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Li M, Yang Y, Xu R, Mu W, Li Y, Mao X, Zheng Z, Bi H, Hao G, Li X, Xu X, Xi Z, Shrestha N, Liu J. A chromosome-level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae). Mol Ecol Resour 2021; 21:1186-1199. [PMID: 33486895 DOI: 10.1111/1755-0998.13334] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 12/01/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022]
Abstract
Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early-diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they survived during repeated climatic oscillations in the Quaternary. We sequenced the genome of Te. sinense and compared it with that of Tr. aralioides. We found that Te. sinense has a smaller genome size (986.3 Mb) than that of Tr. aralioides (1610 Mb). Repetitive elements made the major contribution to the contrasting genome sizes in the two species, with most bursts of repeats occurring within the past four million years when the climate oscillated greatly. These species share two rounds of whole-genome duplications. The mainland species Te. sinense had a larger effective population size than the island species Tr. aralioides after the largest glaciation during the Quaternary climatic oscillation. However, soon after this recovery stage, the effective population sizes of both species continued to decrease, although the current effective population size of Te. sinense is still larger than that of Tr. aralioides. We recovered three distinctly diverged clades through resequencing the genomes of 50 individuals across the distributional range of Te. sinense in China. Our results provide an important genomic resource with which to examine early trait evolution in the core eudicots and assist efforts to conserve this relict tree species.
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Affiliation(s)
- Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Renping Xu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hao Bi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guoqian Hao
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan, China
| | - Xiaojie Li
- Emeishan Biological Resources Experimental Station, Emei, China
| | - Xiaoting Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Wang Z, Jiang Y, Bi H, Lu Z, Ma Y, Yang X, Chen N, Tian B, Liu B, Mao X, Ma T, DiFazio SP, Hu Q, Abbott RJ, Liu J. Hybrid speciation via inheritance of alternate alleles of parental isolating genes. MOLECULAR PLANT 2021; 14:208-222. [PMID: 33220509 DOI: 10.1016/j.molp.2020.11.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/11/2020] [Accepted: 11/13/2020] [Indexed: 05/21/2023]
Abstract
It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change in chromosome number, is an important mechanism of speciation. HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities. HHS requires the establishment of reproductive isolation between a hybrid and its parents, but the underlying genes and genetic mechanisms remain largely unknown. In this study, we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of alternate alleles at genes that determine parental premating isolation. The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron. We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent. In this way, it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation (iron tolerance). These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers.
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Affiliation(s)
- Zefu Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Hao Bi
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China; CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Yazhen Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ningning Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Bin Tian
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry and Grassland Administration, Southwest Forestry University, Kunming 650224, China
| | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan 030006, China
| | - Xingxing Mao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 25606, USA
| | - Quanjun Hu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China.
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews KY16 9TH, UK.
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China; State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China.
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53
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Siddique H, Xu Z, Li X, Saeed S, Liang W, Wang X, Gao C, Dai R, Wang Z, Zhang Z. Anomalous Octahedron Distortion of Bi-Alloyed Cs 2AgInCl 6 Crystal via XRD, Raman, Huang-Rhys Factor, and Photoluminescence. J Phys Chem Lett 2020; 11:9572-9578. [PMID: 33119319 DOI: 10.1021/acs.jpclett.0c02852] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The refinement of XRD patterns only provides the average structure parameters for the alloying materials because of the symmetric protection. Raman vibrational modes can append the detailed information about the bond length and structure. The refinements of XRD patterns for Bi alloying Cs2AgInCl6 revealed the strong structure distortion with the enlarged octahedron of In(Bi)Cl6 and the contracted octahedron of AgCl6 with the increasing Bi. Raman spectra supported the expanded octahedron of InCl6 and the reduced octahedron of AgCl6 but identified the anomalous shortening bond length of Bi-Cl with the increasing Bi. These distorting octahedrons break parity forbidden transition, modify Huang-Rhys factor, and result in the maximum values at 30% Bi alloying and the same variation trend for both photoluminescence and Huang-Rhys factor with the increasing Bi alloying.
