Classical swine fever virus(CSFV) is the causative agent of classical swine fever, a highly contagious disease of pigs. But there is little information on the recombination in natural populations of CSFVs. Therefore, ...Classical swine fever virus(CSFV) is the causative agent of classical swine fever, a highly contagious disease of pigs. But there is little information on the recombination in natural populations of CSFVs. Therefore, a phylogenetic analysis of 62 fulllength genome CSFV strains, isolated from all over the world, was performed to detect potential recombination events, with the recombinant sequences being analyzed with the SimPlot and RDP programs. The results identified a mosaic virus, Chinese CSFV HCLV(2)(AF091507.1), which is the one naturally emerged recombinant CSFV with two recombination breakpoints at 2 484 and 2 900 bp of the genome alignment. Its two putative parental-like strains were CSFV Shimen(AF092448.2) and CSFV strain C/HVRI(AY805221.1). This work demonstrated that homologous recombination did occur in natural CSFV populations. It had significant implications for understanding the molecular epidemiology of CSFV, and revealed that recombination was an important factor for high genetic diversities of CSFV.展开更多
Japanese encephalitis virus（JEV） is a significant causative agent of arthropod-borne encephalitis and what is less clear that the factors cause the virus wide spread. The objective was to confirm whether the homolog...Japanese encephalitis virus（JEV） is a significant causative agent of arthropod-borne encephalitis and what is less clear that the factors cause the virus wide spread. The objective was to confirm whether the homologous recombination imposed on JEV. The phylogenetic and homologous recombination analyses were performed based on 163 complete JEV genomes which were recently isolated. They were still separated into five genotypes（GI-GV） and the most of recently isolated JEVs were GI rather than GIII in Asian areas including China's Mainland. Two recombinant events were identified in JEV and the evidence of the recombination was observed between China and Japan isolates that partitioned into two distinct subclades, but still the same genotype（GIII）. Our data further suggested that most of the nucleotides in JEV genome were under negative selection; however, changes within codon 2 316（amino acid NS4b-44） showed an evidence of the positive selection.展开更多
A controversial taxon,Hipparion plocodus,is reviewed in the present study.Hi.plocodus has been confirmed to be a valid species with definite diagnostic characteristics,represented by cranial specimens from Baode,Shanx...A controversial taxon,Hipparion plocodus,is reviewed in the present study.Hi.plocodus has been confirmed to be a valid species with definite diagnostic characteristics,represented by cranial specimens from Baode,Shanxi Province.The phylogenetic analysis performed in the present study,with a new matrix,shows that Hi.plocodus forms a monophyletic group with a European species,Hippotherium malpassii.Actually,no close relationship between so-called Hm.malpassii and the genus Hippotherium has been identified,and the record of stratigraphic range of this genus in late stage of Late Miocene is currently absent.Herein previously Hi.plocodus and Hm.malpassii have both attributed into“Hipparion”before the discovery of better material.Evolutionary stages and correlative absolute age showed that these two species should derive independently from some primitive clade.During the late stage of the Late Miocene,the development of the Asian summer monsoon enhanced the humidity of China,with forest and wood habitats expanding considerably under this setting.As the result,one Eurasian closed-habitat lineage thus extended its range into China,which had become very suited for it,give rise to“Hi.”plocodus.展开更多
Boehmeria nivea var.strigosa Zeng Y.Wu&Y.Zhao,a new variety of B.nivea(Urticaceae)from Southwest China,is here described based on evidence from morphology and molecular phylogeny.This new variety is mainly charact...Boehmeria nivea var.strigosa Zeng Y.Wu&Y.Zhao,a new variety of B.nivea(Urticaceae)from Southwest China,is here described based on evidence from morphology and molecular phylogeny.This new variety is mainly characterized by its green abaxial leaf blade,partly connate stipules,and densely patent strigose hairs on stems and potioles.The phylogenetic analysis based on rbc L,nrDNA and rbc L+nrDNA datasets,revealed that all individuals of B.nivea var.strigosa formed a monophyletic group.The conservation status of B.nivea var.strigosa is assessed as“Near Threatened”(NT)according to IUCN evaluation criteria.The discovery of this new variety is not only crucial for the taxonomy of ramie,but also provides reference for the exploration and utilization of ramie.展开更多
