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Background: The family Columbidae is known as the pigeon family and contains approximately 351 species and 50 genera. Compared to the wealth of biological and genomic information on these Columba livia var. domesteca, information on Columba rupestris and Streptopelia orientalis has been rather limited. The C. rupestris population size is decreasing in Korea. Objectives: Whole-genome sequencing and identification of population characterization of each species based genome variation on 9 Korean pigeon and dove samples, namely, six hill pigeon (C. rupestris), one rock pigeon (C. livia var. domestica) and two oriental turtle dove (S. orientalis) samples. Results: The whole genome of 9 genotypes were sequenced and mapped to the C. livia reference genome. Sequence alignment showed over 96% identity in C. rupestris and 94% identity in S. orientalis to the reference genome (GenBank assembly accession: GCA_001887795.1). Sequence variations, including single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), and structural variations, revealed that intergenus (Columba vs. Streptopelia) variations were approximately four times higher than intragenus variations (C. livia vs. C. rupestris). Of the two Columba species, C. livia var. domestica is closer to S. orientalis than C. rupestris. Pairwise sequentially Markovian coalescent (PSMC) demographic history analysis revealed that the three species underwent a common population bottleneck between 105 and 120 Kya; since then, the effective population sizes of the rock pigeon and oriental turtle dove have increased. Conclusion: The effective population size of the hill pigeon, an Endangered Species of Grade II in Korea, has increased slowly from the second severe bottleneck that occurred approximately 0.5–1.4 × 104 years ago. Our results showed no relationship between copy number variation in the Norrie disease protein (NDP) regulatory regions and plumage color patterns. We report the first comparative analysis of three pigeon genomes. [ABSTRACT FROM AUTHOR]

Bursaphelenchus xylophilus is an emerging pathogenic nematode that is responsible for a devastating epidemic of pine wilt disease worldwide, causing severe ecological damage and economic losses to forestry. Two forms of this nematode have been reported, i.e., with strong and weak virulence, commonly referred as virulent and avirulent strains. However, the pathogenicity-related genes of B. xylophilus are not sufficiently characterized. In this study, to find pathogenesis related genes we re-sequenced and compared genomes of two virulent and two avirulent populations. We identified genes affected by genomic variation, and functional annotation of those genes indicated that some of them might play potential roles in pathogenesis. The performed analysis showed that both avirulent populations differed from the virulent ones by 1576 genes with high impact variants. Demonstration of genetic differences between virulent and avirulent strains will provide effective methods to distinguish these two nematode virulence forms at the molecular level. The reported results provide basic information that can facilitate development of a better diagnosis for B. xylophilus isolates/strains which present different levels of virulence and better understanding of the molecular mechanism involved in the development of the PWD. [ABSTRACT FROM AUTHOR]

Knowledge of ploidy level and genome size in a germplasm collection is critical before studying genetic diversification of different environmental range in grasses and other plants. We assessed the geographic patterns in ploidy level and genome size of 216 individuals of Cynodon dactylon (L.) Pers. (common bermudagrass) by flow cytometry of accessions sampled from 16 geographic sites along a latitudinal gradient from 22°35′ N to 36°18′ N across China. Flow cytometry histograms combined with mitotic chromosome observations results show that tetraploids were the most frequent ploidy level, constituting 44.91% of all individuals. Nuclear DNA contents were 2.384, 2.419, 2.437, 2.873 and 3.288 pg/2C for the diploid, triploid, tetraploid, pentaploid and hexaploid, respectively. Higher proportions of polyploid individuals were observed within populations at the highest and lowest latitudes. In addition, monoploid genome size of C. dactylon progressively increased with increasing ploidy level. Temperature and precipitation had the influence on ploidy level for all the sites. The relationship between ploidy level and geographic distribution for C. dactylon will facilitate the utilization of this species for biological and genetic research. [ABSTRACT FROM AUTHOR]

Sugarcane bacilliform virus (SCBV), which causes leaf freckle in sugarcane, is a member of the genus Badnavirus. Studies were conducted to characterize SCBV in Saccharum officinarum germplasm and cultivated varieties in India by sequencing the complete genomes of five isolates. Genome lengths ranged from 7,553 to 7,884 nucleotides. Duplications in ORF3 and insertions in the RNase H-domain in some of the isolates were found to contribute to the large size of their genomes. The Indian SCBV isolates share identities of 69-85 % for the complete genomic sequence, indicating wide genetic diversity among them, and share 70-82 % identity with Sugarcane bacilliform Ireng Maleng virus (SCBIMV) and Sugarcane bacilliform Morocco virus (SCBMV), as well as 43-46 % identity with Banana streak virus (BSV) and BSV-related SCBV species from Guadeloupe, indicating that the Indian SCBV isolates are distinct from SCBV isolates reported to date. Irrespective of the region compared, SCBV isolates from India, Australia, and Morocco clustered together. BSV and BSV-related SCBV isolates from Guadeloupe formed another cluster. A phylogenetic analysis based on the partial RT/RNase H-sequence separated SCBV and BSV-related SCBV sequences into 11 SCBV groups viz. SCBV-A to -K. Among the 11 groups, the SCBV sequences separated under H, I, J, and K are newly identified in this study, representing three new species and are tentatively named as SCBBBV, SCBBOV, and SCBBRV. Thus, the PASC and phylogenetic analyses evidenced that the symptoms associated with badnaviruses in sugarcane in India are caused by at least three new species, SCBBBV, SCBBOV, and SCBBRV, besides SCBIMV and SCBMV represented by SCBV-BT and SCBV-Iscam, respectively. [ABSTRACT FROM AUTHOR]

