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Summary: Stature is an important quantitative trait for cattle performance, which influences herd productivity. Previous studies have reported that an SNP (AC_000171.1:g.25015640G>T, rs109815800) in Pleomorphic adenoma gene 1 (PLAG1) on chromosome 14 (CHR14) is associated with bovine stature. To validate whether rs109815800 is associated with the body height of Chinese cattle, we carried out an association analysis using 558 adult cattle samples from seven populations. Then, 1038 samples from 38 Chinese cattle breeds were used to show the geographical distribution of this variant in China. The results showed that the Q allele (G allele) increased the height of cattle. Furthermore, the frequencies of Q allele in Chinese native breeds tend to decrease from northern China to southern China, and the frequency of Q allele in two Chinese beef cattle breeds is much higher than that in another 36 Chinese local cattle breeds. Our data suggest that the prevalence of the Q allele is correlated with latitude in China. [ABSTRACT FROM AUTHOR]

Hymenolepis nanais a common tapeworm that parasitizes in the small intestine of rodent animals and humans. The present study examined the sequence diversity of three mitochondrial (mt) genes namely NADH dehydrogenase subunits 5 (nad5), small subunit ribosomal RNA (rrnS), and ATPase subunit 6 (atp6) ofH. nanafrom mice in different geographical regions of China. A part of thenad5 (pnad5), completerrnS andatp6 genes were amplified separately from individualH. nanaisolates using polymerase chain reaction (PCR) and then sequenced. The sequences of pnad5,rrnS, andatp6 were 710 bp, 704–711 bp, and 516 bp in length, respectively. The A + T contents of the sequences were 70.1–73.5% (pnad5), 70.1–71.7% (rrnS), and 76.6–77.9% (atp6). Sequence variation withinH. nanawas 0–1.4% foratp6, 0–1.7% forrrnS, and 0–0.7% for pnad5. The inter-specific sequence differences betweenH. nanaandHymenolepis diminutawere significantly higher, which was 31.6–31.7% (pnad5), 16.1–17.6% (rrnS), and 26.5–27.1% (atp6). Phylogenetic analysis based on the combined three sequences using the maximum parsimony (MP) method supported thatH. nanais a species complex or “cryptic” species. These findings demonstrated clearly the usefulness of the three mtDNA sequences for population genetics and systematic studies ofH. nanaof human and animal health significance. [ABSTRACT FROM AUTHOR]

Panton-Valentine leukocidin (PVL, encoded by lukSF-PV genes), a bi-component and pore-forming toxin, is carried by different staphylococcal bacteriophages. The prevalence of PVL in Staphylococcus aureus has been reported around the globe. However, the data on PVL-encoding phage types, lukSF-PV gene variation and chromosomal phage insertion sites for PVL-positive S. aureus are limited, especially in China. In order to obtain a more complete understanding of the molecular epidemiology of PVL-positive S. aureus, an integrated and modified PCR-based scheme was applied to detect the PVL-encoding phage types. Phage insertion locus and the lukSF-PV variant were determined by PCR and sequencing. Meanwhile, the genetic background was characterized by staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) gene polymorphisms typing, pulsed-field gel electrophoresis (PFGE) typing, accessory gene regulator (agr) locus typing and multilocus sequence typing (MLST). Seventy eight (78/1175, 6.6%) isolates possessed the lukSF-PV genes and 59.0% (46/78) of PVL-positive strains belonged to CC59 lineage. Eight known different PVL-encoding phage types were detected, and Ф7247PVL/ФST5967PVL (n = 13) and ФPVL (n = 12) were the most prevalent among them. While 25 (25/78, 32.1%) isolates, belonging to ST30, and ST59 clones, were unable to be typed by the modified PCR-based scheme. Single nucleotide polymorphisms (SNPs) were identified at five locations in the lukSF-PV genes, two of which were non-synonymous. Maximum-likelihood tree analysis of attachment sites sequences detected six SNP profiles for attR and eight for attL, respectively. In conclusion, the PVL-positive S. aureus mainly harbored Ф7247PVL/ФST5967PVL and ФPVL in the regions studied. lukSF-PV gene sequences, PVL-encoding phages, and phage insertion locus generally varied with lineages. Moreover, PVL-positive clones that have emerged worldwide likely carry distinct phages. [ABSTRACT FROM AUTHOR]