Chrysosplenium fallax Koldaeva,recently discovered and collected in Yanji,Jilin Province,repre-sents a newly recorded species of Saxifragaceae in China.This species,native to the Russian Far East,was first described a...Chrysosplenium fallax Koldaeva,recently discovered and collected in Yanji,Jilin Province,repre-sents a newly recorded species of Saxifragaceae in China.This species,native to the Russian Far East,was first described as a new species in 2021.Based on precise field investigations and specimen examination,we provide a comprehensive description of C.fallax and its seed micromorphology.Phylogenetic analysis based on chloroplast genomes of 45 Chrysosplenium species confirmed the systematic position of C.fallax in Chrysosplenium.Voucher specimens were deposited in the Herbarium of South-Central Minzu University(HSN).展开更多
Perleididae is a group of stem neopterygian fishes known only from the Triassic.Here,we report the discovery of a new perleidid,Teffichthys wui sp.nov.,based on six well-preserved specimens from the late Smithian(Olen...Perleididae is a group of stem neopterygian fishes known only from the Triassic.Here,we report the discovery of a new perleidid,Teffichthys wui sp.nov.,based on six well-preserved specimens from the late Smithian(Olenekian,Early Triassic)marine deposits of Jurong,Jiangsu and Chaohu,Anhui,China.This new discovery documents the third and youngest species of Teffichthys,which is slightly younger than the Dienerian(Induan)T.elegans from Guizhou and the early Smithian T.madagascariensis from Madagascar.The new species shows diagnostic features of Teffichthys(presence of a spiracular,38-41 lateral line scales,and no more than three epaxial rays in the caudal fin)but differs from T.madagascariensis and T.elegans in some autapomorphies(e.g.,a horizontal opercle/subopercle contact and smooth scales with a nearly straight posterior margin).The diagnostic features for the genus Teffichthys and the family Perleididae are emended based on detailed comparisons of the new taxon with other perleidids.The phylogenetic relationships of perleidids with other stem neopterygians are discussed using a cladistic approach,and the results provide new insights into the phylogeny and classification of main stem neopterygian clades.展开更多
Different from ribosomal genes, which contain highly conserved sequences that are detected in all organisms, the intergenic spacer of rDNA (IGS) appears to be the most rapidly-evolving spacer region. For this reason w...Different from ribosomal genes, which contain highly conserved sequences that are detected in all organisms, the intergenic spacer of rDNA (IGS) appears to be the most rapidly-evolving spacer region. For this reason we tested this region for phylogenetic studies. This report focuses on the study of IGS sequences of isolates belonging to Trichoderma section (T. viride, T. koningii, T. hamatum, T. erinaceus, T. asperellum) and Pachybasium section (T. harzianum, T. crassum, T. fasciculatum, T. oblongisporum, T. virens). Using the primer pair 28STD and CNS1, the Fast Start Taq DNA Polymerase (Roche), and a three temperature PCR protocol, products ranging from ca 1900 to 2400 bp were obtained from all tested isolates. The PCR product of 16 Trichoderma spp. isolates was cloned into a pGEM-TEeasy Vector (Promega) and sequenced. Based on a BLAST search we can conclude that the PCR product represents the whole IGS region. Multiple alignments of IGS sequences revealed two portions with different homology level. Portion A (ca 1660 bp) is the portion that contains 3’ end of 28S gene and is the more variable, while portion B (ca 830 bp), that contains the 3’ end of IGS region and the 5’ end of 18S gene, is the less variable. Comparing all sequences in region A 705 identical pairs occur out of 1704 total nucleotides (41.4%), while in region B identical pairs were 723 out of 832 total nucleotides (86.9%) . Sequence comparison of the two regions at intraspecific level (where it was possible) showed higher variability in region A (0.17%-6.8%) than in region B (0.0%-1.0%) . At interspecific level, performing all possible comparisons, the variability of region A (19.5%-52.7%) and B (0.8%- 16.9%). were significantly higher. Comparing sequences of species belonging to Trichoderma section variability of the two regions appears reduced if compared with that obtained from comparisons of species belonging to Pachybasium