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中国科学院昆明植物研究所知识管理系统
Knowledge Management System of Kunming Institute of Botany,CAS
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GST, P < 0.05) were exhibited by this species. The SAMOVA revealed seven diverging groups of related chlorotypes, six of them had distinct nonoverlapping geographical ranges: one in the northeast comprising 10 populations, a second with a southeast distribution comprising 22 populations, and the remaning four groups comprising 15 populations located in the west part of the species’ range along different river valleys. The genetic clustering of populations into three regions was also supported by analysis of molecular variance, which showed that most genetic variation (82.43%) was found among these three regions. Two clusters were distinguished by both phylogenetic analysis and genealogical analysis of chlorotypes, one consisting of chlorotypes from the western region and the second consisting of those from the eastern region. Significant genetic differences between the two regions might be attributed to vicariance and restricted gene flow, and this vicariance could be explained by the physical environmental heterogeneity on each side of the Tanaka-Kaiyong Line. Following the uplift of the Tibetan Plateau, the reorganization of the major river drainages was primarily caused by river separation and capture events. These historical events could change the distribution of S. davidii from fragmented to continuous (Upper/Lower Jinshajiang and Yalongjiang/Daduhe), and from continuous to fragmented (Nujiang and Jinshajiang/Honghe). However, spatial and temporal patterns of phylogeographic divergence are strongly associated with historical disjunction rather than modern drainage connections. Moreover, the following north-south split in the eastern region and effective isolation with their genetic diversity were essentially modelled by genetic drift. The higher chlorotype richness and genetic divergence for populations in western region compared with other two regions suggests that there were multipe refugia or in situ survival of S. davidii in the Himalayan-Hengduan Mountain region. Fixation of chlorotypes in the northeastern region and near fixation in the southeastern region suggest a recent colonization of these areas. We further found that this species underwent past range expansion around 37-303 thousand years ago (kya). The southeastern populations likely experienced a demographic expansion via unidirectional gene flow along rivers, while northeastern populations underwent a more northward expansion, both from initial populations (s) (21, 22, 23) preserved on eastern refugia (Jinshajiang). This process might have been accompanied with a series of founder effects or bottlenecks making populations genetically impoverished. 3. Phylogeographic analysisbased on nuclear sequence，We sequenced the nuclear (ncpGS) region in all populations sampled, recovering 23 nuclear haplotypes. Compared to cpDNA, both NST (0.470) and GST (0.338) were relatively lower, but NST was also significantly larger than GST. 37.10% of the total variation was distributed among regions which was much lower than that shown by chlorotypes. Thus, more extensive distribution of nuclear haplotypes was exhibited across the geographical range instead of the strong population subdivision observed in chlorotypes. Similarly to the chloroplast data, we found that genetic differentiation of nDNA was positively correlated with the geographical distance, but the increase in the geographical distance between populations did not increase the genetic differentiation of nDNA as rapidly as that of cpDNA. These contrasting levels between the chloroplast and nuclear genomes of S. davidii are likely due to limited gene flow of cpDNA by seeds vs. the extensive gene flow of nDNA by wind-mediated pollen in the population history. We also determined from nuclear markers that haplotype diversity was reduced in the southeastern and northeastern regions due to the loss of rare haplotypes in western region. This reduction of gene diversity is also a signature of founder events or recent bottleneck