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Lin L, Jiang XL, Guo KQ, Byrne A, Deng M. Climate change impacts the distribution of Quercus section Cyclobalanopsis (Fagaceae), a keystone lineage in East Asian evergreen broadleaved forests. PLANT DIVERSITY 2023; 45:552-568. [PMID: 37936812 PMCID: PMC10625921 DOI: 10.1016/j.pld.2023.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 11/09/2023]
Abstract
East Asian evergreen broadleaved forests (EBFLs) harbor high species richness, but these ecosystems are severely impacted by global climate change and deforestation. Conserving and managing EBLFs requires understanding dominant tree distribution dynamics. In this study, we used 29 species in Quercus section Cyclobalanopsis-a keystone lineage in East Asian EBLFs-as proxies to predict EBLF distribution dynamics using species distribution models (SDMs). We examined climatic niche overlap, similarity, and equivalency among seven biogeographical regions' species using 'ecospat'. We also estimated the effectiveness of protected areas in the predicted range to elucidate priority conservation regions. Our results showed that the climatic niches of most geographical groups differ. The western species under the Indian summer monsoon regime were mainly impacted by temperature factors, whereas precipitation impacted the eastern species under the East Asian summer monsoon regime. Our simulation predicted a northward range expansion of section Cyclobalanopsis between 2081 and 2100, except for the ranges of the three Himalayan species analyzed, which might shrink significantly. The greatest shift of highly suitable areas was predicted for the species in the South Pacific, with a centroid shift of over 300 km. Remarkably, only 7.56% of suitable habitat is currently inside protected areas, and the percentage is predicted to continue declining in the future. To better conserve Asian EBLFs, establishing nature reserves in their northern distribution ranges, and transplanting the populations with predicted decreasing numbers and degraded habitats to their future highly suitable areas, should be high-priority objectives.
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Affiliation(s)
- Lin Lin
- School of Ecology and Environmental Sciences, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming 650500, Yunnan, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of BioResources in Yunnan, Yunnan University, Kunming 650500, Yunnan, China
| | - Xiao-Long Jiang
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
| | - Kai-Qi Guo
- College of Forestry, Central South University of Forestry and Technology, Changsha 410004, Hunan, China
- Shanghai Chenshan Botanical Garden, Shanghai 201602, China
| | - Amy Byrne
- The Morton Arboretum, Lile, IL 60532-1293, USA
| | - Min Deng
- School of Ecology and Environmental Sciences, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, Yunnan University, Kunming 650500, Yunnan, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of BioResources in Yunnan, Yunnan University, Kunming 650500, Yunnan, China
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Denk T, Grimm GW, Hipp AL, Bouchal JM, Schulze ED, Simeone MC. Niche evolution in a northern temperate tree lineage: biogeographical legacies in cork oaks (Quercus section Cerris). ANNALS OF BOTANY 2023; 131:769-787. [PMID: 36805162 PMCID: PMC10184457 DOI: 10.1093/aob/mcad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/15/2023] [Indexed: 05/16/2023]
Abstract
BACKGROUND AND AIMS Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Despite being a small clade, they display a range of leaf morphologies comparable to the largest sections (>100 spp.) in Quercus. Their fossil record extends back to the Eocene. Here, we explore how cork oaks achieved their modern ranges and how legacy effects might explain niche evolution in modern species of section Cerris and its sister section Ilex, the holly oaks. METHODS We inferred a dated phylogeny for cork and holly oaks using a reduced-representation next-generation sequencing method, restriction site-associated DNA sequencing (RAD-seq), and used D-statistics to investigate gene flow hypotheses. We estimated divergence times using a fossilized birth-death model calibrated with 47 fossils. We used Köppen profiles, selected bioclimatic parameters and forest biomes occupied by modern species to infer ancestral climatic and biotic niches. KEY RESULTS East Asian and Western Eurasian cork oaks diverged initially in the Eocene. Subsequently, four Western Eurasian lineages (subsections) differentiated during the Oligocene and Miocene. Evolution of leaf size, form and texture was correlated, in part, with multiple transitions from ancestral humid temperate climates to mediterranean, arid and continental climates. Distantly related but ecologically similar species converged on similar leaf traits in the process. CONCLUSIONS Originating in temperate (frost-free) biomes, Eocene to Oligocene ranges of the primarily deciduous cork oaks were restricted to higher latitudes (Siberia to north of Paratethys). Members of the evergreen holly oaks (section Ilex) also originated in temperate biomes but migrated southwards and south-westwards into then-(sub)tropical southern China and south-eastern Tibet during the Eocene, then westwards along existing pre-Himalayan mountain ranges. Divergent biogeographical histories and deep-time phylogenetic legacies (in cold and drought tolerance, nutrient storage and fire resistance) thus account for the modern species mosaic of Western Eurasian oak communities, which are composed of oaks belonging to four sections.