The present study examined genetic variability among Clonorchis sinensis isolates from four different geographical localities (Guangzhou, Nanning, Jiamusi and Daqing) and host species (cats, dogs, human and rabbits) in Mainland China by sequence analyses of two mitochondrial DNA (mtDNA) genes, namely NADH dehydrogenase subunits 2, 5 ( nad2 and nad5) and ribosomal internal transcribed spacer 1 (ITS1). A portion of the ITS1, nad2 (p nad2) and nad5 (p nad5) was amplified by polymerase chain reaction separately from adult C. sinensis individuals and the amplicons were subjected to sequencing from both directions. The length of the sequences of ITS1, p nad2 and p nad5 was 643, 666 and 771 bp, respectively. The intraspecific sequence variations within C. sinensis were 0-1.7% for ITS1, 0-1.4% for p nad2 and 0-0.9% for p nad5. The interspecific sequence variations within other zoonotic trematodes, which were published previously, were 4.5-84.9% for ITS1, 21.9-43.6% for p nad2 and 19.2-48.9% for p nad5. The A+T contents of the sequences were 45.26-45.88% (ITS1), 62.91-63.51% (p nad2) and 58.24-58.63% (p nad5). Phylogenetic analyses using ribosomal and mitochondrial sequence data set, with three different computational algorithms (Bayesian inference, maximum parsimony and maximum likelihood), all revealed distinct groups with high statistical support. These findings demonstrated the existence of low-level intraspecific variations in ribosomal DNA (rDNA) and mtDNA sequences among C. sinensis isolates from four different regions and hosts in China and elucidated that mtDNA sequences and rDNA sequences provided reliable genetic markers for phylogenetic studies of zoonotic trematodes. [ABSTRACT FROM AUTHOR]

Dicrocoelium chinensis is commonly known as the 'lancet fluke' or 'small liver fluke' which lives in the bile ducts and gall bladder of domestic and wild ruminants. In this study, we examined sequence variability in two mitochondrial (mt) genes, namely cytochrome c oxidase subunit 1 ( cox1) and NADH dehydrogenase subunit 1 ( nad1) genes, among D. chinensis isolated from domestic yaks in Gansu and Sichuan provinces, China. A portion of the cox1 (p cox1) and nad1 (p nad1) genes was amplified by PCR separately from the individual adult D. chinensis, and the amplicons were subjected to sequencing from both directions. The lengths of the sequences of p cox1 and p nad1 were 358 and 458 bp, respectively. The A+T contents of the sequences were 58.94-59.22% for p cox1 and 60.04-60.48% for p nad1, respectively. The intra-specific sequence variations within D. chinensis were 0-0.84% for p cox1 and 0-0.87% for p nad1. The inter-specific sequence differences among members of the examined trematodes were significantly higher, being 22.9-29.3% and 33.6-41.5% for p cox1 and p nad1, respectively. Phylogenetic analysis utilizing combined sequences of p cox1 and p nad1 using Bayesian inference revealed that all of the D. chinensis isolates grouped together with high statistical support. These findings demonstrated the existence of low intra-specific variation in mitochondrial DNA (mtDNA) sequences among the D. chinensis isolates from domestic yaks in China and had implications for studying the molecular epidemiology and population genetics of D. chinensis. [ABSTRACT FROM AUTHOR]

