A Chinese Patient with Spastic Paraplegia Type 4 with a De Novo Mutation in the SPAST Gene

Background. Spastic paraplegia type 4 (SPG4) is the most common type of hereditary spastic paraplegia (HSP) caused by mutations in the SPAST gene. Case Presentation. We report the case of a 27-year-old pregnant Chinese woman with HSP in whom we identified a missense mutation in the SPAST gene (c.1496G>A, p.Arg499His) and a nonsense mutation in the NEFH gene (c.289G>T, p.Glu97 ∗ ) via whole-exome sequencing; this finding corroborated that of Sanger sequencing. The patient exhibited the pure SPG4 phenotype with onset during childhood. The SPAST mutation was absent in the parents and paternal relatives. However, the NEFH mutation was identified in five people with no clinical phenotype. Based on theoretical conjecture and the family gene segregation information, we concluded that the SPAST mutation, but not the NEFH mutation, accounted for the proband’s phenotype. Eventually, the woman gave birth to a healthy baby girl with the NEFH mutation. Conclusion. In this report, we identified a missense mutation in the SPAST gene (p.Arg499His) in a 27-year-old pregnant Chinese woman with HSP. We believe that this study expands the knowledge about the clinical parameters and mutation spectrum of SPG4.

Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has been observed in V. parahaemolyticus , including in the genomic regions encoding the O and K antigens. V. parahaemolyticus serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of V. parahaemolyticus have been reported in China. However, the relationships among this serotype of V. parahaemolyticus strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the V. parahaemolyticus serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of V. parahaemolyticus isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of V. parahaemolyticus were acquired from within the genus Vibrio . Hence, we have shown that multiple distinct lineages exist in V. parahaemolyticus serotype O4:K12 and have provided more evidence about the gene segregation found in V. parahaemolyticus isolated in different continents.

The Reproducibility of an Inferred Tree and the Diploidization of Gene Segregation after Genome Duplication

We previously introduced a numerical quantity called the stability (Ps) of an inferred tree and showed that for the tree to be reliable this stability as well as the reliability of the tree, which is usually computed as the bootstrap probability (Pb), must be high. However, if genome duplication occurs in a species, a gene family of the genome also duplicates, and for this reason alone some Ps values can be high in a tree of the duplicated gene families. In addition, the topology of the duplicated gene family can be similar to that of the original gene family if such gene families are identifiable. After genome duplication, however, the gene families are often partially deleted or partially duplicated, and the duplicated gene family may not show the same topology as that of the original family. It is therefore necessary to compute the similarity of the topologies of the duplicated and the original gene families. In this paper, we introduce another quantity called the reproducibility (Pr) for measuring the similarity of the two gene families. To show how to compute the Pr values, we first compute the Pb and Ps values for each of the MHC class II α and β chain gene families, which were apparently generated by genome duplication. We then compute the Pr values for the MHC class II α and β chain gene families. The Pr values for the α and β chain gene families are now low, and this suggests that the diploidization of gene segregation has occurred after the genome duplication. Currently higher animals, defined as animals with complex phenotypic characters, generally have a higher genome size, and this increase in genome size appears to have been caused by genome duplication and diploidization of gene segregation after genome duplication.

Distribusi dan Pola Segregasi Karakter Kuantitatif F2 Persilangan Padi Situ Patenggang dengan IPB 3S

This study aims to determine the distribution and patterns of gene segregation that play a role in the inheritance of quantitative F2 traits resulting from the Situ Patenggang rice crossing with IPB 3S. The method used in this study is an experimental method carried out in July to December 2018 with a single plant cropping pattern. Data distribution was tested by Kolmogorov Smirnov test using SPSS 17.0 software and the suitability of segregation ratio using Chi-Square method with a real level of 5%. The results showed the nature of the number of productive puppies in normal distribution which means the character is controlled by many genes (polygenic). Plant height, number of empty grains and number of filled grains follow Mendel's segregation pattern with a ratio of 15: 1 (double dominant epistasis; controlled by two dominant genes that are both epistasis and regulate the same traits and can replace one another). the nature of the number of non-productive tillers, panicle length, and weight of 1000 grains does not follow the Mendel segregation ratio pattern or its modification for one trait and two traits is assumed because it is controlled by more than two genes (minor genes) so that their individual effects are difficult to distinguish.

