Cytochrome B

The evolutionary history of three out of four birds traditionally classified into the genus Rhodopechys birds has been studied by comparing their mitochondrial cytochrome b DNA sequence with that of greenfinches and other genus Carduelis finches. The desert finch (Rhodopechys obsoleta) or a sister extinct species seems to have existed about 6 million years ago in Asian and perhaps African desert-like areas. This bird has no molecular relationship with other Rhodopechys birds and seems to have given rise to the greenfinches radiation, probably by allopatry of marginal or isolated groups; the latter would have evolved to green plumage colours and more simple song modulations (i.e., greenfinches). The possible role of assortative mating and the newly postulated acquired phenotypic characters in greenfinches speciation are discussed.

To date, no polymerase chain reaction diagnostic technique exists to directly identify mammalian blood meals from mosquitoes by sized DNA fragments following agarose gel electrophoresis. We have developed a vertebrate-specific multiplexed primer set based on mitochondrial cytochrome b to identify the mammalian blood hosts of field-collected mosquitoes. Although designed for the study of African malaria vectors, the application of this tool is not restricted to this disease system. Validation of this diagnostic technique on dried anopheline and culicine field specimens collected in Zambia and Mali demonstrated that blood meals could be identified 2-7 months after collection. Time course experiments showed that host DNA was detectable in frozen mosquito abdomens 24-30 hours post-feeding. Additionally, multiple blood meals from different mammals could be detected in a single mosquito. This diagnostic assay will be a valuable tool for identifying the blood meals of field-collected mosqu...

The fern genus Dryopteris (Dryopteridaceae) is represented in the Hawaiian Islands by 18 endemic taxa and one non-endemic, native species. The goals of this study were to determine whether Dryopteris in Hawai’i is monophyletic and to infer the biogeographical origins of Hawaiian Dryopteris by determining the geographical distributions of their closest living relatives. We sequenced two chloroplast DNA fragments, rbcL and the trnL-F intergenic spacer (IGS), for 18 Hawaiian taxa, 45 non-Hawaiian taxa, and two outgroup species. For individual fragments, we estimated phylogenetic relationships using Bayesian inference and maximum parsimony. We performed a combined analysis of both cpDNA fragments employing Bayesian inference, maximum parsimony, and maximum likelihood. These analyses indicate that Hawaiian Dryopteris is not monophyletic, and that there were at least five separate colonizations of the Hawaiian Islands by different species of dryopteroid ferns, with most of the five groups having closest relatives in SE Asia. The results suggest that one colonizing ancestor, perhaps from SE Asia, gave rise to eight endemic taxa (the glabra group). Another colonizing ancestor, also possibly from SE Asia, gave rise to a group of five endemic taxa (the exindusiate group). Dryopteris fusco-atra and its two varieties, which are endemic to Hawai’i, most likely diversified from a SE Asian ancestor. The Hawaiian endemic Nothoperanema rubiginosum has its closest relatives in SE Asia, and while the remaining two species, D. wallichiana and D. subbipinnata, are sister species, their biogeographical origins could not be determined from these analyses due to the widespread distributions of D. wallichiana and its closest non-Hawaiian relative.

Abstract:  Attempts to prevent illegal trade in bile and gallbladders from Asiatic black bears, Ursus thibetanus, are hampered by difficulties associated with identifying such items. We extracted DNA from bile crystals of unknown species origin and generated partial cytochrome b (cyt b) sequences using either universal primers (positioned in conserved regions of cyt b), or primers designed on existing U. thibetanus sequences (UT). Species origin was determined by aligning resolved sequences to reference sequence data. The universal primers were unsuitable for U. thibetanus identification when multiple species templates were present in the samples. The UT primers amplified U. thibetanus DNA from all sample extracts, including those containing mixed species templates. The amplified fragment can distinguish U. thibetanus from the most closely related species, U. americanus, a distinct advantage of DNA sequencing over the methods currently used to analyze suspected U. thibetanus bile.

An out-of-Africa dispersal route has been proposed for many organisms, including modern man. However, counter examples of in-to-Africa dispersal routes are less common. In the present article, the phylogenetic relationships within the Labeoninae, a subfamily of cyprinid fishes distributed in Asia and Africa, were analyzed to investigate the biogeographic processes governing the modern distribution of these Asian and African cyprinids. The mitochondrial DNA cytochrome b gene was used as a molecular marker. The phylogenetic analysis indicated that the subfamily Labeoninae is a monophyletic group, with some Asian labeonins located at the basal position. Two subclades were found that contained both African and Asian species, which highlighted a need for further biogeographic analysis. Based on this analysis, it is proposed that the centre of origin of the Labeoninae was in East Asia. Molecular clock estimation suggests that the Labeoninae arose by the Early Miocene (~23 MYA) during the period of the second Tibetan uplift. Subsequently, two dispersal events of labeonins from Asia into Africa occured in the Early Miocene (~ 20 MYA) and Late Miocene (~9 MYA) and serve as examples counter to out-of-Africa dispersal.