Abstract: The present study identified and characterized new major sperm protein (MSP) genes from the two nodule worms Oesophagostomum dentatum and Oesophagostomum quadrispinulatum collected from pigs in China. Total genomic DNA was extracted individually from 10 male nematode samples representing O. dentatum, and 4 male nematode samples representing O. quadrispinulatum. A pair of primers (OMSP1F/MSP1R) was designed based on the MSP gene sequences of Ascaris suum and O. dentatum available in GenBank, and used to amplify the MSP genes from the two porcine nodule worms. The PCR products were purified and subsequently cloned into pGEM-T Easy vector. Recombinants were identified by PCR and sequenced. Sequence analysis revealed that there were two different types of MSP sequences in O. dentatum and O. quadrispinulatum, one contained intron, and the other did not. The lengths of the MSP sequences containing introns were 433bp or 439bp in O. dentatum, and 436bp, 439bp or 446bp in O. quadrispinulatum, containing 1 or 2 introns. Five and three new members of the MSP multigene family were identified in O. dentatum and O. quadrispinulatum in this study, respectively. The MSP sequences without introns were 381bp in length, and can be deduced into 126 amino acids. The sequences of MSP genes containing introns seem to be more conserved than those without introns. The identities of deduced amino acid sequences of the MSP genes containing introns were 96.0–100% within and between the two nodule worms, and were 81.1–93.7% compared with other published MSP sequences of the representative nematodes. The present study identified new MSP genes with introns from O. dentatum and O. quadrispinulatum for the first time. The identification and characterization of newly described MSP genes from O. dentatum and O. quadrispinulatum have implications for further studies of molecular biology and reproduction control of Oesophagostomum spp. [Copyright &y& Elsevier]

Chrysanthemum stunt viroid (CSVd) has been detected or isolated from chrysanthemums or other host species in 26 countries. While strains (biological variants) have been described for many viroids, strains have not been described as such specifically for CSVd, despite the determination of 117 sequence variants of CSVd in 16 countries. Tomato has been described as an experimental host, either symptomless, or showing mild, or even severe symptoms, depending on the report; however, most of these studies were done with single isolates of CSVd and one cultivar of tomato plants. Thus, here we re-examined these issues by directly comparing the biological activity of three isolates of CSVd, one each from the USA, China and Australia, varying in their nucleotide sequence. We found that these isolates showed no differences in symptoms induced on either chrysanthemum or tomato plants, suggesting that much of the biological variation reported previously may have been due to cultivar differences and/or environmental effects. [ABSTRACT FROM AUTHOR]

In this study, sequence variation in three mitochondrial DNA regions, namely cytochrome c oxidase subunit ( cox1) and NADH dehydrogenase subunits 1 and 4 ( nad1 and nad4), between Oesophagostomum dentatum and O. quadrispinulatum isolated from pigs in different geographical origins in Mainland China was examined, and their phylogenetic relationships were reconstructed. A partial of the cox1 (p cox1), nad1, and nad4 genes (p nad1 and p nad4) were amplified separately from individual nodule worms by PCR and were subjected to direct sequencing in order to define sequence variations. While the intraspecific sequence variations within each of the two species were 0.3-5.2% for p cox1, 0-4.9% for p nad1, and 0-7.1% for p nad4, the interspecific sequence differences were significantly higher, being 10.7-13.4% for p cox1, 11-14.6% for p nad1, and 14.9-18% for p nad4, respectively. There were a number of nucleotide positions in the p cox1, p nad1, and p nad4 sequences with no apparent intraspecific variation but distinct interspecific differences among those samples of Oesophagostomum spp. examined, which may be used as genetic makers for the identification and differentiation of the Oesophagostomum spp. Phylogenetic analyses using three inference methods, namely Bayesian inference, maximum likelihood, and maximum parsimony based on the combined sequences of p cox1, p nad1, and p nad4 revealed that the O. dentatum and O. quadrispinulatum form monophyletic groups, respectively. These findings demonstrated clearly the usefulness of the three mitochondrial sequences for studying systematics, population genetic structures, and the molecular ecology of Oesophagostomum spp. [ABSTRACT FROM AUTHOR]