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Affiliation(s)
- Thomas Denk
- Department of Palaeobiology, Swedish Museum of Natural History, 10405 Stockholm, Sweden
| | | | | | - Johannes M Bouchal
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | | | - Marco C Simeone
- Department of Agricultural and Forestry Sciences, University of Tuscia, 01100 Viterbo, Italy
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Lu WX, Zhang BH, Zhang YY, Yang SC. Differentiation of Cold Tolerance in an Artificial Population of a Mangrove Species, Kandelia obovata, Is Associated With Geographic Origins. FRONTIERS IN PLANT SCIENCE 2022; 12:695746. [PMID: 35185942 PMCID: PMC8851163 DOI: 10.3389/fpls.2021.695746] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Temperature is one of the climatic factors that shape the geographic distribution of plant populations. Mangroves are temperature-sensitive plants, and their distributions are severely limited by low temperatures. It is unknown, however, to what extent temperature contributes to their population differentiation and evolution. Kandelia obovata (Rhizophoraceae) is a mangrove species with high cold tolerance in the Northern Hemisphere. We investigated the phenotypic responses of an artificial population of K. obovata, with plants transplanted from different source populations, to extremely low temperatures during winter of 2015-2016 in Yueqing County (28°20'N), Zhejiang Province of China. Using two binary traits, "with/without leaves alive on the branches" and "with/without alive buds on the tips of branches," we classified plants in this artificial population into strong, moderate and poor cold resistance groups. We further assessed the genetic diversity, structure and differentiation of these three groups, as well as five natural populations along a latitudinal gradient using ten nuclear and six plastid microsatellite markers. Microsatellite data revealed genetic differentiation among the natural populations along the latitudinal gradient. Molecular data indicated that the cold tolerance of three groups in the artificial population was associated with their geographic origins, and that the most cold-tolerant group came from the northernmost natural population. Our study thus indicates that natural populations of K. obovata may have evolved divergent capacity of cold tolerance.
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Affiliation(s)
- Wen-Xun Lu
- College of the Environment and Ecology, Xiamen University, Xiamen, China
- School of Life Sciences, Peking University, Beijing, China
| | - Bing-Huang Zhang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yuan-Ye Zhang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Sheng-Chang Yang
- College of the Environment and Ecology, Xiamen University, Xiamen, China
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Cardoni S, Piredda R, Denk T, Grimm GW, Papageorgiou AC, Schulze E, Scoppola A, Salehi Shanjani P, Suyama Y, Tomaru N, Worth JRP, Cosimo Simeone M. 5S-IGS rDNA in wind-pollinated trees (Fagus L.) encapsulates 55 million years of reticulate evolution and hybrid origins of modern species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:909-926. [PMID: 34808015 PMCID: PMC9299691 DOI: 10.1111/tpj.15601] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 11/02/2021] [Accepted: 11/18/2021] [Indexed: 05/31/2023]
Abstract
Standard models of plant speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality in wind-pollinated trees with long evolutionary histories is more complex: species evolve from other species through isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Therefore, it can provide unique insights into the dynamic speciation processes of lineages that diversified tens of millions of years ago. Here, we provide the first high-throughput sequencing (HTS) of the 5S intergenic spacers (5S-IGS) for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata - F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4963 unique 5S-IGS variants reflect a complex history of hybrid origins, lineage sorting, mixing via secondary gene flow, and intra-genomic competition between two or more paralogous-homoeologous 5S rDNA lineages. We show that modern species are genetic mosaics and represent a striking case of ongoing reticulate evolution during the past 55 million years.