Effects of mutations in pigeonMc1rimplicate an expanded plumage color patterning regulatory network

Studies in mammals have shown that the Melanocortin 1 receptor occupies a pivotal role as a nexus for integrating paracrine and autocrine signals to regulate pigment production and type-switching between pheomelanin (red/yellow) and eumelanin (black/brown) pigment synthesis in melanocytes. Inactivating mutations in theMc1rgene are responsible for recessive pheomelanic reddening traits in several species, while mutations that increase activity cause dominant eumelanic darkening traits in mammals and birds. Previous efforts to associateMc1rcoding variants with color variation in pigeons (Columba livia) have yielded conflicting results. Applying a reverse genomic approach, we discovered a novel 500 base pair frameshifting deletion in pigeonMc1rthat likely inactivates the single-exon gene. Segregation analysis revealed complete cosegregation (LOD = 12.2) withsmoky(symbolsy), a recessive pigmentation trait reported in these pages by Willard F. Hollander 80 years ago. We coupled these findings with breeding tests to determine thatDirty(V), a dominant darkening trait, is allelic tosy, and identified two independentValleles, one of which is associated with melanic morphs of two other bird species. In contrast to observations thatMc1rinactivation results in uniform pheomelanic pelage in mammals, its loss in otherwise wild-type pigeons occurs without apparent pheomelanism, instead increasing plumage eumelanism while leaving black bar pattern elements of the tail and wing largely intact. These findings require reconsideration of Mc1r’s presumed role in pigment type-switching in birds, and suggest the existence of Mc1r-independent pathways for eumelanic pigmentation pattern regulation unknown in mammals.

A novel c.973G>T mutation in the ε-subunit of the acetylcholine receptor causing congenital myasthenic syndrome in an iranian family

Congenital myasthenic syndrome (CMS) constitutes a group of inherited disorders of neuromuscular junctions. The majority of postsynaptic syndromes result from mutations in the CHRNE gene that causes muscle nicotine acetylcholine deficiency. In this study, we report on a 2 and a half-year-old boy with normal developmental milestones and bilateral ptosis. Clinical courses, electrophysiological studies and molecular genetic analysis were assessed. Polymerase chain reaction (PCR) and direct DNA sequencing of the CHRNE gene were performed for the proband and all the family members. A novel homozygous missense mutation of c.973G>T was found in the CHRNE gene. Segregation studies were suggested to be the genetic cause of the disease. Using three in silico tools and the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant classification guidelines indicated that the novel variant c.973G>T was likely pathogenic. Our results recommended first screening of the CHRNE gene for pathogenic mutations in Iranian origin.

Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

During analysis of kiwifruit derived from hybrids between the high vitamin C (ascorbic acid; AsA) species Actinidia eriantha and A. chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis, we performed whole-genome sequencing on pools of hybrid genotypes with either high or low AsA fruit. Pool-GWAS (genome-wide association study) revealed a single Quantitative Trait Locus (QTL) spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis × A. eriantha) × A. chinensis backcross families, showing that the A. eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNA sequencing (RNASEQ). This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harbouring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.

Molecular Characterization of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

During analysis of kiwifruit derived from hybrids between the high AsA species Actinidia eriantha and A. chinensis var chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis we performed whole-genome sequencing on pools of high and low AsA fruit from tetraploid A. chinensis var. deliciosa x A. eriantha backcross families. Pool-GWAS revealed a single QTL spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis x A. eriantha) x A. chinensis backcross families, showing that the eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNASEQ. This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harboring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.