section. On the basis of sequence alignment, phylogenetic trees were obtained either with entire IGS, with region A, and with region B. Results of this analysis revealed that all isolates belonging to Trichoderma section grouped separately from isolates belonging to Pachybasium section. IGS region allowed us to group species according to their taxonomic position. The topology of the tree did not change substantially, varying in genetic distance only. Performing a GenBank search sequences representing the final portion of the IGS region of other fungal species were found, and we carried out a multiple alignment using also our sequences of Trichoderma spp. and Diaporthe helianthi. The phylogeny inferred from sequence alignment matched the generally accepted morphology-based classification and was identical to other molecular schemes at high taxonomic level. Data analysis was useful in establishing a broad-scale phylogeny of Ascomycota and was also useful in sorting them into statistically-supported clades. The tree showed that Trichoderma occurred in a well-supported terminal subclade of a larger clade that also contained other genera belonging to Hypocreales order. Sequence analysis of the Trichoderma spp. IGS region allowed us to design a specific PCR primer that was successfully used to amplify region A. The new reverse primer LCR2, that recognize all Trichoderma isolates, was identified in region B and confirmed for its specificity on the DNA of fungi belonging to other Ascomycota genera. Results obtained showed that IGS region seems to be an interesting and versatile tool for phylogenetic analysis, for resolving some taxonomic problems and for constructing specific primer useful for different purposes.展开更多
The main cultivated varieties in the world belong to the species of upland cotton(Gossypium hirsutum L.),and their genetic background is very narrow.However,the wild species and races in
The early Silurian Chongqing Lagerstätte(middle Telychian)yields exceptionally preserved articulated jawless and jawed fishes.Here,we describe a new eugaleaspiform(Galeaspida,jawless stem-Gnathostomata),Miaojiaas...The early Silurian Chongqing Lagerstätte(middle Telychian)yields exceptionally preserved articulated jawless and jawed fishes.Here,we describe a new eugaleaspiform(Galeaspida,jawless stem-Gnathostomata),Miaojiaaspis dichotomus gen.et sp.nov.,from the Chongqing Lagerstätte in Xiushan,Chongqing,China.The new form resembles Tujiaaspis vividus in the short medial dorsal canal,and the presence of the branching ends of the lateral transverse canal.They differ in that T.vividus has highly developed subordinate branches of the sensory canals that form a reticulate sensory canal system,and the median dorsal opening is more elongated.Our phylogenetic analysis recovers M.dichotomus and T.vividus as a monophyletic clade(Tujiaaspidae fam.nov.),which is supported by two synapomorphies:the short medial dorsal canal,and the branching ends of the lateral transverse canal.Tujiaaspidae forms a trichotomy with Shuyuidae and a clade comprising Anjiaspis,Sinogaleaspidae,Yongdongaspidae,and the‘eugaleaspid cluster’.The sensory canal patterns in galeaspids are compared to show the transformation sequence of the sensory canal system in Eugaleaspiformes.展开更多
Glutamate decarboxylase （GAD） has been found in animal and higher plant tissues as well as in yeasts and microorganisms. In animals the enzyme plays an important role in central nervous system activity because the e...Glutamate decarboxylase （GAD） has been found in animal and higher plant tissues as well as in yeasts and microorganisms. In animals the enzyme plays an important role in central nervous system activity because the enzyme substrate glutamic acid is a mediator of excitation process and the product, gamma-aminobutyric acid, is the most important mediator of inhibition process in the central nervous system. GAD65 is one form of the glutamate decarboxylases （GAD）, GAD65 has been identified as a major autoantigen in type 1 diabetes, so the GAD65 gene of porcine was cloned by RT-PCR method to construct phylogenetic tree, the homology of 13 glutamate decarboxylases （GAD） of different origin was analyzed by multiple alignment.展开更多
Two new species of Crassulaceae,Sedum baiwanense Yan S.Huang&Q.Fan and S.nankunshanense Yan S.Huang&Q.Fan,from Guangdong,China,are described and illustrated here.Phylogenetic analysis based on the internal tra...Two new species of Crassulaceae,Sedum baiwanense Yan S.Huang&Q.Fan and S.nankunshanense Yan S.Huang&Q.Fan,from Guangdong,China,are described and illustrated here.Phylogenetic analysis based on the internal transcribed spacer(ITS)region of nrDNA suggests that the two new species belong to Acre Clade,and are relative to S.subtile Miq.,S.tianmushanense Y.C.Ho&F.Chai,and S.jiulungshanense Y.C.Ho with high support values(node posterior probabilities=1).With high morphologically differences,we can easily distinguish species in this monophyletic group.展开更多