Hemileia vastatrix is a biotrophic fungus, causing coffee leaf rust in all coffee growing countries, leading to serious social and economic problems. Gene expression studies may have a key role unravelling the transcriptomics of this pathogen during interaction with the plant host. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is currently the golden standard for gene expression analysis, although an accurate normalisation is essential for adequate conclusions. Reference genes are often used for this purpose, but the stability of their expression levels requires validation under experimental conditions. Moreover, pathogenic fungi undergo important biomass variations along their infection process in planta, which raises the need for an adequate method to further normalise the proportion of fungal cDNA in the total plant and fungus cDNA pool. In this work, the expression profiles of seven reference genes [glyceraldehyde-3-phosphate dehydrogenase (GADPH), elongation factor (EF-1), Beta tubulin (β-tubulin), cytochrome c oxidase subunit III (Cyt III), cytochrome b (Cyt b), Hv00099, and 40S ribosomal protein (40S_Rib)] were analysed across 28 samples, obtained in vitro (germinated uredospores and appressoria) and in planta (post-penetration fungal growth phases). Gene stability was assessed using the statistical algorithms incorporated in geNorm and NormFinder tools. Cyt b, 40S_Rib, and Hv00099 were the most stable genes for the in vitro dataset, while 40S_Rib, GADPH, and Cyt III were the most stable in planta. For the combined datasets (in vitro and in planta), 40S_Rib, GADPH, and Hv00099 were selected as the most stable. Subsequent expression analysis for a gene encoding an alpha subunit of a heterotrimeric G-protein showed that the reference genes selected for the combined dataset do not differ significantly from those selected specifically for the in vitro and in planta datasets. Our study provides tools for correct validation of reference genes in obligate biotrophic plant pathogens, as well as the basis for RT-qPCR studies in H. vastatrix.► Reference genes were selected for Hemileia vastatrix in planta RT-qPCR studies. ► Gene stability was assessed using geNorm and NormFinder programmes. ► 40S_Rib, GADPH, and Hv00099 were the most stable reference genes. ► An extra correction step enabled normalisation of fungal biomass in planta.

Abstract: Despite very strict wildlife protection acts in several countries and trading laws such as CITES, illegal trading and poaching of wildlife is still active mostly because of the use of their parts in Chinese medicinal products and ornaments. For successfully identifying wildlife and their parts, mitochondrial DNA sequencing is being used now-a-days. DNA bar coding using fragments of cytochrome b and cytochrome oxidase I genes are frequently utilized for mammalian species identification. This mini review describes some of the mtDNA sequences and STR markers used for mammalian species identification in the field of forensic wildlife along with the problems associated and their possible solutions.

The diverse scincid lizard fauna of the largely submerged subcontinent of Zealandia (which incorporates New Zealand, New Caledonia, Lord Howe Island, Norfolk Island, and the Chatham Islands) forms a monophyletic lineage within the Eugongylus group of skinks. We use 4062 bp of mitochondrial (ND2, ND4, Cytochrome b, 12SrRNA, 16SrRNA) and nuclear (Rag-1) DNA sequence data to recover a molecular phylogeny for the New Zealand skink fauna, and investigate the origin and diversification of skinks in New Zealand. Our phylogeny includes 32 of the 33 extant described New Zealand skink species (Cyclodina and Oligosoma), the Lord Howe Island skink (C. lichenigera), and representatives from several New Caledonian genera. Neighbour-joining, Maximum Parsimony, Maximum Likelihood, and Bayesian phylogenetic analyses are used to demonstrate that the New Zealand skink species form a single monophyletic lineage, with C. lichenigera representing a closely related sister lineage to the New Zealand radiat...

Primer pairs were designed and protocols developed to selectively amplify segments of vertebrate mitochondrial cytochrome oxidase subunit 1 (COI) and cytochrome b (Cyt b) mtDNA from the bloodmeals of mosquitoes (Diptera: Culicidae). The protocols use two pairs of nested COI primers and one pair of Cyt b primers to amplify short segments of DNA. Resultant sequences are then compared with sequences in GenBank, using the BLAST function, for putative host identification. Vertebrate DNA was amplified from 88% of our sample of 162 wild-caught, blood-fed mosquitoes from Oregon, U.S.A. and GenBank BLAST searches putatively identified 98% of the amplified sequences, including one amphibian, seven mammalian and 14 avian species. Criteria and caveats for putative identification of bloodmeals are discussed.