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Proposed nomenclature for microhaplotypes.

ABSTRACT: Microhaplotypes are a new type of genetic marker in forensics and population genetics. A standardized nomenclature is desirable. A simple approach that does not require a central authority for approval is proposed. The nomenclature proposed follows the recommendation of the HUGO Gene Nomenclature Committee ( http://www.genenames.org ): "We strongly encourage naming families and groups of genes related by sequence and/or function using a "root" symbol. This is an efficient and informative way to name related genes, and already works well for a number of established gene families…" The proposal involves a simple root consisting of "mh" followed by the two-digit chromosome number and unique characters established by the authors in the initial publication. We suggest the unique symbol be an indication of the laboratory followed by characters unique to the chromosome and laboratory. For instance, the microhaplotype symbol mh01KK-001 refers to a locus on chromosome 1 published by the Kidd Lab (KK-) as their #001. Publication defines mh01KK-001 as comprised of four single nucleotide polymorphisms (SNPs), rs4648344, rs6663840, rs58111155, and rs6688969.

SUBMITTER: Kidd KK

PROVIDER: S-EPMC4912715 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Proposed nomenclature for microhaplotypes.

Kidd Kenneth K KK

Human genomics 20160617 1

Microhaplotypes are a new type of genetic marker in forensics and population genetics. A standardized nomenclature is desirable. A simple approach that does not require a central authority for approval is proposed. The nomenclature proposed follows the recommendation of the HUGO Gene Nomenclature Committee ( http://www.genenames.org ): "We strongly encourage naming families and groups of genes related by sequence and/or function using a "root" symbol. This is an efficient and informative way to ...[more]

PMID: 27316555

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Project description:The venom enzyme sphingomyelinase D (SMase D) in the spider family Sicariidae (brown or fiddleback spiders [Loxosceles] and six-eyed sand spiders [Sicarius]) causes dermonecrosis in mammals. SMase D is in a gene family with multiple venom-expressed members that vary in functional specificity. We analyze molecular evolution of this family and variation in SMase D activity among crude venoms using a data set that represents the phylogenetic breadth of Loxosceles and Sicarius. We isolated a total of 190 nonredundant nucleotide sequences encoding 168 nonredundant amino acid sequences of SMase D homologs from 21 species. Bayesian phylogenies support two major clades that we name alpha and beta, within which we define seven and three subclades, respectively. Sequences in the alpha clade are exclusively from New World Loxosceles and Loxosceles rufescens and include published genes for which expression products have SMase D and dermonecrotic activity. The beta clade includes paralogs from New World Loxosceles that have no, or reduced, SMase D and no dermonecrotic activity and also paralogs from Sicarius and African Loxosceles of unknown activity. Gene duplications are frequent, consistent with a birth-and-death model, and there is evidence of purifying selection with episodic positive directional selection. Despite having venom-expressed SMase D homologs, venoms from New World Sicarius have reduced, or no, detectable SMase D activity, and Loxosceles in the Southern African spinulosa group have low SMase D activity. Sequence conservation mapping shows >98% conservation of proposed catalytic residues of the active site and around a plug motif at the opposite end of the TIM barrel, but alpha and beta clades differ in conservation of key residues surrounding the apparent substrate binding pocket. Based on these combined results, we propose an inclusive nomenclature for the gene family, renaming it SicTox, and discuss emerging patterns of functional diversification.

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Proposed nomenclature for microhaplotypes.

Publications

Proposed nomenclature for microhaplotypes.

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