基金Supported by the National Natural Science Foundation of China(31370140 31372438)
文摘Classical swine fever virus(CSFV) is the causative agent of classical swine fever, a highly contagious disease of pigs. But there is little information on the recombination in natural populations of CSFVs. Therefore, a phylogenetic analysis of 62 fulllength genome CSFV strains, isolated from all over the world, was performed to detect potential recombination events, with the recombinant sequences being analyzed with the SimPlot and RDP programs. The results identified a mosaic virus, Chinese CSFV HCLV(2)(AF091507.1), which is the one naturally emerged recombinant CSFV with two recombination breakpoints at 2 484 and 2 900 bp of the genome alignment. Its two putative parental-like strains were CSFV Shimen(AF092448.2) and CSFV strain C/HVRI(AY805221.1). This work demonstrated that homologous recombination did occur in natural CSFV populations. It had significant implications for understanding the molecular epidemiology of CSFV, and revealed that recombination was an important factor for high genetic diversities of CSFV.
基金Supported by the National Natural Science Foundation of China(31272569,31270187)Projects in the National Science&Technology Pillar Program during 12th Five-year Plan Period(2013BAD12B04)Harbin Science and Technology Bureau(RC2012XK002003)
文摘Japanese encephalitis virus（JEV） is a significant causative agent of arthropod-borne encephalitis and what is less clear that the factors cause the virus wide spread. The objective was to confirm whether the homologous recombination imposed on JEV. The phylogenetic and homologous recombination analyses were performed based on 163 complete JEV genomes which were recently isolated. They were still separated into five genotypes（GI-GV） and the most of recently isolated JEVs were GI rather than GIII in Asian areas including China's Mainland. Two recombinant events were identified in JEV and the evidence of the recombination was observed between China and Japan isolates that partitioned into two distinct subclades, but still the same genotype（GIII）. Our data further suggested that most of the nucleotides in JEV genome were under negative selection; however, changes within codon 2 316（amino acid NS4b-44） showed an evidence of the positive selection.
文摘A controversial taxon,Hipparion plocodus,is reviewed in the present study.Hi.plocodus has been confirmed to be a valid species with definite diagnostic characteristics,represented by cranial specimens from Baode,Shanxi Province.The phylogenetic analysis performed in the present study,with a new matrix,shows that Hi.plocodus forms a monophyletic group with a European species,Hippotherium malpassii.Actually,no close relationship between so-called Hm.malpassii and the genus Hippotherium has been identified,and the record of stratigraphic range of this genus in late stage of Late Miocene is currently absent.Herein previously Hi.plocodus and Hm.malpassii have both attributed into“Hipparion”before the discovery of better material.Evolutionary stages and correlative absolute age showed that these two species should derive independently from some primitive clade.During the late stage of the Late Miocene,the development of the Asian summer monsoon enhanced the humidity of China,with forest and wood habitats expanding considerably under this setting.As the result,one Eurasian closed-habitat lineage thus extended its range into China,which had become very suited for it,give rise to“Hi.”plocodus.
文摘Boehmeria nivea var.strigosa Zeng Y.Wu&Y.Zhao,a new variety of B.nivea(Urticaceae)from Southwest China,is here described based on evidence from morphology and molecular phylogeny.This new variety is mainly characterized by its green abaxial leaf blade,partly connate stipules,and densely patent strigose hairs on stems and potioles.The phylogenetic analysis based on rbc L,nrDNA and rbc L+nrDNA datasets,revealed that all individuals of B.nivea var.strigosa formed a monophyletic group.The conservation status of B.nivea var.strigosa is assessed as“Near Threatened”(NT)according to IUCN evaluation criteria.The discovery of this new variety is not only crucial for the taxonomy of ramie,but also provides reference for the exploration and utilization of ramie.