Unionicola (Wolcottatax) arcuata (Wolcott, 1898) (Acari: Hydrachnidia: Unionicolidae) commonly occurs in parasitic association with Cristaria plicata (Leach), Anodonta woodiana elliptica (Heude) or Anodonta woodiana pacifica (Heude) during one or more stages of its life cycle. The mitochondrial 12S rRNA gene was sequenced and analysed from U. arcuata obtained from nine populations of these freshwater mussels from six large lakes in the middle and lower reaches of the Yangtze River, China. The 382 base sequence alignments for these nine populations of U. arcuata had two gaps and contained 51 (13.4%) variable nucleotides. The pairwise divergences among U. arcuata sequence data ranged from 0 to 10.9%, with the lowest intraspecific divergences (0–0.5%) observed among U. arcuata obtained from the same host species and the highest intraspecific divergences (6.7–10.9%) found among U. arcuata from different species of hosts. The results of sequence alignment and divergence were consistent with the heterogeneity in sequence data of the 12S rRNA gene observed in other studies of acarines. Maximum parsimony and maximum likelihood analyses each yielded a single tree with the same topology and high bootstrap support. The gene trees indicate three major clades, with U. arcuata from C. plicata, A. woodiana elliptica and A. woodiana pacifica each forming a distinct clade. Overall, the results of this study indicated that host association, rather than patterns of geographic distribution, plays an important role in the degree of genetic divergence among populations of U. arcuata. [ABSTRACT FROM AUTHOR]

Abstract: Background: There are few data in the literature on viral sequence variation between host generations/successive transmission events. Relatively little is known about the sequence heterogeneity of the influenza viruses transmitted within families. Objectives: To study the molecular epidemiology of influenza virus and to determine the sequence variation within an individual, a household and a community during the first wave of influenza pandemic in 2009. Study design: A prospective study of household transmission of influenza A in Hong Kong was conducted during the pandemic in 2009. The HA and NA sequences of pandemic and seasonal influenza A viral isolates identified in this household transmission study were sequences and analyzed. Results: Our results indicated that there were multiple introductions of influenza viruses into Hong Kong. Sequence analysis of these isolates suggested that members of these family clusters acquired the infection by household transmissions. Interestingly, unlike those concluded from previous household transmission studies, we observed sequence variations between sequential samples from the same person and also within the same household. Conclusions: Family clusters of influenza A viral infection are predominantly the result of secondary transmission within a household. Our results also suggested that the intra-host viral sequence variation might be more common that than previously thought. [Copyright &y& Elsevier]

Abstract: Objective: To identify genetic variants in the E6 gene of HPV 16 and to examine the association between these variants and cervical cancer development. Methods: Cervical samples were collected from 72 patients with cervical cancer and 72 age-matched control subjects, all from Hubei Province, China. HPV 16 sequence was detected with E6 gene-specific polymerase chain reaction, and variants were identified by DNA sequencing. Results: HPV 16 was detected in 81% of the patients and 43% of control subjects, respectively. The rank orders of incidence of HPV 16 prototype and E6 variants were as follows: D25E (62%), the prototype (17%), E113D (9%), L83V (6%) in case subjects; the prototype (71%), D25E (23%), L83V/E113D (7%) in control subjects. The odds ratio of HPV 16 E6 variant was higher than that of prototype (RR=11.73, 95% CI=4.18–32.94, P =0.0001). Conclusion: The D25 E variant is the most prevalent E6 genomic variant in Hubei, China. The presence of HPV 16 E6 variant in cervical intraepithelial neoplasia (CIN) lesions may serve as a useful predictor of clinical outcome of the disease. [Copyright &y& Elsevier]

Wheat microsatellite XGWM261, due to its closely linked to the dwarfing gene Rht8, has been adopted as the diagnostic molecular marker of Rht8. Screening 408 Chinese and 98 exotic varieties showed 13 allele variants in locus of XGWM261, with 6 alleles only to be found in Chinese varieties and 2 only in exotic varieties, respectively. Sequencing results of the 13 alleles revealed their absolute fragment sizes with 216, 212, 210, 206, 204, 202, 200, 196, 194, 192, 190, 174, and 164 bp, respectively. Allelic distribution analysis showed that the 204, 192, 174, and 164 bp alleles were prevailing in Chinese varieties, and the diagnostic 192 bp allele to Rht8 had a very high percentage in the Yellow and Huai River Valleys Facultative Wheat Zone than in the Northern Winter Wheat Zone in China. The GT → AC substitution at position 35 was found in 216, 200, and 174 bp alleles. Moreover, the AG insertion immediately at the end of CT-repeat region was also found in 216, 200, 174, and 164 bp alleles. [ABSTRACT FROM AUTHOR]

