[1] |
BAELE G,SUCHARD M A,RAMBAUT A,et al.Emerging concepts of data integration in pathogen phylodynamics[J]. Syst Biol,2017,66(1):e47-e65.
|
[2] |
STEGLICH M,NÜBEL U. The challenge of detecting indels in bacterial genomes from short-read sequencing data[J]. J Biotechnol,2017,250:11-15.
|
[3] |
JETTEN L,van IERSEL L. Nonbinary tree-based phylogenetic networks[J]. IEEE/ACM Trans Comput Biol Bioinform,2018,15(1):205-217.
|
[4] |
ZOU Q,WAN S,ZENG X,et al.Reconstructing evolutionary trees in parallel for massive sequences[J]. BMC Syst Biol,2017,11(Suppl 6):100.
|
[5] |
FALK T,HERNDON N,GRAU E,et al.Growing and cultivating the forest genomics database,TreeGenes[J]. Database(Oxford),2018,2018:1-11.
|
[6] |
WAILAN A M,COLL F,HEINZ E,et al.rPinecone:define sub-lineages of a clonal expansion via a phylogenetic tree[J]. Microb Genom,2019,5(4):e000264.
|
[7] |
FRANCIS A,HUBER K T,MOULTON V.Tree-based unrooted phylogenetic networks[J]. Bull Math Biol,2018,80(2):404-416.
|
[8] |
HARRIS K.From a database of genomes to a forest of evolutionary trees[J]. Nat Genet,2019,51(9):1306-1307.
|
[9] |
HAYAMIZU M.On the existence of infinitely many universal tree-based networks[J]. J Theor Biol,2016,396:204-206.
|
[10] |
PÉREZ-LOSADA M,ARENAS M,GALÁN J C,et al. High-throughput sequencing(HTS) for the analysis of viral populations[J]. Infect Genet Evol,2020,80:104208.
|
[11] |
GRAY R D,WATTS J.Cultural macroevolution matters[J]. Pro Nat Acad Sci U S A,2017,114(30):7846-7852.
|
[12] |
LU Y,YANG L,MENG J,et al. Microevolution of vibrio parahaemolyticus isolated from clinical,acute hepatopancreatic necrosis disease infecting shrimps,and aquatic production in China[J]. Microbes Environ,2020,35(2):ME19095.
|
[13] |
DIDELOT X,FALUSH D.Inference of bacterial microevolution using multilocus sequence data[J]. Genetics,2007,175(3):1251-1266.
|
[14] |
LIN Y,RAJAN V,MORET B M.A metric for phylogenetic trees based on matching[J]. IEEE/ACM Tran Comput Biol Bioinform,2012,9(4):1014-1022.
|
[15] |
BASGALUPP M P,FREITAS A A,DE CARVALHO A C P L,et al. Evolutionary design of decision-tree algorithms tailored to microarray gene expression data sets[J]. IEEE transactions on evolutionary computation:a publication of the IEEE Neural Networks Council,2014,18(6):873-892.
|
[16] |
FISCHER M.On the uniqueness of the maximum parsimony tree for data with up to two substitutions:an extension of the classic Buneman theorem in phylogenetics[J]. Mol Phylogenet Evol,2019,137:127-137.
|
[17] |
SAITOU N.Property and efficiency of the maximum likelihood method for molecular phylogeny[J]. J Mol Evol,1988,27(3):261-273.
|
[18] |
ANSARI M A,DIDELOT X.Bayesian inference of the evolution of a phenotype distribution on a phylogenetic tree[J]. Genetics,2016,204(1):89-98.
|
[19] |
LEMANCEAU P,BLOUIN M,MULLER D,et al.Let the core microbiota be functional[J]. Trends Plant Sci,2017,22(7):583-595.
|
[20] |
SMILLIE C S,SMITH M B,FRIEDMAN J,et al.Ecology drives a global network of gene exchange connecting the human microbiome[J]. Nature,2011,480(7376):241-244.
|
[21] |
JOLLEY K A,MAIDEN M C J. Using multilocus sequence typing to study bacterial variation:prospects in the genomic era[J]. Future Microbiol,2014,9(5):623-630.
|
[22] |
ACHTMAN M,WAIN J,WEILL F X,et al.Multilocus sequence typing as a replacement for serotyping in Salmonella enterica[J]. PLoS Pathog,2012,8(6):e1002776.
|
[23] |
李薇薇,郭云昌,占利,等. 2017年中国即食食品中单核细胞增生李斯特菌的分子流行病学特征[J]. 中华预防医学杂志,2020,54(2):175-180.
|
[24] |
KIMURA B.Will the emergence of core genome MLST end the role of in silico MLST?[J]. Food Microbiol,2018,75:28-36.