during post-glacial colonization. However, nuclear diversity within populations remains high. This provides evidence that regionally pollen flow might be sufficiently high to blur the genetic identity of founder populations over a reasonably large spatial scale.3. Relationships among three varieties，The phylogenetic analysis identified two phylogroups of chlorotypes, corresponding to S. davidii var. davidii and var. chuansinesis. The former was distinguished by the abscence of predonminant nuclear haplotype H1 of the latter. The monophyletic group of chlorotypes in var. davidii and var. liangshanesis showed their relatively close relationship. And their genetic divergence from the third variety appears to be relative to their slight morphological difference in leaf size and the divergent environmental niche spaces they occupy. Thus, the observed differences in morphological characters between var. chuansinesis and other two varieties can be explained by the seed dispersal limitation illustrated above (as inferred by geographical separation) and by environmental heterogeneity (as inferred by precipitation or elevation) or by a combination of both. After all, the geological changes, drainage reorganization, and floristic differences following the Himalayan uplift have been suggested to affect the genetic structure of S. davidii. These results provide new insights into the phylogeographic pattern of plants in China. In addition, the unique population genetic structure found in S. davidii has provided important insights into the evolutionary history of this species. The genetic profile uncovered in this study is also critical for its conservation management. Our study has uncovered the existence of at least two ‘evolutionary significant units’ independent units within S. davidii, corresponding to var. davidii from eastern region and var. chuansinensis from western region. The conservation efforts should first focus on most western populations and on the southeastern ones exhibiting high levels of genetic diversity, while the genetically homogeneous northeastern populations located in the degraded Loess Plateau should require much greater conservation 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Differences in pseudogene evolution contributed to the contrasting flavors of turnip and Chiifu, two Brassica rapa subspecies
期刊论文
PLANT COMMUNICATIONS, 2023, 卷号: 4, 期号: 1, 页码: 100427
作者:
Yin,Xin
;
Yang,Danni
;
Zhao,Youjie
;
Yang,Xingyu
;
Zhou,Zhili
;
Sun,Xudong
;
Kong,Xiangxiang
;
Li,Xiong
;
Wang,Guangyan
;
Duan,Yuanwen
;
Yang,Yunqiang
;
Yang,Yongping
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提交时间：2024/07/17
turnip genome
comparative genomics
pseudogene evolution
GSL biosynthesis
flavor
Brassicaceae lineage -specific polyploidization events (whole
WHOLE-GENOME TRIPLICATION
PHYLOGENETIC ANALYSIS
GLUCOSINOLATE CONTENT
ARABIDOPSIS
IDENTIFICATION
OLERACEA
EXPRESSION
SEQUENCE
ORIGIN
DIVERSIFICATION
Phylogenomic insights into the reticulate evolution of Camellia sect. Paracamellia Sealy (Theaceae)
期刊论文
JOURNAL OF SYSTEMATICS AND EVOLUTION, 2023
作者:
Qin,Sheng-Yuan
;
Chen,Kai
;
Zhang,Wen-Ju
;
Xiang,Xiao-Guo
;
Zuo,Zheng-Yu
;
Guo,Cen
;
Zhao,Yao
;
Li,Lin-Feng
;
Wang,Yu-Guo
;
Song,Zhi-Ping
;
Yang,Ji
;
Yang,Xiao-Qiang
;
Zhang,Jian
;
Jin,Wei-Tao
;
Wen,Qiang
;
Zhao,Song-Zi
;
Chen,Jia-Kuan
;
Li,De-Zhu
;
Rong,Jun
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浏览/下载：6/2
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提交时间：2024/07/10
Camellia oleifera
hybridization
phylogenomics
plastome
polyploidization
transcriptome
EVERGREEN BROADLEAVED FORESTS
HISTORY
DYNAMICS
OLEIFERA
CHINA
PHYLOGEOGRAPHY
ALIGNMENT
TREE
A clue to the evolutionary history of modern East Asian flora: Insights from phylogeography and diterpenoid alkaloid distribution pattern of the Spiraea japonica complex
期刊论文
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2023, 卷号: 184, 页码: 107772
作者:
Luo,Dong
;
Song,Min-shu
;
Xu,Bo
;
Zhang,Yu
;
Zhang,Jian-wen
;
Ma,Xiang-guang
;
Hao,Xiao jiang
;
Sun,Hang
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浏览/下载：1/1
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提交时间：2024/07/25
ampliative Spiraea japonica complex