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Affiliation(s)
- Simone Cardoni
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Roberta Piredda
- Department of Veterinary MedicineUniversity of Bari ‘Aldo Moro’Valenzano70010Italy
| | - Thomas Denk
- Swedish Museum of Natural HistoryStockholm10405Sweden
| | | | | | | | - Anna Scoppola
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
| | - Parvin Salehi Shanjani
- Natural Resources Gene Bank, Research Institute of Forests and RangelandsAgricultural Research, Education and Extension OrganizationTehranIran
| | - Yoshihisa Suyama
- Graduate School of Agricultural ScienceTohoku UniversityOsakiMiyagi989‐6711Japan
| | - Nobuhiro Tomaru
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaAichi464‐8601Japan
| | - James R. P. Worth
- Ecological Genetics LaboratoryForestry and Forest Products Research Institute (FFPRI)TsukubaIbaraki305‐8687Japan
| | - Marco Cosimo Simeone
- Department of Agricultural and Forestry Science (DAFNE)Università degli studi della TusciaViterbo01100Italy
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Oyundelger K, Harpke D, Herklotz V, Troeva E, Zheng Z, Li Z, Oyuntsetseg B, Wagner V, Wesche K, Ritz CM. Phylogeography of Artemisia frigida (Anthemideae, Asteraceae) based on genotyping-by-sequencing and plastid DNA data: Migration through Beringia. J Evol Biol 2021; 35:64-80. [PMID: 34792226 DOI: 10.1111/jeb.13960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/03/2021] [Accepted: 11/10/2021] [Indexed: 12/20/2022]
Abstract
Artemisia frigida is a temperate grassland species that has the largest natural range among its genus, with occurrences across the temperate grassland biomes of Eurasia and North America. Despite its wide geographic range, we know little about the species' distribution history. Hence, we conducted a phylogeographical study to test the hypothesis that the species' distribution pattern is related to a potential historical migration over the 'Bering land bridge'. We applied two molecular approaches: genotyping-by-sequencing (GBS) and Sanger sequencing of the plastid intergenic spacer region (rpl32 - trnL) to investigate genetic differentiation and relatedness among 21 populations from North America, Middle Asia, Central Asia and the Russian Far East. Furthermore, we identified the ploidy level of individuals based on GBS data. Our results indicate that A. frigida originated in Asia, spread northwards to the Far East and then to North America across the Bering Strait. We found a pronounced genetic structuring between Middle and Central Asian populations with mixed ploidy levels, tetraploids in the Far East, and nearly exclusively diploids in North America except for one individual. According to phylogenetic analysis, two populations of Kazakhstan (KZ2 and KZ3) represent the most likely ancestral diploids that constitute the basally branching lineages, and subsequent polyploidization has occurred on several occasions independently. Mantel tests revealed weak correlations between genetic distance and geographical distance and climatic conditions, which indicates that paleoclimatic fluctuations may have more profoundly influenced A. frigida's spatial genetic structure and distribution than the current environment.
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Affiliation(s)
- Khurelpurev Oyundelger
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Dörte Harpke
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Seeland, Germany
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Elena Troeva
- Institute for Biological Problems of Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Zhenzhen Zheng
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Zheng Li
- School of Life Sciences, Henan University, Kaifeng, China
| | - Batlai Oyuntsetseg
- Department of Biology, School of Arts and Sciences, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Viktoria Wagner
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Karsten Wesche
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Christiane M Ritz
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany.,Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
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Kahl SM, Kappel C, Joshi J, Lenhard M. Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions. Ecol Evol 2021; 11:13986-14002. [PMID: 34707833 PMCID: PMC8525116 DOI: 10.1002/ece3.8103] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/15/2021] [Accepted: 08/23/2021] [Indexed: 01/03/2023] Open
Abstract
To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between F ST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.