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Affiliation(s)
- Hassan Siddique
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zilong Xu
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiangdong Li
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Sara Saeed
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wentao Liang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiangqi Wang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chan Gao
- The Centre for Physical Experiments, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rucheng Dai
- The Centre for Physical Experiments, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhongping Wang
- The Centre for Physical Experiments, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zengming Zhang
- The Centre for Physical Experiments, University of Science and Technology of China, Hefei, Anhui 230026, China
- Key Laboratory of Strongly-Coupled Quantum Matter Physics, Chinese Academy of Sciences, School of Physical Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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54
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Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data. FORESTS 2020. [DOI: 10.3390/f11111192] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Research highlights: Our study is the first to explore the genetic composition of ancient Cryptomeria trees across a distribution range in China. Background and objectives: Cryptomeria japonica var. sinensis is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike Cryptomeria in Japan, genetic Chinese Cryptomeria has seldom been studied, although there is ample evidence of its great ecological and economic value. Materials and methods: Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese Cryptomeria through ddRAD-seq technology. Results: The results reveal a lower genetic variation but higher genetic differentiation (Ho = 0.143, FST = 0.1204) than Japanese Cryptomeria (Ho = 0.245, FST = 0.0455). The 86% within-population variation is based on an analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. Structure analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. A demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese Cryptomeria had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that the strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species’ unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.
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Ye Z, Chen D, Yuan J, Zheng C, Yang X, Wang W, Zhang Y, Wang S, Jiang K, Bu W. Are population isolations and declines a threat to island endemic water striders? A lesson from demographic and niche modelling of Metrocoris esakii (Hemiptera: Gerridae). Mol Ecol 2020; 29:4573-4587. [PMID: 33006793 DOI: 10.1111/mec.15669] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 12/14/2022]
Abstract
Genetic stochasticity and bottlenecking in the course of Pleistocene glaciations have been identified as threatening the survival of local endemics. However, the mechanisms by which local endemic species balance the influences of these two events remain poorly understood. Here, we generated a double-digest restriction site-associated DNA sequencing (ddRAD-seq) data set, mined mitochondrial sequences and constructed ecological niche models for the island endemic water strider Metrocoris esakii (Hemiptera: Gerridae). We found that M. esakii comprised three divergent lineages (i.e., north, central and south) isolated by geographical barriers and generally experienced population declines with the constriction of suitable areas during the Last Glacial Maximum (LGM). Further demographic model testing and stairway plots revealed a history of recent gene flow among the neighbouring lineages and rapid recovery at the end of the LGM, indicating that M. esakii at least had the potential for an adaptive response to population fragmentation and bottlenecking. The northern lineage did not show genetic bottlenecking during the LGM, which was probably due to its large effective population size (Ne ) from migration, which improved its adaptive potential. Relative to the ddRAD-seq data set, the demographic results based on mitochondrial sequences were less conclusive, showing weak differentiation and oversimplified demographic trajectories for the three genetic lineages. Overall, this study provides some degree of optimism for the survival of island endemic water striders from a demographic perspective, but further evaluation of their extinction risk under the impacts of human activities is required.
