BGI Shenzhen Shenzhen China

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BGI Shenzhen Shenzhen China

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Campbell B.C.,University of Queensland | Gilding E.K.,University of Queensland | Tai S.,BGI Shenzhen Shenzhen China | Tao Y.,University of Queensland | And 4 more authors.
Plant Biotechnology Journal | Year: 2016

Next-generation sequencing of complete genomes has given researchers unprecedented levels of information to study the multifaceted evolutionary changes that have shaped elite plant germplasm. In conjunction with population genetic analytical techniques and detailed online databases, we can more accurately capture the effects of domestication on entire biological pathways of agronomic importance. In this study, we explore the genetic diversity and signatures of selection in all predicted gene models of the storage starch synthesis pathway of Sorghum bicolor, utilizing a diversity panel containing lines categorized as either 'Landraces' or 'Wild and Weedy' genotypes. Amongst a total of 114 genes involved in starch synthesis, 71 had at least a single signal of purifying selection and 62 a signal of balancing selection and others a mix of both. This included key genes such as STARCH PHOSPHORYLASE 2 (SbPHO2, under balancing selection), PULLULANASE (SbPUL, under balancing selection) and ADP-glucose pyrophosphorylases (SHRUNKEN2, SbSH2 under purifying selection). Effectively, many genes within the primary starch synthesis pathway had a clear reduction in nucleotide diversity between the Landraces and wild and weedy lines indicating that the ancestral effects of domestication are still clearly identifiable. There was evidence of the positional rate variation within the well-characterized primary starch synthesis pathway of sorghum, particularly in the Landraces, whereby low evolutionary rates upstream and high rates downstream in the metabolic pathway were expected. This observation did not extend to the wild and weedy lines or the minor starch synthesis pathways. © 2016 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.


Xu Y.,Sun Yat Sen University | Guan L.,BGI Shenzhen Shenzhen China | Xiao X.,Sun Yat Sen University | Zhang J.,BGI Shenzhen Shenzhen China | And 7 more authors.
Clinical Genetics | Year: 2015

In our previous studies, mutations in known candidate genes were detected in approximately 50% of Chinese patients with various forms of retinal degeneration. The next stage, identifying additional causative mutations in patients with various forms of genetic eye diseases based on whole exome sequencing of 1220 samples, revealed frequent homozygous or compound heterozygous null mutations in ALMS1, which are known to associate with Alström syndrome as well as individuals diagnosed with Leber congenital amaurosis (LCA) or early-onset severe cone-rod dystrophy (CORD) without signs of systemic phenotypes except that one had a congenital heart abnormity. Sanger sequencing, co-segregation analysis and analysis of normal individuals identified a total of 13 null mutations in ALMS1 in 11 probands, including 4 probands with homozygous mutations and 7 with compound heterozygous mutations. Follow-up examinations revealed absent or mild systemic manifestations of Alström syndrome in those available: 9 of 15 patients in 11 families. These findings not only expand the spectrum of phenotypes associated with ALMS1 mutations but also suggest that ALMS1 should be regarded as a candidate causative gene in patients diagnosed with isolated LCA and early-onset severe CORD. © 2015 John Wiley & Sons A/S.


Lin N.,Fujian Agriculture and forestry University | Liu Z.,BGI Shenzhen Shenzhen China | Zhou J.,The 4th Peoples Hospital Foshan City | Wang S.,Fujian Agriculture and forestry University | Fleming J.,CAS Institute of Biophysics
FEMS Microbiology Letters | Year: 2013

The prevalence of drug-resistance in Mycobacterium tuberculosis is already having a negative impact on the control of tuberculosis. We report the draft genome sequences of two super-extensively drug-resistant M. tuberculosis isolates from China, FJ05194 (lineage 2) and GuangZ0019 (lineage 4), and compare them with the H37Rv reference strain to identify possible sources of genetic variation associated with their extensive drug resistance. Our results suggest that their extensive drug resistance probably results from the stepwise accumulation of resistances to individual drugs. © 2013 Federation of European Microbiological Societies.


Zhang C.,BGI Shenzhen Shenzhen China | Wang Y.,South China University of Technology | Huang C.,BGI Shenzhen Shenzhen China | Zhang M.,BGI Shenzhen Shenzhen China | And 4 more authors.
Tissue Antigens | Year: 2013

Twenty-seven novel human leukocyte antigen (HLA) class II alleles in Chinese Marrow Donors are described: 10 HLA-DRB1 alleles and 17 HLA-DQB1 alleles. © 2013 John Wiley & Sons A/S.

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