#comparative sequence analysis

The two chief difficulties arise from marker density and sequence orthology. However, there are problems in the interpretation and use of comparative genetic maps based on recombinational mapping of DNA markers. These large rearrangements are most commonly observed, as one might expect, between distantly related species ( Paterson et al., 1996) but can also occur in a relatively short period of time within some lineages ( Devos et al., 1993 Zhang et al., 1998). Comparative genetic maps based on shared restriction fragment length polymorphism probes indicate many large chromosomal rearrangements, some arising specifically during the origin of a particular family of plants ( Moore et al., 1995 Gale and Devos, 1998). Gene order is somewhat more variable, however. These comparisons have been greatly extended, particularly in the grasses (reviewed in Gale and Devos, 1998), revealing significant conservation of gene content and order across plant species that diverged from a common ancestor 90%) of plant genes have close homologs within most other plant genomes. Initial comparisons of the chromosome sets within polyploid species ( Helentjaris et al., 1988 Chao et al., 1989) and of diploid genomes between closely related species ( Bonierbale et al., 1988 Hulbert et al., 1990) indicated extensive colinearity of genetic maps. The advent of DNA marker technology not only facilitated the rapid generation of detailed plant genetic maps but also allowed map comparisons when common DNA markers were employed. Moreover, comparative genetic analyses have begun to show that different plant species often use homologous genes for very similar functions ( Fatokun et al., 1992 Ahn et al., 1993 Paterson et al., 1995 Lagercrantz et al., 1996). Despite this diversity, plant geneticists have recently found that plants exhibit extensive conservation of both gene content and gene order ( Bennetzen and Freeling, 1993). Plant genomes tend to be large and complex, varying in size from ∼38 Mb (1 C) for the crucifer Cardamine amara to >87,000 Mb for Fritillaria assyriaca, a member of the Lilliaceae ( Flavell et al., 1974 Bennett and Leitch, 1995). The flowering plants comprise some 250,000 species and are tremendously diverse in growth habit, environmental adaptation, and nuclear genome structure.

Toll-like receptors (TLRs) play a central role in innate immunity. Furthermore, the super-repeat in the TLR7 family suggests strongly that "bacterial" and "typical" LRRs evolved from a common precursor. These central parts are inferred to play a key role in the structure and/or function of their TLRs. The central parts of the TLR1 and TLR7 families and of TLR4 have more irregular or longer LRR motifs. ConclusionĮach of the six major TLR families is characterized by their constituent LRR motifs, their repeat numbers, and their patterns of cysteine clusters. The LRRs in TLRs form one or two horseshoe domains and are mostly flanked by two cysteine clusters including two or four cysteine residue. The super-repeat is represented by STTSTTSTT or _TTSTTSTT. The LRRs at the N-terminal part have a super-motif of STT with about 80 residues. The TLR7 family (TLR7, TLR8, and TLR9) contain 27 LRRs. The LRRs found in TLRs frequently consists of LxxLxLxxNxLxxLxxxxF/LxxLxx (" T") and sometimes short motifs including LxxLxLxxNxLxxLPx(x)LPxx (" S"). The repeat numbers of the LRRs ranges from 16 to 28. TLRs from thirty-four vertebrate were analyzed. The new method utilizes known LRR structures to recognize and align new LRR motifs in TLRs and incorporates multiple sequence alignments and secondary structure predictions. We identified and aligned LRRs in TLRs by a new method described here. The repeat numbers of LRRs and their "phasing" in TLRs differ with isoforms and species they are aligned differently in various databases. All known domain structures adopt an arc or horseshoe shape. There are seven classes of LRRs including "typical" (" T") and "bacterial" (" S"). All LRRs include the highly conserved segment, LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. The LRR domains in TLRs have been inferred to be responsible for molecular recognition. TLRs recognize and respond to molecules such as lipopolysaccharide, peptidoglycan, flagellin, and RNA from bacteria or viruses. TLRs are membrane glycoproteins and contain leucine rich repeat (LRR) motif in the ectodomain.

The 5′ two-thirds of the genome (nucleotide positions 312 to 20416) encodes the replicase protein, which is associated with RNA replication and transcription. The FCoV genome is approximately 29 kilobases (kb) in length and contains eight genes flanked by a 5′ untranslated region (5′UTR) and a 3′UTR (nucleotide positions 311 and 276, respectively). It is a single-stranded positive-sense RNA virus with a 5′ cap and 3′ poly-A tail. Our findings provide updated information about the molecular characteristics of the accessory and nucleocapsid genes of FCoV strains in circulation that were not previously documented in this country.įeline coronavirus (FCoV) is a member of the family Coronaviridae and the genus Alphacoronavirus. The accessory gene sequence divergence may be responsible for driving the periodic emergence and continued persistence of FCoVs in Thai domestic cat populations. Amino acid deletions were observed in the N, ORF3c, and ORF7b proteins of Thai FCoV sequences. Truncation of the 3a gene product was found in Thai FCoV strains of group 2. In the ORF3ab sequences, some Thai strains were more than 99% identical to the DF-2 prototype strain. Comparative sequence analysis suggested that the Thai FCoV isolates were most closely related to strains reported in the Netherlands, the USA, and China. In this study, we investigated the genetic diversity and genetic relationships among the current Thai and global FCoV strains in the accessory and nucleocapsid genes using a virus-specific PCR method. Of these, the S gene is more divergent and is responsible for the two FCoV serotypes, while ORF3c harbors mutations that result either in early termination or destruction of the protein. Most studies involving molecular surveillance and evaluation of FCoV field strains have examined the genetic diversity of the spike and accessory ORF3c coding regions. There have been numerous studies on FIP worldwide, whereas information about this disease in Thailand is still limited. Feline infectious peritonitis virus (FIPV) is a mutant type of FCoV that is characterized by causing fibrinous serositis with effusions in the pleural and abdominal cavities (wet form) and/or granulomatous-necrotizing inflammatory lesions in several organs (dry form). Feline infectious peritonitis (FIP) is a lethal infectious disease of domestic cats caused by feline coronavirus (FCoV) infection.