PHYLOGENY ,GENETIC speciation - Abstract
Based on sequence data of the nuclear ITS and plastid matK, trnL-F and psbA-trnH markers of 162 species (169 accessions), the relationships and monophyly of tribe Hedysareae and its close relatives were assessed, with special reference to the infrageneric phylogeny of Hedysarum. The results showed that Hedysareae sensu Lock is not monophyletic, and its relationships with tribe Galegeae are unclear. Tribe Galegeae is polyphyletic. Fledysareae sensu Lock includes two strongly supported clades: the Caraganean clade and the Hedysaroid clade. Tribe Caraganeae Ranjbar was supported to be recognized based on the Caraganean clade, but it is herein suggested to be re-circumscribed by excluding Chesneya and Gueldenstaedtia. Our results support treating the Hedysaroid clade as tribe Hedysareae, comprising nine genera: Alhagi, Corethrodendron, Ebenus, Eversmannia, Greuteria, Hedysarum, Onobrychis, Sulla and Taverniera. Hedysarum as delimited here consists of three main clades: the first clade (the mesic group) corresponds to H. sect. Hedysarum; the second clade (the xeric group) is the re-defined H. sect. Multicaulia, consisting of the core group of H. sect. Multicaulia plus the former genus Sartorio-, and the third clade (the psychrophilic group) includes the monospecific H. sect. Stracheya (with H. tibeticum) and two species previously placed in H. sect. Multicaulia (H. kumaonense, H. lehmannianum). [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
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