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Affiliation(s)
- Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Danyang Chen
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Juanjuan Yuan
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xin Yang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenwu Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yaoyao Zhang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Siqi Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Kun Jiang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin, China
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56
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Rougemont Q, Moore JS, Leroy T, Normandeau E, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon. PLoS Genet 2020; 16:e1008348. [PMID: 32845885 PMCID: PMC7478589 DOI: 10.1371/journal.pgen.1008348] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/08/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored. Reconstruction of a species’ past demographic history from genetic data can highlight historical factors that have shaped the distribution of genetic diversity along its genome and its geographic range. Here, we combine genotyping-by-sequencing with demographic modelling to address these issues in the Coho salmon, a Pacific salmon of conservation concern in some parts of its range, notably in the south. Our demographic reconstructions reveal a linear decrease in genetic diversity toward the north of the species range, supporting the hypothesis of a northern route of postglacial recolonization from a single major southern refugium. As predicted by theory, we also observed a higher proportion of deleterious mutations in the most distant populations from this refugium. Beyond this general pattern, among-site variation in the proportion of deleterious mutations is consistent with different local trends in effective population sizes. Our results highlight the potential importance of understanding historical factors that have shaped geographic patterns of the distribution of deleterious mutations in order to implement effective management programs for the conservation of wild populations. Such fundamental knowledge of human historical demography is now having major impacts on health sciences, and we argue it is time to integrate such approaches in conservation science as well.
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Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Thibault Leroy
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B. Rondeau
- Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ruth E. Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M. Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, United States of America
| | - Penelope A. Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service and Institute of Marine Sciences, University of California–Santa Cruz, Santa Cruz, California, United States of America
| | - Terry D. Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F. Koop
- Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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Chen Z, Ai F, Zhang J, Ma X, Yang W, Wang W, Su Y, Wang M, Yang Y, Mao K, Wang Q, Lascoux M, Liu J, Ma T. Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world's southernmost poplar (Populus ilicifolia). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:430-442. [PMID: 32168389 DOI: 10.1111/tpj.14744] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 02/04/2020] [Accepted: 03/02/2020] [Indexed: 05/16/2023]
Abstract
Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome-wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (Ne ) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome-wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species.
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Affiliation(s)
- Zeyuan Chen
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Fandi Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Junlin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Xinzhi Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Wenlu Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Weiwei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yutao Su
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Mingcheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Qingfeng Wang
- Key Laboratory of Aquatic Botany and Watershed Ecology, The Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen, 18D 75326, Uppsala, Sweden
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, 610065, China
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Sun Y, Deng T, Zhang A, Moore MJ, Landis JB, Lin N, Zhang H, Zhang X, Huang J, Zhang X, Sun H, Wang H. Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization. iScience 2020; 23:101124. [PMID: 32428861 PMCID: PMC7232092 DOI: 10.1016/j.isci.2020.101124] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/20/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.
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Affiliation(s)
- Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Tao Deng
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Aidi Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | | | - Jacob B Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA; School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, USA
| | - Nan Lin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC, USA
| | - Xiujun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.
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Leitwein M, Duranton M, Rougemont Q, Gagnaire PA, Bernatchez L. Using Haplotype Information for Conservation Genomics. Trends Ecol Evol 2020; 35:245-258. [DOI: 10.1016/j.tree.2019.10.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/18/2019] [Accepted: 10/28/2019] [Indexed: 12/19/2022]
