Multiple BAC-FISH is a powerful tool for modern cytogenetic researching in both animals and plants.But in cotton,this technique is unavailable due to the high percentage of repetitive sequences.
The constant evolution of pathogens poses a threat to wheat resistance against diseases,endangering food security.Developing resistant wheat varieties is the most practical approach for circumventing this problem.As a...The constant evolution of pathogens poses a threat to wheat resistance against diseases,endangering food security.Developing resistant wheat varieties is the most practical approach for circumventing this problem.As a close relative of wheat,Aegilops geniculata,particularly accession SY159,has evolved numerous beneficial traits that could be applied to improve wheat.In this study,we established the karyotype of SY159 by fluorescence in situ hybridization(FISH)using the oligonucleotide probes Oligo-pTa535 and Oligo-pSc119.2 and a complete set of wheat–Ae.geniculata accession TA2899 addition lines as a reference.Using specific-locus amplified fragment sequencing(SLAF-seq)technology,400 specific markers were established for detecting the SY159 chromosomes with efficiencies reaching 81.5%.The SY159-specific markers were used to classify the different homologous groups of SY159 against the wheat-Ae.geniculata addition lines.We used these specific markers on the 7Mg chromosome after classification,and successfully confirmed their suitability for studying the different chromosomes of SY159.This study provides a foundation for accelerating the application of SY159 in genetic breeding programs designed to improve wheat.展开更多
BACKGROUND Cri du chat syndrome(CdCS),also known as 5p deletion syndrome(5p-)is a syndrome caused by partial deletion of the 5p chromosome in human beings.The incidence accounts for 1/50000 and the cause of CdCS is re...BACKGROUND Cri du chat syndrome(CdCS),also known as 5p deletion syndrome(5p-)is a syndrome caused by partial deletion of the 5p chromosome in human beings.The incidence accounts for 1/50000 and the cause of CdCS is related to partial deletion of chromosome 5 short arm(p).CdCS is a sporadic event.Only one case of CdCS was detected by chromosome screening in 125 and 170 pregnant Iranian women[1].The most prominent clinical manifestations of CdCS are typical high-pitched cat calls,severe mental retardation or mental retardation and is most harmful to both language and growth retardation[2].CdCS is a chromosome mutation disease which occurs during embryonic development and the symptoms of some cases are extremely atypical.It is difficult to make an early diagnosis and screening in clinic.We can suspect the disease from its atypical manifestations in the weak crying of cats,and chromosome karyotype analysis can find some questionable gene deletion fragments to assist the clinical diagnosis and prognosis of CdCS.CASE SUMMARY A 2-d-old male child who was admitted to our hospital with a poor postnatal reaction and poor milk intake.The baby’s crying and sucking is weak,reaction and feeding time is poor and the baby has nausea and vomiting.Karyotype analysis showed that the chromosomes were 46,XY,deletion(5)p15.Whole genome microarray analysis(named ISCN2013)showed that the chromosomes of the child were male karyotypes and contained three chromosomal abnormalities.Among them,loss of 5p15.2pter(113576-13464559)was associated with cat call syndrome.After 3 mo of follow-up,the child still vomited repeatedly,had poor milk intake,did not return to normal growth,had developmental retardation and a poor directional response.CONCLUSION Therefore,when cat crying and laryngeal sounds occur in the neonatal period,it should be considered that they are related to CdCS.Chromosome karyotype and genome analysis are helpful for the diagnosis of CdCS.展开更多
Background Prenatal diagnoses are extremely advantageous for pregnant women with high-risk indicators and can help prevent the birth of malformed infants. However, no large-scale statistical study analyzing the correl...Background Prenatal diagnoses are extremely advantageous for pregnant women with high-risk indicators and can help prevent the birth of malformed infants. However, no large-scale statistical study analyzing the correlation between fetal chromosome disorders and abnormal indicators during pregnancy has been done in China. The objectives of this study were to diagnose and analyze fetal chromosome abnormalities, determine the feasibility of the various prenatal test methods and establish diagnostic guidelines for the early, middle, and late trimesters. Methods From January 2004 to May 2009, 2782 pregnant women at high-risk underwent prenatal diagnoses. Categorized data expressed as either actual counts or percentages were analyzed by the chi-square or Fisher＇s exact test. Chorionic villus sampling was performed in the early-trimester （10-12 weeks of gestation）, amniocentesis in mid-trimester （16-28 weeks of gestation）, and umbilical cord blood collection in mid- or late-trimester （16-37 weeks of gestation）. In 51 cases either autopsy samples from intrauterine fetal deaths or placental tissues from aborted fetuses were tested. Results Chromosomal abnormalities were observed in 3.99% （111/2782） of the samples. Overall, the success rate of cytogenetic analysis for high-risk pregnancy groups was 98.17% （2731/2782）. It was significantly less successful when used to analyze data from the chorionic villus sampling compared with that from amniocentesis and umbilical cord blood （P=-0.000）. Abnormal chromosome carriers had the highest percentage of abnormal chromosomes （67.86%） when compared with chromosomal abnormalities in patients with ultra-sonographic ＂soft markers＂ （11.81%）, advanced maternal age （4.51%） and those who had positive serum screening results （P=-0.000）. Conclusions Invasive prenatal diagnostic techniques are feasible tools for confirming fetal chromosomal abnormalities. Abnormal chromosomes detected in one of the parents carrying abnormal chromosome, ultrasound soft markers, advanced maternal age or positive serum screening results were associated with a higher frequency of fetal genetic diseases.展开更多
Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene colline...Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(https://github.com/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.展开更多
文摘Multiple BAC-FISH is a powerful tool for modern cytogenetic researching in both animals and plants.But in cotton,this technique is unavailable due to the high percentage of repetitive sequences.