文摘Chrysosplenium fallax Koldaeva,recently discovered and collected in Yanji,Jilin Province,repre-sents a newly recorded species of Saxifragaceae in China.This species,native to the Russian Far East,was first described as a new species in 2021.Based on precise field investigations and specimen examination,we provide a comprehensive description of C.fallax and its seed micromorphology.Phylogenetic analysis based on chloroplast genomes of 45 Chrysosplenium species confirmed the systematic position of C.fallax in Chrysosplenium.Voucher specimens were deposited in the Herbarium of South-Central Minzu University(HSN).
文摘Perleididae is a group of stem neopterygian fishes known only from the Triassic.Here,we report the discovery of a new perleidid,Teffichthys wui sp.nov.,based on six well-preserved specimens from the late Smithian(Olenekian,Early Triassic)marine deposits of Jurong,Jiangsu and Chaohu,Anhui,China.This new discovery documents the third and youngest species of Teffichthys,which is slightly younger than the Dienerian(Induan)T.elegans from Guizhou and the early Smithian T.madagascariensis from Madagascar.The new species shows diagnostic features of Teffichthys(presence of a spiracular,38-41 lateral line scales,and no more than three epaxial rays in the caudal fin)but differs from T.madagascariensis and T.elegans in some autapomorphies(e.g.,a horizontal opercle/subopercle contact and smooth scales with a nearly straight posterior margin).The diagnostic features for the genus Teffichthys and the family Perleididae are emended based on detailed comparisons of the new taxon with other perleidids.The phylogenetic relationships of perleidids with other stem neopterygians are discussed using a cladistic approach,and the results provide new insights into the phylogeny and classification of main stem neopterygian clades.
文摘Different from ribosomal genes, which contain highly conserved sequences that are detected in all organisms, the intergenic spacer of rDNA (IGS) appears to be the most rapidly-evolving spacer region. For this reason we tested this region for phylogenetic studies. This report focuses on the study of IGS sequences of isolates belonging to Trichoderma section (T. viride, T. koningii, T. hamatum, T. erinaceus, T. asperellum) and Pachybasium section (T. harzianum, T. crassum, T. fasciculatum, T. oblongisporum, T. virens). Using the primer pair 28STD and CNS1, the Fast Start Taq DNA Polymerase (Roche), and a three temperature PCR protocol, products ranging from ca 1900 to 2400 bp were obtained from all tested isolates. The PCR product of 16 Trichoderma spp. isolates was cloned into a pGEM-TEeasy Vector (Promega) and sequenced. Based on a BLAST search we can conclude that the PCR product represents the whole IGS region. Multiple alignments of IGS sequences revealed two portions with different homology level. Portion A (ca 1660 bp) is the portion that contains 3’ end of 28S gene and is the more variable, while portion B (ca 830 bp), that contains the 3’ end of IGS region and the 5’ end of 18S gene, is the less variable. Comparing all sequences in region A 705 identical pairs occur out of 1704 total nucleotides (41.4%), while in region B identical pairs were 723 out of 832 total nucleotides (86.9%) . Sequence comparison of the two regions at intraspecific level (where it was possible) showed higher variability in region A (0.17%-6.8%) than in region B (0.0%-1.0%) . At interspecific level, performing all possible comparisons, the variability of region A (19.5%-52.7%) and B (0.8%- 16.9%). were significantly higher. Comparing sequences of species belonging to Trichoderma section variability of the two regions appears reduced if compared with that obtained from comparisons of species belonging to Pachybasium section. On the basis of sequence alignment, phylogenetic trees were obtained either with entire IGS, with region A, and with region B. Results of this analysis revealed that all isolates belonging to Trichoderma section grouped separately from isolates belonging to Pachybasium section. IGS region allowed us to group species according to their taxonomic position. The topology of the tree did not change substantially, varying in genetic distance only. Performing a GenBank search sequences representing the final portion of the IGS region of other fungal species were found, and we carried out a multiple alignment using also our sequences of Trichoderma spp. and Diaporthe helianthi. The phylogeny inferred from sequence alignment matched the generally accepted morphology-based classification and was identical to other molecular schemes at high taxonomic level. Data analysis was useful in establishing a broad-scale phylogeny of Ascomycota and was also useful in sorting them into statistically-supported clades. The tree showed that Trichoderma occurred in a well-supported terminal subclade of a larger clade that also contained other genera belonging to Hypocreales order. Sequence analysis of the Trichoderma spp. IGS region allowed us to design a specific PCR primer that was successfully used to amplify region A. The new reverse primer LCR2, that recognize all Trichoderma isolates, was identified in region B and confirmed for its specificity on the DNA of fungi belonging to other Ascomycota genera. Results obtained showed that IGS region seems to be an interesting and versatile tool for phylogenetic analysis, for resolving some taxonomic problems and for constructing specific primer useful for different purposes.
