本文用生物素标记的人类1号、2号、4号染色体DNA探针进行染色体原位抑制(chromosomal in situ suppression,简称CISS)杂交以研究人和猕猴染色体的同源性。结果表明:人1号染色体与猕猴1号染色体同源。其中与猕猴lpter→lq33的同源程度高...本文用生物素标记的人类1号、2号、4号染色体DNA探针进行染色体原位抑制(chromosomal in situ suppression,简称CISS)杂交以研究人和猕猴染色体的同源性。结果表明:人1号染色体与猕猴1号染色体同源。其中与猕猴lpter→lq33的同源程度高,与猕猴lq33→lqter的同源程度相对较低;人2号染色体与猕猴13号染色体长臂、9号染色体长臂和部分短臂同源;人4号染色体与猕猴2号染色体同源。结合染色体带型比较分析,本文对人和猕猴染色体的演化关系进行了探讨,该研究进一步证明了染色体重排可能是灵长类染色体进化的主要机制。展开更多
Miiuy croaker,Miichthys miiuy is an ecologically important teleost species which is widely distributed in southeast coast of China.In this study,we present a chromosomal-scale genome assembly of the miiuy croaker whic...Miiuy croaker,Miichthys miiuy is an ecologically important teleost species which is widely distributed in southeast coast of China.In this study,we present a chromosomal-scale genome assembly of the miiuy croaker which is an important Sciaenidae fish and economical species.We adopted Oxford Nanopore and Hi-C sequencing techniques to achieve an assembly with high accuracy and completeness.The investigation of genome characteristic and functional features may provide insights into the study of phylogenetic diversity of miiuy croaker.This study can also be beneficial to improve molecular assisted breeding techniques.Moreover,it can be a great resource to better conduct further study of other sciaenids.展开更多
Segmental duplications on rice (Oryza sativa L.) chromosomes 8, 9, 11, and 12 were studied by examining the distributions of sequences resolved by 13 probes detecting multiple copies of DNA sequences. Four of the hyb...Segmental duplications on rice (Oryza sativa L.) chromosomes 8, 9, 11, and 12 were studied by examining the distributions of sequences resolved by 13 probes detecting multiple copies of DNA sequences. Four of the hybridization bands detected by a repetitive sequence probe, rTRS, were mapped to the ends of all the four chromosomes. Two or three of the bands detected by each of the other 12 probes were also mapped to different chromosomes. The bands detected by the same probe usually occurred in similar locations of different chromosomes. Loci detected by different DNA probes were often similarly arranged on different chromosomes. Chromosomes 8 and 9 showed colinearity of marker loci arrangement indicating a possible common origin. A segment on chromosome 9 was also very similar to the previously reported duplicated fragments on the ends of chromosomes 11 and 12 which were also detected in this study, indicating a likely common origin. Moreover, the various degrees of distributional similarity of the segments suggest a complex relationship among the chromosomes in the evolution of the rice genome. These results support the proposition that chromosome duplication and diversification may be a mechanism for the origin and evolution of the chromosomes in the rice genome.展开更多
The blackspotted croaker(Protonibea diacanthus)is an endangered coastal marine fish.It is also a valuable species that is cultured on the southeast coast of China.While some genetic studies have been conducted to prot...The blackspotted croaker(Protonibea diacanthus)is an endangered coastal marine fish.It is also a valuable species that is cultured on the southeast coast of China.While some genetic studies have been conducted to protect this species,genomic resources are lacking.Here,we report a chromosome-scale assembly of P.diacanthus genome by high-depth genome sequencing,assembly,and annotation.The genome scale was 635.69 Mb with contig and scaffold N50 length of 3.33 Mb and 25.60 Mb,respectively.Hi-C scaffolding of the genome resulted in 24 chromosomes of 94.15%total genome.We predicted 23,971 protein-coding genes.In addition,we constructed a phylogenetic tree using 2755 single-copy gene families and identified 462 unique gene families in P.diacanthus genome compared to three other sciaenids.What’s more,from the analysis of gene families,we found that several gene families related to innate immunity were significantly expanded in the blackspotted croaker genome compared to other teleost genomes.The high-quality genome can improve our understanding of the molecular mechanisms behind economically valuable traits and provide insights into characteristics of the immune system.展开更多
