Amino acid sequence of photosystem I subunit IV from the cyanobacterium Synechocystis PCC 6803

We describe here the complete amino acid sequence of photosystem I subunit IV from Synechocystis 6803. The molecular mass of 8.0 kDa is lower than in higher plants and Chlamydomonas, due to the lack of a characteristic, proline-rich, N-terminal sequence. The remaining sequence exhibits a good conservation, with a hydrophilic and strongly basic N-tenninal head followed by two hydrophobic domains. There is no possibility of classical membrane-spanning alpha helices. This component is likely to be one of the most stroma accessible subunits of photosystem I.     

Exome resequencing reveals signatures of demographic and adaptive processes across the genome and range of black cottonwood (Populus trichocarpa)

Extant variation in temperate and boreal plant species has been influenced by both demographic histories associated with Pleistocene glacial cycles and adaptation to local climate. We used sequence capture to investigate the role of these neutral and adaptive processes in shaping diversity in black cottonwood (Populus trichocarpa). Nucleotide diversity and Tajima's D were lowest at replacement sites and highest at intergenic sites, while LD showed the opposite pattern. With samples grouped into three populations arrayed latitudinally, effective population size was highest in the north, followed by south and centre, and LD was highest in the south followed by the north and centre, suggesting a possible northern glacial refuge. F_ST outlier analysis revealed that promoter, 5′‐UTR and intronic sites were enriched for outliers compared with coding regions, while no outliers were found among intergenic sites. Codon usage bias was evident, and genes with synonymous outliers had 30% higher average expression compared with genes containing replacement outliers. These results suggest divergent selection related to regulation of gene expression is important to local adaptation in P. trichocarpa. Finally, within‐population selective sweeps were much more pronounced in the central population than in putative northern and southern refugia, which may reflect the different demographic histories of the populations and concomitant effects on signatures of genetic hitchhiking from standing variation.     

The NADPH-dependent electron flow in chloroplasts of the higher plants

The NADPH-dependent reduction of some photosynthetic electron carriers in the dark, and the reduction of NADP+ associated with the glycolytic sequence and the oxidative pentose phosphate pathway in chloroplasts are reviewed. The postulated pathways of electron transports sensitive and insensitive to antimycin A are also evaluated. It is proposed that the electron flow, predominantly through cytochrome bf complex, may be also involved in the pathway of NADPH-dependent and antimycin A-insensitive back electron transport. An information on the chlororespiration in higher plants is also included. This revised version was published online in June 2006 with corrections to the Cover Date.     

Impact of altitude and topography on the genetic diversity of Quercus serrata populations in the Chichibu Mountains, central Japan

In order to elucidate the factors affecting the genetic diversity of Quercus serrata in secondary forests in mountainous regions, we evaluated the level and distribution of genetic variation within and between 15 populations using seven microsatellite markers. The populations were at altitudes ranging from 140 to 1200 m in and around the Chichibu Mountains, central Japan.The expected heterozygosity (H_E) ranged from 0.766 to 0.837. The two populations that exhibited the highest and the second highest values of H_E are located beside a river and a lake, respectively. The two populations exhibiting the lowest and the second lowest values of H_E are, in contrast, located on a summit and a ridge. The observed heterozygosity (H_O) varied between 0.638 and 0.844, and the value of this variable was also higher for the populations beside water than those on summits or ridges. The soils at the waterside are wet, in contrast to those on ridges and summits, which tend to be shallow and subject to rapid desiccation. These results suggest that a lack of soil moisture is likely to inhibit the development and regeneration of Q. serrata, and that genetic diversity is reduced in arid areas. The genetic differentiation was low (F_ST=0.013) among the investigated populations, although all five populations in Yamanashi prefecture clustered together in an UPGMA tree. According to a multiple regression analysis, there was no significant isolation by distance among the populations along either the horizontal or vertical axes. Therefore, genetic variation within populations is affected by topography, but variation between populations is hardly affected by geographical factors. Furthermore, the results of this study suggest two conclusions. First, that altitude is not always a useful variable when estimating the genetic diversity of plant populations in mountainous regions. Second, that genetic diversity can vary even among the undifferentiated plant populations in small areas like the Chichibu Mountains.     

SSR markers for a critically endangered species Euryodendron excelsum and a distantly related species Ternstroemia gymnanthera (Ternstroemiaceae)

Euryodendron excelsum is a critically endangered tertiary relict plant endemic to China. It has only one population remaining in Ba Jia Zhen of Yangchun, Guangdong. In this study, we discovered 25 microsatellite markers from E. excelsumusing a Fast Isolation by Amplified Fragment Length Polymorphism of Sequences COntaining Repeats (FIASCO) protocol. Thirteen loci demonstrated polymorphisms, with the number of alleles per locus ranging from 2 to 13. Values for observed and expected heterozygosity ranged from 0.176 to 1.000 and from 0.261 to 0.889, respectively. Three loci (ZXM-17, ZXM-54, and ZXM-92) were found to significantly deviate from Hardy-Weinberg equilibrium. In addition, five of 13 loci could be successfully cross-amplified in Ternstroemia gymnanthera. These microsatellite loci may help to further survey the adaptive evolution and genetic variation of E. excelsum for guiding its conservation.     

Nucleotide sequence of the ethidium efflux gene from Escherichia coli

The nucleotide sequence of the gene specifying the ethidium efflux system of Escherichia coli has been determined. The translated open reading frame has identified a membrane-bound polypeptide of 110 amino acids (11,960 Da) which shares 42% identity with a staphylococcal protein specifying resistance to ethidium.     

Nucleotide sequence and characterization of a maize cytoplasmic ribosomal protein S11 cDNA

We isolated a Zea mays cDNA encoding the 40S subunit cytoplasmic ribosomal protein S11. The nucleotide sequence was determined and the derived amino acid sequence compared to the corresponding Arabidopsis thaliana protein showing an homology of 90%. This ribosomal protein is encoded by a small multigene family of at least two members. The mRNA steady-state level is about one order of magnitude higher in rapidly growing parts of the plant such as the roots and shoots of seedlings compared to fully expanded leaf tissue.     

Identification and characterization of ten polymorphic microsatellite loci in the red panda Ailurus fulgens

Ten polymorphic microsatellite loci were characterized from two genomic DNA-enriched libraries of the red panda (Ailurus fulgens). The number of observed alleles among 35 samples of red pandas ranged from five to 12. Observed and expected heterozygosities were 0.286–0.971 and 0.443–0.894, and the mean polymorphic information content was 0.712. All loci followed Hardy–Weinberg expectations except Aifu-14 and Aifu-16, which may due to the presence of inbreeding or null alleles. Three pairs of loci exhibited significant linkage disequilibrium after Bonferroni correction for multiple comparisons. These microsatellites would be useful to strengthen population management, genetic diversity exploration, and demographic history speculation of this species.