Investigation of genetic diversity and epidemiological characteristics of <i>Pasteurella multocida</i> isolates from poultry in southwest China by population structure, multi-locus sequence typing and virulence-associated gene profile analysis

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.

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Population structure and genetic diversity of Vibrio parahaemolyticus from a coastal area of China based on a multi-locus sequence typing (MLST) scheme

Antonie van Leeuwenhoek ◽

10.1007/s10482-019-01252-0 ◽

2019 ◽

Vol 112 (8) ◽

pp. 1199-1211

Author(s):

Yu Li ◽

Hong-Qiu Yin ◽

Jun Xia ◽

Hong Luo ◽

Ming-Yi Wang

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Coastal Area ◽

Vibrio Parahaemolyticus ◽

Multi Locus Sequence Typing ◽

Mlst Scheme

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Genetic Diversity and Population Structure of Gerbera delavayi (Asteraceae) in Southwest China: Implications for Conservation

Annales Botanici Fennici ◽

10.5735/085.054.0623 ◽

2017 ◽

Vol 54 (4-6) ◽

pp. 409-422

Author(s):

Xiao-Dan Xu ◽

Wei Zheng ◽

Long-Qing Chen ◽

Jun Wen

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Southwest China

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Genetic diversity and population structure of Gerbera delavayi Franch. revealed by newly developed genic-SSR markers

10.7287/peerj.preprints.2656v1 ◽

2016 ◽

Author(s):

Wei Zheng ◽

Xiaodan Xu

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Habitat Fragmentation ◽

Genetic Differentiation ◽

Ssr Markers ◽

Southwest China ◽

Perennial Herb ◽

Genetic Barrier ◽

Genic Ssr ◽

Wild Resources

Background: Gerbera delavayi Franch., a perennial herb native to southwest China, is of important and special value in textile and culture. Its abaxial leaves have a layer of soft fibers, which can be manually peeled, twisted into a yarn, and applied in textiles for hand-made clothes. The particular craftsmanship, unique all over the world, is a part of the intangible cultural heritage in Yunnan and Sichuan Province. To date, the wild species has become endangered because its leaves are excessively harvested for textile applications. Estimating the genetic variation of plant species is crucial for plant conservation and breeding. So, the aim of this study was to (1) provide an accurate outline of the genetic diversity and population structure of G. delavayi and (2) propose targeted conservation strategies for these wild resources. Methods: Simple sequence repeats (SSR) markers were developed from the G. delavayi transcriptome for its genetic analysis. A total of 5,179 genic-SSR markers were identified and 350 primer pairs were selected for PCR validation. After primary screening , 19 polymorphic and neutral primer pairs were used to analyze the genetic diversity and population structure of nine wild fireweed populations (a total of 204 individuals) collected from Southwest China. Results: Moderate genetic diversity (allelic richness (Ar)=3.436, Shannon’s information index (I)=0.789 , observed heterozygosity (Ho)=0.304 , and expected heterozygosity (He)=0.415) and moderate differentiation (FST=0.110, P=0.000) were found among nine populations. The lowest genetic diversity (Ar=2.351, I=0.497, Ho=0.178, and He=0.284) and highest inbreeding (inbreeding coefficient (FIS)=0.365) were both detected within the isolated population PE. Furthermore, high genetic differentiation, limited gene flow, and clear genetic barrier were detected between PE and other populations, showing the significant effects of habitat fragmentation on the genetic differentiation of these G. delavayi populations. Conclusions: Our results showed that human overexploitation has led to moderate genetic diversity in G.delavayi populations. Furthermore, habitat fragmentation has resulted in clear genetic barrier and high differentiation between the isolated and concentrated populations. Upon the genetic features of wild G. delavayi populations, we proposed several strategies for protecting and utilizing the current wild resources.

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Genetic diversity and population structure of Ottelia acuminata var. jingxiensis, an endangered endemic aquatic plant from southwest China

Aquatic Botany ◽

10.1016/j.aquabot.2018.09.004 ◽

2019 ◽

Vol 152 ◽

pp. 20-26 ◽

Cited By ~ 10

Author(s):

Zhi-Zhong Li ◽

Meng-Xue Lu ◽

Andrew W. Gichira ◽

Md. Rabiul Islam ◽

Qing-Feng Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Aquatic Plant ◽

Southwest China

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Isolation and Characterization of 17 Polymorphic Microsatellite Loci for Musella lasiocarpa (Musaceae)

HortScience ◽

10.21273/hortsci.44.7.2041 ◽

2009 ◽

Vol 44 (7) ◽

pp. 2041-2042 ◽

Cited By ~ 2

Author(s):

