A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced t...A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript as- sembly contigs （TACs） with an N50 of 1510 bp, the largest one being -8 kb. Of the 21 434 TACs, 16 622 （77.5%） could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content （PIC） value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.展开更多
BACKGROUND Kidney transplantation is the standard treatment for end-stage renal disease.Particularly,rare and specific pathogenic infections which are asymptomatic are often difficult to diagnose,causing delayed and i...BACKGROUND Kidney transplantation is the standard treatment for end-stage renal disease.Particularly,rare and specific pathogenic infections which are asymptomatic are often difficult to diagnose,causing delayed and ineffective treatment and thus seriously affecting prognosis.Tropheryma whipplei(T.whipplei)is a Gram-positive actinomycete widely found in soil,sewage,and other external environments and is present in the population as an asymptomatic pathogen.There is relatively little documented research on T.whipplei in renal transplant patients,and there are no uniform criteria for treating this group of post-transplant patients.This article describes the treatment of a 42-year-old individual with post-transplant T.whipplei infection following kidney transplantation.CASE SUMMARY To analyze clinical features of Whipple’s disease and summarize its diagnosis and treatment effects after renal transplantation.Clinical data of a Whipple’s disease patient treated in the affiliated hospital of Guizhou Medical University were collected and assessed retrospectively.The treatment outcomes and clinical experience were then summarized via literature review.The patient was admitted to the hospital due to recurrent diarrhea for 1 mo,shortness of breath,and 1 wk of fever,after 3 years of renal transplantation.The symptoms of the digestive and respiratory systems were not significantly improved after adjusting immunosuppressive regimen and anti-diarrheal,empirical antibiotic treatments.Bronchoscopic alveolar fluid was collected for meta-genomic next-generation sequencing(mNGS).The deoxyribonucleic acid sequence of Tropheryma whipplei was detected,and Whipple’s disease was diagnosed.Meropenem,ceftriaxone,and other symptomatic treatments were given,and water-electrolyte balance was maintained.Symptoms resolved quickly,and the patient was discharged after 20 d of hospitalization.The compound sulfamethoxazole tablet was continued for 3 mo after discharge.No diarrhea,fever,and other symptoms occurred during the 6-month follow-up.CONCLUSION Whipple’s disease is rare,with no specific symptoms,which makes diagnosis difficult.Polymerase chain reaction or mNGS should be immediately performed when the disease is suspected to confirm the diagnosis.展开更多
文摘A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript as- sembly contigs （TACs） with an N50 of 1510 bp, the largest one being -8 kb. Of the 21 434 TACs, 16 622 （77.5%） could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content （PIC） value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.
基金Supported by Guiyang Science and Technology Program,No.2019-9-1-39.
文摘BACKGROUND Kidney transplantation is the standard treatment for end-stage renal disease.Particularly,rare and specific pathogenic infections which are asymptomatic are often difficult to diagnose,causing delayed and ineffective treatment and thus seriously affecting prognosis.Tropheryma whipplei(T.whipplei)is a Gram-positive actinomycete widely found in soil,sewage,and other external environments and is present in the population as an asymptomatic pathogen.There is relatively little documented research on T.whipplei in renal transplant patients,and there are no uniform criteria for treating this group of post-transplant patients.This article describes the treatment of a 42-year-old individual with post-transplant T.whipplei infection following kidney transplantation.CASE SUMMARY To analyze clinical features of Whipple’s disease and summarize its diagnosis and treatment effects after renal transplantation.Clinical data of a Whipple’s disease patient treated in the affiliated hospital of Guizhou Medical University were collected and assessed retrospectively.The treatment outcomes and clinical experience were then summarized via literature review.The patient was admitted to the hospital due to recurrent diarrhea for 1 mo,shortness of breath,and 1 wk of fever,after 3 years of renal transplantation.The symptoms of the digestive and respiratory systems were not significantly improved after adjusting immunosuppressive regimen and anti-diarrheal,empirical antibiotic treatments.Bronchoscopic alveolar fluid was collected for meta-genomic next-generation sequencing(mNGS).The deoxyribonucleic acid sequence of Tropheryma whipplei was detected,and Whipple’s disease was diagnosed.Meropenem,ceftriaxone,and other symptomatic treatments were given,and water-electrolyte balance was maintained.Symptoms resolved quickly,and the patient was discharged after 20 d of hospitalization.The compound sulfamethoxazole tablet was continued for 3 mo after discharge.No diarrhea,fever,and other symptoms occurred during the 6-month follow-up.CONCLUSION Whipple’s disease is rare,with no specific symptoms,which makes diagnosis difficult.Polymerase chain reaction or mNGS should be immediately performed when the disease is suspected to confirm the diagnosis.