In the Dongting water system, the Carassius auratus(Crucian carp) complex is characterized by the coexistence of diploid forms(2n=100, 2n CC) and polyploid forms. Chromosomal and karyotypic analyses have suggested tha...In the Dongting water system, the Carassius auratus(Crucian carp) complex is characterized by the coexistence of diploid forms(2n=100, 2n CC) and polyploid forms. Chromosomal and karyotypic analyses have suggested that the polyploid C. auratus has a triploid(3n=150, 3n CC) and a tetraploid origin(4n=200), respectively. However, there is a lack of direct genetic evidence to support this conclusion. In this paper, analysis of the 5S r DNA chromosomal locus revealed that the 3n CC is of triploid origin. Analysis of the species-specific chromosomal centromere locus revealed that 3n CC individuals possess three sets of C. auratus-derived chromosomes. Our results provide direct cytogenetic evidence suggesting that individuals with 150 chromosomes are of autotriploid origin within the C. auratus complex. It marks an important contribution to the study of polyploidization and the evolution of vertebrates.展开更多
The plasmid-expression system is routinely plagued by potential plasmid instability. Chromosomal integration is one powerful approach to overcome the problem. Herein we report a plasmid-free hyper-producer E.coli stra...The plasmid-expression system is routinely plagued by potential plasmid instability. Chromosomal integration is one powerful approach to overcome the problem. Herein we report a plasmid-free hyper-producer E.coli strain for coenzyme Q10 production. A series of integration expression vectors, pxKC3T5b and pxKT5b, were constructed for chemically inducible chromosomal evolution(multiple copy integration) and replicon-free and markerless chromosomal integration(single copy integration), respectively. A coenzyme Q10 hyper-producer Escherichia coli TBW20134 was constructed by applying chemically inducible chromosomal evolution,replicon-free and markerless chromosomal integration as well as deletion of menaquinone biosynthetic pathway.The engineered E. coli TBW20134 produced 10.7 mg per gram of dry cell mass(DCM) of coenzyme Q10 when supplemented with 0.075 g·L-1of 4-hydroxy benzoic acid; this yield is unprecedented in E. coli and close to that of the commercial producer Agrobacterium tumefaciens. With this strain, the coenzyme Q10 production capacity was very stable after 30 sequential transfers and no antibiotics were required during the fermentation process. The strategy presented may be useful as a general approach for construction of stable production strains synthesizing natural products where various copy numbers for different genes are concerned.展开更多
Sciaenops ocellatus,also known as red drum,is a valuable commercial fish that is widely cultured in China.In recent years,while the genetic research and molecular breeding on S.ocellatus has been widely performed,whol...Sciaenops ocellatus,also known as red drum,is a valuable commercial fish that is widely cultured in China.In recent years,while the genetic research and molecular breeding on S.ocellatus has been widely performed,whole-genome resources are lacking.In our study,we assembled the S.ocellatus genome by high-quality genome sequencing,followed by complete annotation.The size of final genome was 686.62 Mb and N50 length of contig and scaffold is 99.71 Kb and 25.62 Mb,respectively.Using the Hi-C technology,we obtained 24 pseudochromosomes containing 87.82%of the total scaffolds.We annotated 20,053 protein-coding genes in S.ocellatus genome,of which 99.93%were homologous to proteins in different database.Totally,we detected 133.54 Mb repeat sequences,which accounts for 19.45%of the assembly.According to the phylogenetic analysis,S.ocellatus is most closed to L.croea with a divergence time about 30 million years ago.We assembled a high-quality genome that will be a valuable resource to further study the biology of S.ocellatus and will inform how to breed the red drum to enhance its economic traits.展开更多
The karyotype of Caspian goby was studied, which has been identified as Caspian bighead goby-Neogobius gorlap before. The results of cytogenetic analyses have shown that the diploid set of goby varies from 38 to 40 ch...The karyotype of Caspian goby was studied, which has been identified as Caspian bighead goby-Neogobius gorlap before. The results of cytogenetic analyses have shown that the diploid set of goby varies from 38 to 40 chromosomes, which is different from bighead goby （2n = 43-46）. We assumed that Caspian goby has independence as a species.展开更多