High genetic diversity and low differentiation present challenges in taxonomy and systematics of Salix. Chloroplast (cp) genome sequencing is efficient for providing new genomic information and elucidating phylogenetic relationships. Salix spathulifolia Seemen, S. cupularis Rehder, and S. annulifera C.Marquand & Airy Shaw are three shrubby willows spread in high-altitude regions in western China. In this study, the integrated circular cp genomes were sequenced and analyzed, and a phylogeny of Salix was constructed on the basis of the cp genomes. The results of chloroplast assembly and annotation information were used to characterize genome feature and interspecific variation. The phylogenetic position of the three willows was evaluated using phylogenetic analysis. Full-length cp genomes were 155,566–155,680 bp with a typical double-stranded circular quadripartite structure, containing one large single-copy region (LSC, 84,431–4552 bp), one small single-copy region (SSC: 16,206–16,221 bp), and two inverted repeats (IR: 27,453–27,461 bp). The cp genomes encoded 130 genes, including 8 rRNA genes, 37 tRNA genes, and 85 protein-coding genes. The guanine-cytosine (GC) content of the overall genome was 36.7%. Comparison among the three willows' cp genomes revealed high similarity. Phylogenetic analysis indicated that S. spathulifolia was a basal taxon of clade I, while S. annulifera formed a monophyletic group with S. rorida Laksch.; S. cupularis was sister to S. suchowensis W.C. Cheng and S. psammophila Z. Wang & Chang Y. Yang. The complete chloroplast genomes of the three willows provides an additional sequence-based resource for studying the phylogeny and evolutionary history of Salicaceae. [ABSTRACT FROM AUTHOR]

Ramie fibers, one of the most important natural fibers in China, are mainly composed of lignin, cellulose, and hemicellulose. As the high lignin content in the fibers results in a prickly texture, the lignin content is deemed to be an important trait of the fiber quality. In this study, the genetic basis of the fiber lignin content was evaluated, resulting in the identification of five quantitative trait loci (QTLs). Three genes, whole_GLEAN_10021050, whole_GLEAN_10026962, and whole_GLEAN_10009464 that were identified on the QTL regions of qLC7, qLC10, and qLC13, respectively, were found to be homologs of the Arabidopsis lignin biosynthetic genes. Moreover, all three genes displayed differential expression in the barks located in the top and middle parts of the stem, where lignin was not being synthesized and where it was being biosynthesized, respectively. Sequence comparison found that these three genes had wide variations in their coding sequences (CDSs) and putative promoter regions between the two parents, especially the MYB gene whole_GLEAN_10021050, whose protein had insertions/deletions of five amino acids and substitutions of two amino acids in the conserved domain. This evidence indicates that these three genes are potentially involved in lignin biosynthesis in ramie fibers. The QTLs identified from this study provide a basis for the improvement of lignin content and fiber quality in ramie breeding. The characterization of the three candidate genes here will be helpful for the future clarification of their functions in ramie. [ABSTRACT FROM AUTHOR]

Capillary electrophoresis (CE) is widely used in forensic genetics to study short tandem repeats (STRs). Recently, next-generation sequencing (NGS) platforms have facilitated the development of new strategies for forensic DNA typing. Several studies have shown that NGS successfully analyzes challenging samples. However, because NGS is complicated and time-consuming, it remains unclear whether NGS platforms offer significant advantages over CE for all forensic cases. Here, the MiSeq FGx system was used to test some cases that had previously been analyzed using CE. These cases included paternity test cases in which some samples exhibited locus inconsistencies; samples with off-ladder (OL) alleles; samples with triallelic patterns; and samples with amelogenin test abnormalities. The results generated by MiSeq FGx were compared to those previously generated by CE. The MiSeq FGx and CE results were consistent with the exception of three samples, where inconsistencies were observed at the Penta D locus. For all three incongruent samples, the MiSeq FGx results were correct. Sequence analysis indicated that, in two cases, mismatches were due to undetected alleles rather than mutations. In two additional cases, mutation sources were identified, and in a fifth case, mutation step size was reconsidered. MiSeq FGx was used to identify OL alleles and samples with amelogenin test abnormalities. For cases where verification was required via CE analysis, the simultaneous NGS amplification of several types of multiple genetic markers improved testing efficiency. In addition, we identified additional sequence variants at autosomal, Y chromosomal, and X chromosomal STR loci in the Han Chinese population from northern China. Our results will be useful for future forensic analyses of STR genotypes in Chinese populations. It is likely that NGS would be more widely used in forensic genetics if costs and procedure complexity were reduced.