East Asian flora
Transition belt
Phylogeography
Diterpenoid alkaloids
MOLECULAR PHYLOGEOGRAPHY
SECONDARY METABOLITES
HENGDUAN MOUNTAINS
QUATERNARY CLIMATE
PLANT DIVERSITY
ROSACEAE
DNA
CHLOROPLAST
COALESCENT
CHINA
Deciphering complex reticulate evolution of Asian Buddleja (Scrophulariaceae): insights into the taxonomy and speciation of polyploid taxa in the Sino-Himalayan region
期刊论文
ANNALS OF BOTANY, 2023
作者:
Yang,Fengmao
;
Ge,Jia
;
Guo,Yongjie
;
Olmstead,Richard
;
Sun,Weibang
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浏览/下载：35/4
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提交时间：2024/05/09
Buddleja
phylogenomics
reticulate evolution
polyploidy
plastid genome
low-copy nuclear gene
HYBRIDIZATION
ALIGNMENT
DIVERSIFICATION
ALLOPOLYPLOIDY
PHYLOGENETICS
FRAMEWORK
NUCLEAR
ROBUST
FLOW
Genome size variation and polyploidy prevalence in the genus Eragrostis are associated with the global dispersal in arid area
期刊论文
FRONTIERS IN PLANT SCIENCE, 2023, 卷号: 14, 页码: 1066925
作者:
Hutang,Ge-Ran
;
Tong,Yan
;
Zhu,Xun-Ge
;
Gao,Li-Zhi
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浏览/下载：21/4
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提交时间：2024/05/09
genome size
phylogeny
Eragrostis
adaptation
environmental factors
GRASS SUBFAMILY CHLORIDOIDEAE
NUCLEAR-DNA CONTENT
TEF ZUCC TROTTER
CHROMOSOME-NUMBERS
PHYLOGENETIC SIGNAL
NICHE CONSERVATISM
MOLECULAR PHYLOGENY
DROUGHT TOLERANCE
MODEL SELECTION
SOUTH-AFRICAN
Gradual genome size evolution and polyploidy in Allium from the Qinghai-Tibetan Plateau
期刊论文
ANNALS OF BOTANY, 2022
作者:
Wang, Guangyan
;
Zhou, Ning
;
Chen, Qian
;
Yang, Ya
;
Yang, Yongping
;
Duan, Yuanwen
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浏览/下载：39/10
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提交时间：2024/04/30
Genome size evolution
polyploidy
adaptation
ecological factors
seed mass
Allium
Qinghai-Tibetan Plateau
NUCLEAR-DNA CONTENT
CONSTRAINT HYPOTHESIS
FLOW-CYTOMETRY
PLANT TRAITS
C-VALUE
MECHANISMS
ASTERACEAE
PHYLOGENY
AMARYLLIDACEAE
INFORMATION
Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms
期刊论文
nature plants, 2021
作者:
Gregory W. Stull
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浏览/下载：331/100
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提交时间：2021/08/23
Gradual genome size evolution and polyploidy in Allium from the Qinghai-Tibetan Plateau
期刊论文
ANNALS OF BOTANY, 2021
作者:
Wang,Guangyan
;
Zhou,Ning
;
Chen,Qian
;
Yang,Ya
;
Yang,Yongping
;
Duan,Yuanwen
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浏览/下载：73/0
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提交时间：2022/04/02
Genome size evolution
polyploidy
adaptation
ecological factors
seed mass
Allium
Qinghai-Tibetan Plateau
NUCLEAR-DNA CONTENT
CONSTRAINT HYPOTHESIS
FLOW-CYTOMETRY
PLANT TRAITS
C-VALUE
MECHANISMS
ASTERACEAE
PHYLOGENY
AMARYLLIDACEAE
INFORMATION
Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae
期刊论文
MOLECULAR PLANT, 2021, 卷号: 14, 期号: 5, 页码: 748-773
作者:
Zhao,Yiyong
;
Zhang,Rong
;
Jiang,Kai-Wen
;
Qi,Ji
;
Hu,Yi
;
Guo,Jing
;
Zhu,Renbin
;
Zhang,Taikui
;
Egan,Ashley N.
;
Yi,Ting-Shuang
;
Huang,Chien-Hsun
;
Ma,Hong
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浏览/下载：78/0
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提交时间：2022/04/02
Fabaceae
Leguminosae
nuclear phylogeny
divergence times
whole-genome duplication
rhizobial nodulation
COMPARATIVE GENOMICS
PHYLOGENETIC PERSPECTIVES
EARLY DIVERSIFICATION
PENALIZED LIKELIHOOD
ANCESTRAL POLYPLOIDY
MOLECULAR EVOLUTION
LOTUS-JAPONICUS
ANALYSES REVEAL
GENE
LEGUMINOSAE
Expansion and expression diversity of FAR1/FRS-like genes provides insights into flowering time regulation in roses
期刊论文
PLANT DIVERSITY, 2021, 卷号: 43, 期号: 2, 页码: 173-179
作者:
Zhong,Mi-Cai
;
Jiang,Xiao-Dong
;
Cui,Wei-Hua
;
Hu,Jin-Yong
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Adobe PDF(3291Kb)
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浏览/下载：190/47
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提交时间：2022/04/02
Rose
FAR1/FRS-Like genes
Gene family expansion
Flowering time
Shoot growth behavior
RED ELONGATED HYPOCOTYL3
TRANSCRIPTION FACTORS
ARABIDOPSIS FHY3
LIGHT
RESPONSES
BIOSYNTHESIS
DUPLICATION
PHYTOCHROME
EVOLUTION
ROKSN