采用脉冲场强凝胶电泳技术对4种34个S accharom y ces属广义酵母样本的染色体核型进行了分析,观察到丰富的染色体数目和大小的多态性.染色体数目在所研究的广义酵母中从8到16都有出现,但小于0.5 M b的染色体仅见于S accharom y ces ex i...采用脉冲场强凝胶电泳技术对4种34个S accharom y ces属广义酵母样本的染色体核型进行了分析,观察到丰富的染色体数目和大小的多态性.染色体数目在所研究的广义酵母中从8到16都有出现,但小于0.5 M b的染色体仅见于S accharom y ces ex iguus.广义酵母染色体数目和大小的多态在所受试样品中普遍出现,表明在进化过程中酵母基因组发生了迅速而广泛的重排.展开更多
文摘本文用生物素标记的人类1号、2号、4号染色体DNA探针进行染色体原位抑制(chromosomal in situ suppression,简称CISS)杂交以研究人和猕猴染色体的同源性。结果表明:人1号染色体与猕猴1号染色体同源。其中与猕猴lpter→lq33的同源程度高,与猕猴lq33→lqter的同源程度相对较低;人2号染色体与猕猴13号染色体长臂、9号染色体长臂和部分短臂同源;人4号染色体与猕猴2号染色体同源。结合染色体带型比较分析,本文对人和猕猴染色体的演化关系进行了探讨,该研究进一步证明了染色体重排可能是灵长类染色体进化的主要机制。
基金supported by the National Key Research and Development Project(2018YFD0900301)the National Natural Science Foundation of China(31802325).
文摘Miiuy croaker,Miichthys miiuy is an ecologically important teleost species which is widely distributed in southeast coast of China.In this study,we present a chromosomal-scale genome assembly of the miiuy croaker which is an important Sciaenidae fish and economical species.We adopted Oxford Nanopore and Hi-C sequencing techniques to achieve an assembly with high accuracy and completeness.The investigation of genome characteristic and functional features may provide insights into the study of phylogenetic diversity of miiuy croaker.This study can also be beneficial to improve molecular assisted breeding techniques.Moreover,it can be a great resource to better conduct further study of other sciaenids.
文摘Segmental duplications on rice (Oryza sativa L.) chromosomes 8, 9, 11, and 12 were studied by examining the distributions of sequences resolved by 13 probes detecting multiple copies of DNA sequences. Four of the hybridization bands detected by a repetitive sequence probe, rTRS, were mapped to the ends of all the four chromosomes. Two or three of the bands detected by each of the other 12 probes were also mapped to different chromosomes. The bands detected by the same probe usually occurred in similar locations of different chromosomes. Loci detected by different DNA probes were often similarly arranged on different chromosomes. Chromosomes 8 and 9 showed colinearity of marker loci arrangement indicating a possible common origin. A segment on chromosome 9 was also very similar to the previously reported duplicated fragments on the ends of chromosomes 11 and 12 which were also detected in this study, indicating a likely common origin. Moreover, the various degrees of distributional similarity of the segments suggest a complex relationship among the chromosomes in the evolution of the rice genome. These results support the proposition that chromosome duplication and diversification may be a mechanism for the origin and evolution of the chromosomes in the rice genome.
基金the National Key Research and Development Project(2018YFD0900301)the National Natural Science Foundation of China(31802325).
文摘The blackspotted croaker(Protonibea diacanthus)is an endangered coastal marine fish.It is also a valuable species that is cultured on the southeast coast of China.While some genetic studies have been conducted to protect this species,genomic resources are lacking.Here,we report a chromosome-scale assembly of P.diacanthus genome by high-depth genome sequencing,assembly,and annotation.The genome scale was 635.69 Mb with contig and scaffold N50 length of 3.33 Mb and 25.60 Mb,respectively.Hi-C scaffolding of the genome resulted in 24 chromosomes of 94.15%total genome.We predicted 23,971 protein-coding genes.In addition,we constructed a phylogenetic tree using 2755 single-copy gene families and identified 462 unique gene families in P.diacanthus genome compared to three other sciaenids.What’s more,from the analysis of gene families,we found that several gene families related to innate immunity were significantly expanded in the blackspotted croaker genome compared to other teleost genomes.The high-quality genome can improve our understanding of the molecular mechanisms behind economically valuable traits and provide insights into characteristics of the immune system.