文摘The main cultivated varieties in the world belong to the species of upland cotton(Gossypium hirsutum L.),and their genetic background is very narrow.However,the wild species and races in
文摘The early Silurian Chongqing Lagerstätte(middle Telychian)yields exceptionally preserved articulated jawless and jawed fishes.Here,we describe a new eugaleaspiform(Galeaspida,jawless stem-Gnathostomata),Miaojiaaspis dichotomus gen.et sp.nov.,from the Chongqing Lagerstätte in Xiushan,Chongqing,China.The new form resembles Tujiaaspis vividus in the short medial dorsal canal,and the presence of the branching ends of the lateral transverse canal.They differ in that T.vividus has highly developed subordinate branches of the sensory canals that form a reticulate sensory canal system,and the median dorsal opening is more elongated.Our phylogenetic analysis recovers M.dichotomus and T.vividus as a monophyletic clade(Tujiaaspidae fam.nov.),which is supported by two synapomorphies:the short medial dorsal canal,and the branching ends of the lateral transverse canal.Tujiaaspidae forms a trichotomy with Shuyuidae and a clade comprising Anjiaspis,Sinogaleaspidae,Yongdongaspidae,and the‘eugaleaspid cluster’.The sensory canal patterns in galeaspids are compared to show the transformation sequence of the sensory canal system in Eugaleaspiformes.
基金Supported in part by Heilongjiang Province Tackle Key Problem Item (GB01B104)
文摘Glutamate decarboxylase （GAD） has been found in animal and higher plant tissues as well as in yeasts and microorganisms. In animals the enzyme plays an important role in central nervous system activity because the enzyme substrate glutamic acid is a mediator of excitation process and the product, gamma-aminobutyric acid, is the most important mediator of inhibition process in the central nervous system. GAD65 is one form of the glutamate decarboxylases （GAD）, GAD65 has been identified as a major autoantigen in type 1 diabetes, so the GAD65 gene of porcine was cloned by RT-PCR method to construct phylogenetic tree, the homology of 13 glutamate decarboxylases （GAD） of different origin was analyzed by multiple alignment.
基金Supported by Forest Ecosystem Monitoring Project of Baiwan Provincial Nature Reserve,Qingxin,Guangdong(QCCG2025-003)Guangdong Provincial EQI Monitoring Project(GPCGD241115FG155F)Preliminary Survey and Monitoring and Conservation of Rare and Endangered Plant Species in Qingyuan Karst Mountain Botanical Garden(HT-99982024-0030)。
文摘Two new species of Crassulaceae,Sedum baiwanense Yan S.Huang&Q.Fan and S.nankunshanense Yan S.Huang&Q.Fan,from Guangdong,China,are described and illustrated here.Phylogenetic analysis based on the internal transcribed spacer(ITS)region of nrDNA suggests that the two new species belong to Acre Clade,and are relative to S.subtile Miq.,S.tianmushanense Y.C.Ho&F.Chai,and S.jiulungshanense Y.C.Ho with high support values(node posterior probabilities=1).With high morphologically differences,we can easily distinguish species in this monophyletic group.
