The complete coding region of the maxicircle as a superior phylogenetic marker for exploring evolutionary relationships between members of the Leishmaniinae

Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.

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ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes

BMC Genomics ◽

10.1186/s12864-017-4327-9 ◽

2018 ◽

Vol 19 (S1) ◽

Cited By ~ 20

Author(s):

Yu-Wei Wu

Keyword(s):

Evolutionary Relationships ◽

Marker Genes ◽

Phylogenetic Marker ◽

Automated Pipeline

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Characterization of the Original Christmas Disease Mutation (Cysteine 206 → Serine): From Clinical Recognition to Molecular Pathogenesis

Thrombosis and Haemostasis ◽

10.1055/s-0038-1648381 ◽

1992 ◽

Vol 67 (01) ◽

pp. 063-065 ◽

Cited By ~ 6

Author(s):

Sherryl A M Taylor ◽

Jacalyn Duffin ◽

Cherie Cameron ◽

Jerome Teitel ◽

Bernadette Garvey ◽

...

Keyword(s):

Nucleotide Substitution ◽

Novel Mutation ◽

Factor Ix ◽

Causative Mutation ◽

Coding Region ◽

Body Of Knowledge ◽

Polymerase Chain ◽

Splice Junctions

SummaryChristmas disease was first reported as a distinct clinical entity in two manuscripts published in 1952 (1, 2). The eponym associated with this disorder, is the surname of the first patient examined in detail and reported by Biggs and colleagues in a paper describing the clinical and laboratory features of seven affected individuals (3). This patient has severe factor IX coagulant deficiency (less than 0.01 units/ml) and no detectable circulating factor IX antigen (less than 0.01 units/ml). Coding sequence and splice junctions of the factor IX gene from this patient have been amplified in vitro through the polymerase chain reaction (PCR). One nucleotide substitution was identified at nucleotide 30,070 where a guanine was replaced by a cytosine. This mutation alters the amino acid encoded at position 206 in the factor IX protein from cysteine to serine. The non conservative nature of this substitution, the absence of this change in more than 200 previously sequenced factor IX genes and the fact that the remainder of the coding region of this gene was normal, all provide strong circumstantial evidence in favour of this change being the causative mutation in this patient. The molecular characterization of this novel mutation in the index case of Christmas disease, contributes to the rapidly expanding body of knowledge pertaining to Christmas disease pathogenesis.

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