基金funded by the National Natural Science Foundation of China(31471481)the Project of Science and Technology of Shaanxi Province of China(2021NY-081 and 2023YBNY-033)。
文摘The constant evolution of pathogens poses a threat to wheat resistance against diseases,endangering food security.Developing resistant wheat varieties is the most practical approach for circumventing this problem.As a close relative of wheat,Aegilops geniculata,particularly accession SY159,has evolved numerous beneficial traits that could be applied to improve wheat.In this study,we established the karyotype of SY159 by fluorescence in situ hybridization(FISH)using the oligonucleotide probes Oligo-pTa535 and Oligo-pSc119.2 and a complete set of wheat–Ae.geniculata accession TA2899 addition lines as a reference.Using specific-locus amplified fragment sequencing(SLAF-seq)technology,400 specific markers were established for detecting the SY159 chromosomes with efficiencies reaching 81.5%.The SY159-specific markers were used to classify the different homologous groups of SY159 against the wheat-Ae.geniculata addition lines.We used these specific markers on the 7Mg chromosome after classification,and successfully confirmed their suitability for studying the different chromosomes of SY159.This study provides a foundation for accelerating the application of SY159 in genetic breeding programs designed to improve wheat.
文摘BACKGROUND Cri du chat syndrome(CdCS),also known as 5p deletion syndrome(5p-)is a syndrome caused by partial deletion of the 5p chromosome in human beings.The incidence accounts for 1/50000 and the cause of CdCS is related to partial deletion of chromosome 5 short arm(p).CdCS is a sporadic event.Only one case of CdCS was detected by chromosome screening in 125 and 170 pregnant Iranian women[1].The most prominent clinical manifestations of CdCS are typical high-pitched cat calls,severe mental retardation or mental retardation and is most harmful to both language and growth retardation[2].CdCS is a chromosome mutation disease which occurs during embryonic development and the symptoms of some cases are extremely atypical.It is difficult to make an early diagnosis and screening in clinic.We can suspect the disease from its atypical manifestations in the weak crying of cats,and chromosome karyotype analysis can find some questionable gene deletion fragments to assist the clinical diagnosis and prognosis of CdCS.CASE SUMMARY A 2-d-old male child who was admitted to our hospital with a poor postnatal reaction and poor milk intake.The baby’s crying and sucking is weak,reaction and feeding time is poor and the baby has nausea and vomiting.Karyotype analysis showed that the chromosomes were 46,XY,deletion(5)p15.Whole genome microarray analysis(named ISCN2013)showed that the chromosomes of the child were male karyotypes and contained three chromosomal abnormalities.Among them,loss of 5p15.2pter(113576-13464559)was associated with cat call syndrome.After 3 mo of follow-up,the child still vomited repeatedly,had poor milk intake,did not return to normal growth,had developmental retardation and a poor directional response.CONCLUSION Therefore,when cat crying and laryngeal sounds occur in the neonatal period,it should be considered that they are related to CdCS.Chromosome karyotype and genome analysis are helpful for the diagnosis of CdCS.
文摘Background Prenatal diagnoses are extremely advantageous for pregnant women with high-risk indicators and can help prevent the birth of malformed infants. However, no large-scale statistical study analyzing the correlation between fetal chromosome disorders and abnormal indicators during pregnancy has been done in China. The objectives of this study were to diagnose and analyze fetal chromosome abnormalities, determine the feasibility of the various prenatal test methods and establish diagnostic guidelines for the early, middle, and late trimesters. Methods From January 2004 to May 2009, 2782 pregnant women at high-risk underwent prenatal diagnoses. Categorized data expressed as either actual counts or percentages were analyzed by the chi-square or Fisher＇s exact test. Chorionic villus sampling was performed in the early-trimester （10-12 weeks of gestation）, amniocentesis in mid-trimester （16-28 weeks of gestation）, and umbilical cord blood collection in mid- or late-trimester （16-37 weeks of gestation）. In 51 cases either autopsy samples from intrauterine fetal deaths or placental tissues from aborted fetuses were tested. Results Chromosomal abnormalities were observed in 3.99% （111/2782） of the samples. Overall, the success rate of cytogenetic analysis for high-risk pregnancy groups was 98.17% （2731/2782）. It was significantly less successful when used to analyze data from the chorionic villus sampling compared with that from amniocentesis and umbilical cord blood （P=-0.000）. Abnormal chromosome carriers had the highest percentage of abnormal chromosomes （67.86%） when compared with chromosomal abnormalities in patients with ultra-sonographic ＂soft markers＂ （11.81%）, advanced maternal age （4.51%） and those who had positive serum screening results （P=-0.000）. Conclusions Invasive prenatal diagnostic techniques are feasible tools for confirming fetal chromosomal abnormalities. Abnormal chromosomes detected in one of the parents carrying abnormal chromosome, ultrasound soft markers, advanced maternal age or positive serum screening results were associated with a higher frequency of fetal genetic diseases.
基金This work was supported equally by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31000000)the National Natural Science Foundation of China(grant numbers 31590821 and 91731301 to J.L.and 32070669to X.W.)+1 种基金the National Key Research and Development Program of China(2017YFC0505203 to Z.X.)also by the Fundamental Research Funds for the Central Universities(SCU2019D013 and 2020SCUNL207)and theNational High-Level Talents Special Support Plan(10 Thousand People Plan)。
文摘Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(https://github.com/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots.
