Allelic sequence polymorphisms in the intron region of the nuclear-encoded GapC gene preceded the speciation of three closely related Abies species (Pinaceae)

The DNA sequences of GapC intron 8 were determined for three closely related Abies species, Abies firma, Abies homolepis and Abies veitchii, and ten alleles were identified. Although, in most cases, an allele was specifically detected in one species, some rare alleles were found in two species. The phylogenetic analysis of those alleles showed that they trace back to different ancestral sequences, and that a species possessed the different originated alleles. The polymorphism of the GapC gene observed in the three Abies species seemed to have preceded their evolutionary divergence. Received: 1 February 2000 / Accepted: 10 May 2000     

Transcription of intergenic DNA deposits nucleosomes on promoter to silence gene expression

Comment on: Hainer SJ, et al. Genes Dev. 2011; 25:29-40     

Nuclear internal transcribed spacer‐1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio

The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples. In the DNA extracted from the brain and gill tissues and intestinal contents, CytB was detected at 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from mesocosm, pond and lake water, the copy numbers of ITS1 were about 160, 300 and 150 times higher than those of CytB, respectively. The minimum volume of pond water required for quantification was 33 and 100 mL for ITS1 and CytB, respectively. These results suggested that ITS1 is a more sensitive genetic marker for eDNA studies of C. carpio.     

Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae,Cyprinidae, Teleostei) inferred from mitochondrial genome analysis

The distribution of freshwater taxa is a good biogeographic model to study pattern and process of vicariance and dispersal. The subfamily Leuciscinae (Cyprinidae, Teleostei) consists of many species distributed widely in Eurasia and North America. Leuciscinae have been divided into two phyletic groups, leuciscin and phoxinin. The phylogenetic relationships between major clades within the subfamily are poorly understood, largely because of the overwhelming diversity of the group. The origin of the Far Eastern phoxinin is an interesting question regarding the evolutionary history of Leuciscinae. Here we present phylogenetic analysis of 31 species of Leuciscinae and outgroups based on complete mitochondrial genome sequences to clarify the phylogenetic relationships and to infer the evolutionary history of the subfamily.     

Transcription of intergenic DNA deposits nucleosomes on promoter to silence gene expression

Comment on: Hainer SJ, et al. Genes Dev. 2011; 25:29-40