Genetica最新文献

Phylogenetic relationships within Oxytropis DC. sect. Gloeocephala Bunge from Northeast Asia were studied using plastid intergenic spacers (psbA-trnH + trnL-trnF + trnS-trnG) and ITS nrDNA. Populations of O. anadyrensis Vass., O. borealis DC., O. middendorffii Trautv., O. trautvetteri Meinsh., and O. vasskovskyi Jurtz. were monomorphic or characterised by a low level of chloroplast genetic diversity (h varied from 0.143 to 0.692, and π from 0.0001 to 0.0005). Presumably, the low genetic diversity was a result of the severe bottlenecks during Pleistocene glaciation-interglacial cycles. Twenty chlorotypes were identified; species studied had no shared chlorotypes. Chlorotypes of O. anadyrensis, O. borealis, and O. middendorffii formed two lineages each, while the chlorotypes of O. trautvetteri and O. vasskovskyi formed one separate lineage each in the phylogenetic network. There were specific diagnostic markers of cpDNA in each lineage, excluding O. vasskovskyi. The presence of a species-specific diagnostic marker in O. trautvetteri and specific markers in two lineages of O. anadyrensis support circumscribing these taxa as independent species. Regarding ITS nrDNA polymorphism, five ribotypes were detected. The differences revealed in plastid and nuclear genomes of Oxytropis sect. Gloeocephala confirmed that the Asian sector of Megaberingia was the main centre of diversification of arctic legumes.

Sinhalese and Vedda people are respectively the major ethnic group and the descendants of the probably earliest inhabitants of Sri Lanka, both believed to have a long history of settlement on the island. However, very little information is available on the origin and possible migration patterns of the two populations. Some studies have focused on (CA) dinucleotide repeat variations located in the mitochondrial hypervariable region 3 (HVS3) (base pairs 514-524) as a useful biomarker to understand migration patterns of different populations. Hence, here we analyze these repeat variations in these two ethnic groups to understand their historical roots and possible patterns of gene flow. Blood samples were collected from healthy, maternally unrelated individuals (N = 109) and mitochondrial D-loop was amplified and sequenced. The (CA)₄ dinucleotide repeat in hypervariable region 3 was detected in the majority of Vedda samples while the remaining samples were defined by a (CA)₅ cluster. In contrast, the (CA)₅ repeat was the most frequent among Sinhalese followed by (CA)₄ and (CA)₇ repeats. Haplogroup diversity of (CA)₄ variation indicated that the majority of Sinhalese individuals grouped into the M30 haplogroup while Vedda clustered into the R5a2b and U7a2 haplogroups. No significant differences in diversity measures were observed among the two populations. However, Multidimensional Scaling indicated a separate clustering for aboriginal Vedda and contemporary Sinhalese populations. Results from this study can be used together with mitochondrial DNA information from hypervariable regions 1 and 2 to perform anthropological and forensic investigations in the two populations studied.

Penaeid shrimp embryos undergo holoblastic division, gastrulation by invagination, and hatching as a nauplius larva. Posterior segments form and differentiate during larval development. Hedgehog (Hh) pathway genes from penaeid shrimp and other pancrustaceans were identified by in silico analysis of genomes and transcriptomes, and mapped onto a recent pancrustacean phylogeny to determine patterns of intron gains and losses. Penaeus vannamei, P. japonicus, and P. monodon Hh proteins were encoded by four exons. Amphipod, isopod, and ostracod hh were also encoded by four exons, but hh from other arthropod groups contained three conserved exons. The novel hh intron is hypothesized to have arisen independently in the malacostracan ancestor and Ostracoda by a transposon insertion. Shared patterns of ptc, smo, and ci exon structure were found for Malacostraca, Branchiopoda + Hexapoda, Hexanauplia (Thecostraca + Copepoda), Multicrustacea (Thecostraca + Copepoda + Malacostraca), and Pancrustacea minus Oligostraca. mRNA expression of P. vannamei of hh, ptc, and ci from developmental transcriptomes of zygotes through postlarvae showed low expression from zygote to gastrula, which increased at limb bud, peaked at unhatched nauplius, and declined in nauplius and later larval stages. smo expression was found in zygotes, peaked in gastrula, and declined in limb bud and later stages. These results are consistent with a role for Hh signaling during segmentation in penaeid shrimp.

Messenger RNA (mRNA) and long noncoding RNA (lncRNA) targets interact via competitive microRNA (miRNA) binding. However, the roles of cancer-specific lncRNAs in the competing endogenous RNA (ceRNA) networks of low-grade glioma (LGG) remain unclear. This study obtained RNA sequencing data for normal solid tissue and LGG primary tumour tissue from The Cancer Genome Atlas database. We used a computational method to analyse the relationships among the mRNAs, lncRNAs, and miRNAs in these samples. Gene ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was used to predict the biological processes (BPs) and pathways associated with these genes. Kaplan-Meier survival analysis was used to evaluate the association between the expression levels of specific mRNAs, lncRNAs, and miRNAs and overall survival. Finally, we created a ceRNA network describing the relationships among these mRNAs, lncRNAs, and miRNAs using Cytoscape 3.5.1. A total of 2555 differentially expressed (DE) mRNAs, 218 DElncRNAs, and 192 DEmiRNAs were identified using R. In addition, GO and KEGG pathway analysis of the mRNAs and lncRNAs in the ceRNA network identified 10 BPs, 10 cell components, 10 molecular functions, and 48 KEGG pathways as selectively enriched. A total of 55 lncRNAs, 50 miRNAs, and 10 mRNAs from this network were shown to be closely associated with overall survival in LGG. Finally, 59 miRNAs, 235 mRNAs, and 17 lncRNAs were used to develop a ceRNA network comprising 313 nodes and 1046 edges. This study helps expand our understanding of ceRNA networks and serves to clarify the underlying pathogenesis mechanism of LGG.

Across human protein-coding genes, the human neuron-specific genes, RIT2 and GPM6B, contain the two longest GA short tandem repeats (STRs) of 11 and 9-repeats, respectively, the length ranges of which are functional, and result in gene expression alteration. Here we sequenced the RIT2 and GPM6B STRs in 600 human subjects, consisting of late-onset neurocognitive disorder (n = 200), multiple sclerosis (n = 200), and controls (n = 200). Furthermore, we selected two large human databases, including the general-population-based gnomAD ( https://gnomad.broadinstitute.org ) and a mainly disease-phenotype-archiving database, TOPMed ( https://www.nhlbiwgs.org ), to compare allele frequencies in the general populations vs. the disease compartment. The RIT2 and GPM6B GA-repeats were monomorphic in the human subjects studied, at lengths of 11 and 9-repeats, respectively, and were predominantly human-specific in formula. Exception included a 9/11 genotype of the RIT2 GA-STR in an isolate case of female multiple sclerosis. Exceedingly rare alleles of the two GA repeats were significantly enriched in TOPMed vs. the gnomAD. We report prime instances of predominant monomorphism for specific lengths of STRs in human, and possible enrichment of rare divergent alleles in the disease phenotype compartment. While STRs are most attended because of their high polymorphic nature, STR monomorphism is an underappreciated feature, which may have a link with natural selection and disease.