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Affiliation(s)
- Sandra M. Kahl
- Biodiversity Research/Systematic BotanyInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB)BerlinGermany
| | - Christian Kappel
- GeneticsInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Jasmin Joshi
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB)BerlinGermany
- Institute for Landscape and Open SpaceEastern Switzerland University of Applied SciencesRapperswilSwitzerland
| | - Michael Lenhard
- GeneticsInstitute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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Piredda R, Grimm GW, Schulze ED, Denk T, Simeone MC. High-throughput sequencing of 5S-IGS in oaks: Exploring intragenomic variation and algorithms to recognize target species in pure and mixed samples. Mol Ecol Resour 2020; 21:495-510. [PMID: 32997899 DOI: 10.1111/1755-0998.13264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 11/30/2022]
Abstract
Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex patterns of morphological, ecological, biogeographical and genetic differentiation collide with traditional taxonomy, which measures biodiversity in number of species (or higher taxa). In this pilot study, we generated high-throughput sequencing amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S-IGS) in oaks, using six mock samples that differ in geographical origin, species composition and pool complexity. The potential of the marker for automated genotaxonomy applications was assessed using a reference data set of 1,770 5S-IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (blast) and evolutionary approaches (maximum-likelihood trees and Evolutionary Placement Algorithm). Both methods performed equally well, allowing correct identification of species in sections Ilex and Cerris in the pure and mixed samples, and main lineages shared by species of sect. Quercus. Application of different cut-off thresholds revealed that medium- to high-abundance (>10 or 25) sequences suffice for a net species identification of samples containing one or a few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogous to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units and in situ (natural) contamination. Our pipeline is highly promising for future assessments of intraspecific and interpopulation diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programmes worldwide.
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Affiliation(s)
| | - Guido W Grimm
- Orléans, France.,Department of Palaeontology, University of Vienna, Vienna, Austria
| | | | - Thomas Denk
- Swedish Museum of Natural History, Stockholm, Sweden
| | - Marco Cosimo Simeone
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli studi della Tuscia, Viterbo, Italy
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Zhang RS, Yang J, Hu HL, Xia RX, Li YP, Su JF, Li Q, Liu YQ, Qin L. A high level of chloroplast genome sequence variability in the Sawtooth Oak Quercus acutissima. Int J Biol Macromol 2020; 152:340-348. [PMID: 32109476 DOI: 10.1016/j.ijbiomac.2020.02.201] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/18/2022]
Abstract
The Sawtooth Oak, Quercus acutissima Carruth., is an economically and ecologically important tree species in the family Fagaceae with a wide distribution in China. Here, we examined its intraspecific chloroplast (cp) genome variability using available and a newly sequenced genome. The new cp genome comes from a Q. acutissima individual collected from Shenyang (Northeast China; "Q. acutissima Shenyang" in the following), and then is compared with two recently published cp genomes from Tongchuan (Northwest China) and Nanjing (East China). The cp genome of Q. acutissima Shenyang exhibits a slightly larger genome size than the other two individuals, although each encodes 86 protein-coding genes, 40 tRNA genes and eight rRNA genes. We also found the length difference for the IR/SC boundary region among the three cp genomes. Sequence comparison revealed a high intraspecific genetic divergence: the three cp genomes differ by 332 sequence patterns including 77 single nucleotide polymorphisms, and 255 indels (each gap considered) scattering across 67 regions. Phylogenetic analyses based on the cp genome recovered the split between the subgenus Cerris and the subgenus Quercus, but revealed that three Q. acutissima individuals did not cluster together, indicating that even complete cp genome data fail to reproduce species boundaries in Asian members of section Cerris. Our results show that more complete plastomes covering remote ranges needs to be sequenced to provide a solid backbone for future population-scale in-depth studies and phylogenetic analysis of section Cerris.
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Affiliation(s)
- Ru-Song Zhang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jian Yang
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Hua-Lei Hu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Run-Xi Xia
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Yu-Ping Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Jun-Fang Su
- Center for Experimental Teaching, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Qun Li
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
| | - Yan-Qun Liu
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China.
| | - Li Qin
- Department of Sericulture, College of Bioscience and Biotechnology, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
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