|
[25] |
SAHL J W,STEINSLAND H,REDMAN J C,et al.A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation[J]. Infect Immun,2011,79(2):950-960.
|
[26] |
朱健铭,姜如金,吴康乐,等. 肺炎克雷伯菌单基因分子进化分析及多位点序列分型与基因组系统学研究[J]. 中华医院感染学杂志,2014,24(12):2861-2864.
|
[27] |
RINN J L,CHANG H Y.Genome regulation by long noncoding RNAs[J]. Annu Rev Biochem,2012,81:145-166.
|
[28] |
ULLTSKY I,BARTEL D P. lincRNAs:genomics,evolution,and mechanisms[J]. Cell,2013,154(1):26-46.
|
[29] |
WHITE O,EISEN J A,HEIDELBERG J F,et al.Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1[J]. Science,1999,286(5444):1571-1577.
|
[30] |
CASTAGENONE SERENO P,MULET K,DANCHIN E G J,et al. Gene copy number variations as signatures of adaptive evolution in the parthenogenetic,plant-parasitic nematode Meloidogyne incognita[J]. Mol Ecol,2019,28(10):2559-2572.
|
[31] |
李黎,毛培宏. 低能N~+注入介导的沙漠寡营养细菌基因组SNP研究[J]. 基因组学与应用生物学,2016,35(12):3425-3429.
|
[32] |
BENTKOWSKI P,RADWAN J.Evolution of major histocompatibility complex gene copy number[J]. PLoS Comput Biol,2019,15(5):e1007015.
|
[33] |
NOVICK R P.Pathogenicity islands and their role in staphylococcal biology[J]. Microbiol Spectr,2019,7(3),DOI:10.1128/microbiolspec.GPP3-0062-2019.
|
[34] |
BANASZKIEWICZ S,CALLAND J K,MOURKAS E,et al.Genetic diversity of composite enterotoxigenic staphylococcus epidermidis pathogenicity islands[J]. Genome Biol Evol,2019,11(12):3498-3509.
|
[35] |
BOUYIOUKOS C,REVERCHON S,KÉPÈS F. From multiple pathogenicity islands to a unique organized pathogenicity archipelago[J]. Sci Rep,2016,6:27978.
|
[36] |
MUÑOZ-RAMÍREZ Z Y,MENDEZ-TENORIO A,KATO I,et al. Whole genome sequence and phylogenetic analysis show Helicobacter pylori strains from latin America have followed a unique evolution pathway[J]. Front Cell Infect Microbiol,2017,7:50.
|
[37] |
COMMON J,WESTRA E R.CRISPR evolution and bacteriophage persistence in the context of population bottlenecks[J]. RNA Biol,2019,16(4):588-594.
|
[38] |
IPOUTCHA T,TSARMPOPOULOS I,TALENTON V,et al.Multiple origins and specific evolution of CRISPR/Cas9 systems in minimal bacteria(Mollicutes)[J]. Front Microbiol,2019,10:2701.
|
[39] |
BAUMDICKER F,HUEBNER A M I,PFAFFELHUBER P. The independent loss model with ordered insertions for the evolution of CRISPR spacers[J]. Theor Popul Biol,2018,119:72-82.
|
[40] |
ANDERSEN J M,SHOUP M,ROBINSON C,et al.CRISPR diversity and microevolution in clostridium difficile[J]. Genome Biol Evol,2016,8(9):2841-2855.
|
[41] |
XIE X,HU Y,XU Y,et al.Genetic analysis of Salmonella enterica serovar Gallinarum biovar Pullorum based on characterization and evolution of CRISPR sequence[J]. Vet Microbiol,2017,203:81-87.
|
[42] |
LOUWEN R,STAALS R H,ENDTZ H P,et al.The role of CRISPR-cas systems in virulence of pathogenic bacteria[J]. Microbiol Mol Biol Rev,2014,78(1):74-88.
|
[43] |
MANGAS E L,RUBIO A,ÁLVAREZ-MARÍN R,et al. Pangenome of Acinetobacter baumannii uncovers two groups of genomes,one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation[J]. Microb Genom,2019,5(11):e000309.
|
[44] |
FOUQUIER J,RIDEOUT J R,BOLYEN E,et al.Ghost-tree:creating hybrid-gene phylogenetic trees for diversity analyses[J]. Microbiome,2016,4:11.
|
[45] |
GUZOW-KRZEMISKA B,GSIOR T,SZALEWSKA-PAASZ A.Phylogenetic relationship of the stringent response-related genes of marine bacteria[J]. Acta Biochim Pol,2015,62(4):773-783.
|