基金supported by the National Natural Science Foundation of China (31201987, 31430088, 31210103918)the Doctoral Fund of Ministry of Education of China (20124306120006)+4 种基金the Natural Science Foundation of Hunan Province (14JJ6008)Training Program of the Major Research Plan of the National Natural Science Foundation of China (91331105)the National Key Basic Research Program of China (2012CB722305)the Cooperative Innovation Center of Engineering and New Products for Developmental Biology (20134486)the Construct Program of the Key Discipline in Hunan Province, China
文摘In the Dongting water system, the Carassius auratus(Crucian carp) complex is characterized by the coexistence of diploid forms(2n=100, 2n CC) and polyploid forms. Chromosomal and karyotypic analyses have suggested that the polyploid C. auratus has a triploid(3n=150, 3n CC) and a tetraploid origin(4n=200), respectively. However, there is a lack of direct genetic evidence to support this conclusion. In this paper, analysis of the 5S r DNA chromosomal locus revealed that the 3n CC is of triploid origin. Analysis of the species-specific chromosomal centromere locus revealed that 3n CC individuals possess three sets of C. auratus-derived chromosomes. Our results provide direct cytogenetic evidence suggesting that individuals with 150 chromosomes are of autotriploid origin within the C. auratus complex. It marks an important contribution to the study of polyploidization and the evolution of vertebrates.
基金Supported by the National Natural Science Foundation of China(30970089,20876181,21276289)the Natural Science Foundation of Guangdong Province(9351027501000003,S2011010001396)
文摘The plasmid-expression system is routinely plagued by potential plasmid instability. Chromosomal integration is one powerful approach to overcome the problem. Herein we report a plasmid-free hyper-producer E.coli strain for coenzyme Q10 production. A series of integration expression vectors, pxKC3T5b and pxKT5b, were constructed for chemically inducible chromosomal evolution(multiple copy integration) and replicon-free and markerless chromosomal integration(single copy integration), respectively. A coenzyme Q10 hyper-producer Escherichia coli TBW20134 was constructed by applying chemically inducible chromosomal evolution,replicon-free and markerless chromosomal integration as well as deletion of menaquinone biosynthetic pathway.The engineered E. coli TBW20134 produced 10.7 mg per gram of dry cell mass(DCM) of coenzyme Q10 when supplemented with 0.075 g·L-1of 4-hydroxy benzoic acid; this yield is unprecedented in E. coli and close to that of the commercial producer Agrobacterium tumefaciens. With this strain, the coenzyme Q10 production capacity was very stable after 30 sequential transfers and no antibiotics were required during the fermentation process. The strategy presented may be useful as a general approach for construction of stable production strains synthesizing natural products where various copy numbers for different genes are concerned.
基金This work was supported by National Key Research and Development Project(2018YFD0900301).
文摘Sciaenops ocellatus,also known as red drum,is a valuable commercial fish that is widely cultured in China.In recent years,while the genetic research and molecular breeding on S.ocellatus has been widely performed,whole-genome resources are lacking.In our study,we assembled the S.ocellatus genome by high-quality genome sequencing,followed by complete annotation.The size of final genome was 686.62 Mb and N50 length of contig and scaffold is 99.71 Kb and 25.62 Mb,respectively.Using the Hi-C technology,we obtained 24 pseudochromosomes containing 87.82%of the total scaffolds.We annotated 20,053 protein-coding genes in S.ocellatus genome,of which 99.93%were homologous to proteins in different database.Totally,we detected 133.54 Mb repeat sequences,which accounts for 19.45%of the assembly.According to the phylogenetic analysis,S.ocellatus is most closed to L.croea with a divergence time about 30 million years ago.We assembled a high-quality genome that will be a valuable resource to further study the biology of S.ocellatus and will inform how to breed the red drum to enhance its economic traits.
文摘The karyotype of Caspian goby was studied, which has been identified as Caspian bighead goby-Neogobius gorlap before. The results of cytogenetic analyses have shown that the diploid set of goby varies from 38 to 40 chromosomes, which is different from bighead goby （2n = 43-46）. We assumed that Caspian goby has independence as a species.
文摘采用脉冲场强凝胶电泳技术对4种34个S accharom y ces属广义酵母样本的染色体核型进行了分析,观察到丰富的染色体数目和大小的多态性.染色体数目在所研究的广义酵母中从8到16都有出现,但小于0.5 M b的染色体仅见于S accharom y ces ex iguus.广义酵母染色体数目和大小的多态在所受试样品中普遍出现,表明在进化过程中酵母基因组发生了迅速而广泛的重排.