Chun-yan Yang ◽

Yuan Huang ◽

Chunlin Long

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Southwest China ◽

Microsatellite Primers ◽

Genetic Population ◽

Allele Number ◽

Isolation And Characterization ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite

Seventeen microsatellite markers were isolated from 24 wild individuals collected from three populations of Musella lasiocarpa (Franch.) C. Y. Wu ex H. W. Li, a plant endemic to southwest China. The average allele number of these markers was 3.6 per locus, ranging from two to seven. The expected (He) and observed (Ho) heterozygosities varied from 0.4672 to 0.8183 and from 0.0417 to 1, respectively. Eleven loci were significantly deviated from Hardy-Weinberg equilibrium as a result of the heterozygote deficiency. These microsatellite primers will be used for studying genetic population structure and genetic diversity of M. lasiocarpa.

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Multi-locus sequence typing of Mycoplasma bovis to assess its genetic diversity from 2009-2018 in Ningxia Hui Autonomous Region, China

10.21203/rs.3.rs-23294/v1 ◽

2020 ◽

Author(s):

Yanan Guo ◽

Haifeng Luo ◽

Shuqiang Guo ◽

Yuanyuan Lei ◽

Yong Li ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Scientific Basis ◽

Multi Locus Sequence Typing ◽

Mycoplasma Bovis ◽

Autonomous Region ◽

Mlst Analysis ◽

Ningxia Hui Autonomous Region ◽

And Control ◽

First Time

Abstract Background: Mycoplasma bovis (M. bovis) is a highly contagious cattle pathogen spreading worldwide and especially in Ningxia province in China. Methods: For investing epidemiology and population structure, we isolated 65 strains of M. bovis from infectious cattle with pneumonia or mastitis or arthritis. Multi-locus sequence typing (MLST) analysis were used to compare these 65 strains isolated from 2009 to 2018. The molecular epidemiology and population structure of M. bovis of these strains were further compared to PG45 strain and HB0801 reported for the first time in China and others strains isolated from different province of China through MLST analysis. Seven gene sequences of 65 strains in Ningxia and the strains of different STs in China and PG45 reference strains were concatenated to constructe a phylogenetic tree. Results: Totally two types of ST, ST10 and ST134, were identified in Ningxia. 37 Ningxia strains were classified to ST10 and 28 Ningxia strains were classified to ST134. ST134 strain was a new ST and first found in 2009 and was only widely distributed in Ningxia at present. The M. bovis of ST10 was widely spread in many provinces in China and was widespread in Ningxia since 2010. It is speculated that the prevalence of M. bovis ST10 in Ningxia began in 2010. Conclusion: This study is the first report on the genetic diversity of M. bovis from 2009 to 2018 in Ningxia Hui Autonomous Region and provides the epidemiological information, thus is meaningful for providing a scientific basis for the prevention and control of M.bovis in Ningxia, China.

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Genetic Diversity and Structure of Coix lacryma-jobi L. from Its World Secondary Diversity Center, Southwest China

International Journal of Genomics ◽

10.1155/2019/9815697 ◽

2019 ◽

Vol 2019 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Yu-Hua Fu ◽

Chenglong Yang ◽

Qiuyi Meng ◽

Fanzhi Liu ◽

Gang Shen ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Southwest China ◽

Great Influence ◽

Medicinal Value ◽

Hilly Region ◽

Geographical Regions ◽

Genetic Diversity And Structure ◽

Geographical Populations ◽

Local Breeding

Coix lacryma-jobi L. is an important minor cereal with a high nutritional and medicinal value in Asian countries. The hilly region of South China is the secondary center of diversity of Coix lacryma-jobi L. In the present study, we took a sample of 139 Coix lacryma-jobi L. genotypes from four geographical regions in Southwest China and analyzed the genetic diversity and population structure using AFLP markers. Six primer combinations detected a total of 743 (89.52%) polymorphic loci. The percentage of polymorphic bands within the four geographical populations ranged from 56.02% (Guangxi) to 86.75% (Guizhou). The overall genetic diversity of 139 Coix lacryma-jobi L. was relatively low (h ranged from 0.1854 to 0.2564). The neighbor-joining method grouped all Coix lacryma-jobi L. genotypes into two clusters with no geographical affinity observed among genotypes within the same group. The Fst indicated the two clusters existed great genetic differentiation. AMOVA analysis showed the molecular variation within populations was much higher than that among populations of geographical regions and subpopulations derived from STRUCTURE. Human activities and the natural outcrossing system of Coix lacryma-jobi L. may have a great influence on its distribution, genetic diversity, and population structure. Our study provides useful information for local breeding programs of Coix lacryma-jobi L. as well.

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