Toxoplasma gondii is a eukaryotic parasite of the phylum Apicomplexa, which infects all warm-blood animals, including humans. In the present study, we examined sequence variation in dense granule 20 (GRA20) genes among T. gondii isolates collected from different hosts and geographical regions worldwide. The complete GRA20 genes were amplified from 16 T. gondii isolates using PCR, sequence were analyzed, and phylogenetic reconstruction was analyzed by maximum parsimony (MP) and maximum likelihood (ML) methods. The results showed that the complete GRA20 gene sequence was 1,586 bp in length among all the isolates used in this study, and the sequence variations in nucleotides were 0-7.9% among all strains. However, removing the type III strains (CTG, VEG), the sequence variations became very low, only 0-0.7%. These results indicated that the GRA20 sequence in type III was more divergence. Phylogenetic analysis of GRA20 sequences using MP and ML methods can differentiate 2 major clonal lineage types (type I and type III) into their respective clusters, indicating the GRA20 gene may represent a novel genetic marker for intraspecific phylogenetic analyses of T. gondii.

Background: Several studies have demonstrated that variants on chromosome 9p21 confer susceptibility to ischemic stroke (IS) disease. But, the results of variants' roles in Chinese IS population are blank or inconsistent., Methods: We performed a case-control analysis in 116 patients with IS and 118 non-IS controls of Han background to determine whether 4 single nucleotide polymorphisms were associated with IS. DNA was extracted from saliva using a magnetic nanoparticles-based method., Results: After we adjusted for clinical parameters, we found that the rs10757278-GG genotype conveyed 1.88-fold (95% confidence interval [CI], 1.1-3.1; P = .015), the rs1537378-C allele conveyed 2.0-fold (95% CI, 1.2-3.5; P = .008), and the rs1333047-TT genotype conveyed 1.64-fold (95% CI, 1.02-2.6; P = .041) increased risk of IS, respectively. In addition, there is a significant difference of the lipids level between GG genotype compared with that of AA genotype in rs10757278 (P < .05)., Conclusions: This study is the first one to demonstrate that the rs10757278-GG genotype, the rs1537378-C allele, and rs1333047-TT genotype are associated with IS in Chinese Han populations. More importantly, the variant of rs10757278 may have different degrees of influence on lipids level., (Copyright © 2015 National Stroke Association. Published by Elsevier Inc. All rights reserved.)

Background: DNA sequence variation including base(s) changes and insertion or deletion in the primer binding region may cause a null allele and, if this changes the length of the amplified fragment out of the allelic ladder, off-ladder (OL) alleles may be detected., Aim: In order to provide accurate and reliable DNA evidence for forensic DNA analysis, it is essential to clarify sequence variations in prevalently used STR loci., Subjects and Methods: Suspected null alleles and OL alleles of PlowerPlex16® System from 21,934 unrelated Chinese individuals were verified by alternative systems and sequenced., Results: A total of 17 cases with null alleles were identified, including 12 kinds of point mutations in 16 cases and a 19-base deletion in one case. The total frequency of null alleles was 7.751 × 10(-4). Eight hundred and forty-four OL alleles classified as being of 97 different kinds were observed at 15 STR loci of the PowerPlex®16 system except vWA. All the frequencies of OL alleles were under 0.01., Conclusion: Null alleles should be confirmed by alternative primers and OL alleles should be named appropriately. Particular attention should be paid to sequence variation, since incorrect designation could lead to false conclusions.