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Chen Y, Ma T, Zhang L, Kang M, Zhang Z, Zheng Z, Sun P, Shrestha N, Liu J, Yang Y. Genomic analyses of a “living fossil”: The endangered dove‐tree. Mol Ecol Resour 2020; 20. [DOI: 10.1111/1755-0998.13138] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 12/18/2022]
Affiliation(s)
- Yang Chen
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Tao Ma
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Lushui Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Minghui Kang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Zhiyang Zhang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Pengchuan Sun
- School of Life Sciences North China University of Science and Technology Caofeidian, Tangshan China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Jianquan Liu
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
| | - Yongzhi Yang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of Education & State Key Lab of Hydraulics & Mountain River Engineering College of Life Sciences Sichuan University Chengdu China
- State Key Laboratory of Grassland Agro‐Ecosystem Institute of Innovation Ecology Lanzhou University Lanzhou China
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Yang X, Wang Z, Zhang L, Hao G, Liu J, Yang Y. A chromosome-level reference genome of the hornbeam, Carpinus fangiana. Sci Data 2020; 7:24. [PMID: 31964866 PMCID: PMC6972722 DOI: 10.1038/s41597-020-0370-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/11/2019] [Indexed: 11/24/2022] Open
Abstract
Betulaceae, the birch family, comprises six living genera and over 160 species, many of which are economically valuable. To deepen our knowledge of Betulaceae species, we have sequenced the genome of a hornbeam, Carpinus fangiana, which belongs to the most species-rich genus of the Betulaceae subfamily Coryloideae. Based on over 75 Gb (~200x) of high-quality next-generation sequencing data, we assembled a 386.19 Mb C. fangiana genome with contig N50 and scaffold N50 sizes of 35.32 kb and 1.91 Mb, respectively. Furthermore, 357.84 Mb of the genome was anchored to eight chromosomes using over 50 Gb (~130x) Hi-C sequencing data. Transcriptomes representing six tissues were sequenced to facilitate gene annotation, and over 5.50 Gb high-quality data were generated for each tissue. The structural annotation identified a total of 27,381 protein-coding genes in the assembled genome, of which 94.36% were functionally annotated. Additionally, 4,440 non-coding genes were predicted. Measurement(s) | DNA • RNA • sequence_assembly • sequence feature annotation | Technology Type(s) | DNA sequencing • RNA sequencing • genome assembly • sequence annotation | Sample Characteristic - Organism | Carpinus fangiana |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11382390
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Affiliation(s)
- Xiaoyue Yang
- Stat Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000, Lanzhou, China
| | - Zefu Wang
- Stat Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610000, Sichuan, China
| | - Lei Zhang
- Stat Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610000, Sichuan, China
| | - Guoqian Hao
- Sichuan Tea College, Yibin University, Yibin, 644007, Sichuan, China
| | - Jianquan Liu
- Stat Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000, Lanzhou, China.,Stat Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610000, Sichuan, China
| | - Yongzhi Yang
- Stat Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000, Lanzhou, China.
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Lim DU, Choi S, Kim S, Choi YJ, Lee S, Kang MS, Kim YH, Cho JH. All-Inkjet-Printed Vertical Heterostructure for Wafer-Scale Electronics. ACS NANO 2019; 13:8213-8221. [PMID: 31260260 DOI: 10.1021/acsnano.9b03428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, we fabricated an array of all-inkjet-printed vertical Schottky barrier (SB) transistors and various logic gates on a large-area substrate. All of the electronic components, including the indium-gallium-zinc-oxide (IGZO) semiconductor, reduced graphene oxide (rGO), and indium-tin-oxide (ITO) electrodes, and the ion-gel gate dielectric, were directly and uniformly printed onto a 4 in. wafer. The vertical SB transistors had a vertically stacked structure, with the inkjet-printed IGZO semiconductor layer placed between the rGO source electrode and the ITO drain electrode. The ion-gel gate dielectric was also inkjet-printed in a coplanar gate geometry. The channel current was controlled by adjusting the SB height at the rGO/IGZO heterojunction under application of an external gate voltage. The high intrinsic capacitance of the ion-gel gate dielectric facilitated modulation of the SB height at the source/channel heterojunction to around 0.5 eV at a gate voltage lower than 2 V. The resulting vertical SB transistors exhibited a high current density of 2.0 A·cm-2, a high on-off current ratio of 106, and excellent operational and environmental stabilities. The simple device structure of the vertical SB transistors was beneficial for the fabrication of all-inkjet-printed low-power logic circuits such as the NOT, NAND, and NOR gates on a large-area substrate.
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Affiliation(s)
- Dong Un Lim
- Department of Chemical and Biomolecular Engineering , Yonsei University , Seoul 03722 , Korea
| | | | | | | | | | - Moon Sung Kang
- Department of Chemical and Biomolecular Engineering , Sogang University , Seoul 04107 , Korea
| | | | - Jeong Ho Cho
- Department of Chemical and Biomolecular Engineering , Yonsei University , Seoul 03722 , Korea
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