Halobacterium salinarum NRC-1 contains multiple TBP and TFB proteins required for the recruitment of RNA polymerase for transcription initiation. The presence and the expression of genes encoding TFB were investigated in the two Hbt. salinarum strains NRC-1 and PHH1 and the mutant strain PHH4. The plasmid-encoded tfbC and tfbE genes of NRC-1 were lacking in PHH1 and PHH4. The 5′-end of the tfbF transcript was determined and contained a 5′-untranslated region of 39 nucleotides able to form a stem-loop structure. The expression of these tfb genes was studied in cultures growing at 15, 37°C and under heat shock conditions. Cold temperatures reduced growth and except for tfbF also the amounts of all tfb transcripts. However, the formation of gas vesicles increased in PHH1 and NRC-1. Heat shock reduced growth of PHH1 and NRC-1, but PHH4 was not affected. A 100-fold increase in tfbA and tfbB mRNA was observed in PHH1 and PHH4, whereas NRC-1 reduced the amounts of these transcripts and increased the expression of tfbG. All TFB proteins tested were able to interact with the transcription activator GvpE involved in gas vesicle formation that thus is able to recruit TFB to the gvp promoter. [ABSTRACT FROM AUTHOR]

Understanding genetic variation between populations is important because it affects the portability of human genome-wide analytical methods. We compared genetic variation and substructure between Malawians and other African and non-African HapMap populations. Allele frequencies and adjacent linkage disequilibrium (LD) were measured for 617 715 single nucleotide polymorphisms (SNPs) across subject genomes. Allele frequencies in the Malawian population (N=226) were highly correlated with allele frequencies in HapMap populations of African ancestry (AFA, N=376), namely Yoruban in Ibadan, Nigeria (Spearman's r2=0.97), Luhya in Webuye, Kenya (r2=0.97), African Americans in the southwest United States (r2=0.94) and Maasai in Kinyawa, Kenya (r2=0.91). This correlation was much lower between Malawians and other ancestry populations (r2<0.52). LD correlations between Malawians and HapMap populations were strongest for the populations of AFA (AFA r2>0.82, other ancestries r2<0.57). Principal components analyses revealed little population substructure within our Malawi sample but provided clear distinction between Malawians, AFA populations and two European populations. Five SNPs within the lactase gene (LCT) had substantially different allele frequencies between the Malawi population and Maasai in Kenyawa, Kenya (rs3769013, rs730005, rs3769012, rs2304370; P-values <1 × 10−33). [ABSTRACT FROM AUTHOR]

A series of 14 contiguous restriction fragments of yeast mitochondrial DNA that cover a 5.2 kb segment including the oli2 gene provided a set of hybridization probes that were used to analyze gel fractionated mitochondrial RNA immobilized on diazotized paper. Of the nine oli2 region transcripts in grande strain J69-1B (class I), the five largest (5,100, 4,500 (most prominent), 3,900, 3,600 and 3,000 nucleotides) contain the oli2 coding sequence; all appear to have the same 3′ end. The four smallest J69-1B transcripts (1,900, 1,700, 800 and 600 nucleotides) contain only sequences down-stream of the oli2 gene. A 1.8 kb DNA region specifying these four transcripts is deleted from grande strain JM6 (class 11); these transcripts are thus dispensible for respiratory function. The five oli2 transcripts of JM6 (3,000, 2,400 (most prominent), 2,000, 1,700 and 1,150 nucleotides) all contain the oli2 coding sequence and are each related to a corresponding J69-1B transcript; the 5′ and 3′ ends match in each case, but the JM6 transcripts are about 2,000 nucleotides shorter. In particular, the putative oli2 mRNA has a 5′ leader of about 1,400 nucleotides, a coding region of 780 nucleotides, and a variant 3′ tail that is about 2,300 nucleotides in J69-1 B, and about 200 nucleotides in JM6. [ABSTRACT FROM AUTHOR]