Yumei Li

Complete mitochondrial genome sequence of Chestnut-flanked white-eye (Zosterops erythropleurus)

Abstract The Chestnut-flanked white-eye (Zosterops erythropleurus) is a species of family Zosteropidae, which is distributed widely in the world. In the present study, the complete mitochondrial genome sequence of Chestnut-flanked white-eye was determined. It has a total length of 17 811 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions. The total base composition was 30.2% for A, 31.0% for C, 14.2% for G and 24.6% for T. The phylogenetic tree of Chestnut-flanked white-eye and 13 other species belonging to the order Passeriformes was built. The molecular data presented here will be useful to study the evolutionary relationships and genetic diversity of Chestnut-flanked white-eye.

Development and characterization of polymorphic microsatellite markers for Chinese raccoon dog (Nyctereutes procyonoides procyonoides).

Chinese raccoon dog (Nyctereutes procyonoides procyonoides) is one of the most important fur-bearing animal species. Information about the genetic background of farmed Chinese raccoon dogs is limited. In this study, 17 polymorphic microsatellite markers were isolated and identified from an (AC)n-microsatellite-enriched library of Chinese raccoon dogs. The number of alleles per locus ranged from 2 to 8 based on 48 individuals tested. The expected and observed heterozygosity and polymorphism information content per locus ranged from 0.383 to 0.8378, 0.3200 to 0.8696, and 0.3047 to 0.7947, respectively. Cross-species amplification of these loci in 2 other Canidae species indicated that 9 and 11 of these loci could also be amplified successfully in the arctic and silver fox, respectively. These microsatellite loci developed in the present report will provide useful tools for population genetic studies, individual identification, and phylogenetic analysis in the Chinese raccoon dog and other Canidae species.

Complete mitochondrial genome of the Spotted dove (Streptopelia chinensis).

Abstract The Spotted dove (Streptopelia chinensis) is a member of the bird family Columbidae. In this study, we report the complete mitochondrial genome of this species. The mitochondrial genome of Spotted dove is a circular molecule of 16,966 bp in size and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition is 30.1% for A, 32.1% for C, 13.9% for G, and 23.9% for T. These data will be useful for the phylogenetic and population diversity analyses of birds, especially Columbidae species.

Cloning and identification of the ASIP gene in Chinese raccoon dog (Nyctereutes procyonoides procyonoides).

The quantity, quality, and distribution of eumelanin and pheomelanin determine a wide variety of coat colors in animals. Three coat color variants exist in farmed wild-type Chinese raccoon dog (Nyctereutes procyonoides procyonoides), which is an important fur-bearing animal species. The ASIP gene is an important candidate gene for coat color variation in some species. In this study, the complete cDNA sequences of ASIP were amplified from a wild-type Chinese raccoon dog. Sequence analysis revealed the coding region of ASIP in Chinese raccoon dog to be 396-bp in length and two transcripts (accession Nos. KT224450 and KT224451) were identified due to the alternative use of exon 1 (1A and 1C). However, the alternative splicing pattern and the coding sequence of ASIP in three types of coat color variants were the same as those identified in the wild-type individual. Based on the results obtained in this study, we can exclude a role for alternative splicing of exon 1 and the coding sequence of ASIP in coat color variation in Chinese raccoon dog.

Cloning and association analysis of KIT and EDNRB polymorphisms with dominant white coat color in the Chinese raccoon dog (Nyctereutes procyonoides procyonoides).

The Chinese raccoon dog (Nyctereutes procyonoides procyonoides) is one of the most important fur-bearing animal species. The dominant white individual, a coat color variant in farmed Chinese raccoon dog, shows a completely white phenotype over the entire body. The KIT and EDNRB genes have been reported to be associated with the dominant white coat color in some mammalian species. In the present study, the full-length coding sequences of KIT and EDNRB were amplified from a dominant white and a wild-type Chinese raccoon dog. Sequence analysis revealed that the coding region of KIT and EDNRB in Chinese raccoon dog was 2919 and 1332 base pairs in length (accession No. KM083121 and KM083122), respectively, and 2 single-nucleotide polymorphisms (SNPs; c.600C>T and c.967G>A) in KIT and 1 SNP (c.259A>C) in EDNRB was found only in the dominant white individual. An alternative splicing site at the boundary of 4 and 5 of the KIT gene was identified in both individuals. We further investigated the association between the 3 SNPs of KIT and EDNRB and dominant white coat color by genotyping 18 individuals. We found no association between these SNPs and dominant white coat color. Based on these results, we can exclude the coding regions of the KIT and EDNRB genes as determinants of the dominant white coat color in Chinese raccoon dog.

Isolation and characterization of novel microsatellite markers from the sika deer (Cervus nippon) genome

Microsatellite markers are widely and evenly distributed, and are highly polymorphic. Rapid and convenient detection through automated analysis means that microsatellite markers are widely used in the construction of plant and animal genetic maps, in quantitative trait loci localization, marker-assisted selection, identification of genetic relationships, and genetic diversity and phylogenetic tree construction. However, few microsatellite markers remain to be isolated. We used streptavidin magnetic beads to affinity-capture and construct a (CA)n microsatellite DNA-enriched library from sika deer. We selected sequences containing more than six repeats to design primers. Clear bands were selected, which were amplified using non-specific primers following PCR amplification to screen polymorphisms in a group of 65 unrelated sika deer. The positive clone rate reached 82.9% by constructing the enriched library, and we then selected positive clones for sequencing. There were 395 sequences with CA repeats, and the CA repeat number was 4-105. We selected sequences containing more than six repeats to design primers, of which 297 pairs were designed. We next selected clear bands and used non-specific primers to amplify following PCR amplification. In total, 245 pairs of primers were screened. We then selected 50 pairs of primers to randomly screen for polymorphisms. We detected 47 polymorphic and 3 monomorphic loci in 65 unrelated sika deer. These newly isolated and characterized microsatellite loci can be used to construct genetic maps and for lineage testing in deer. In addition, they can be used for comparative genomics between Cervidae species.

Complete mitochondrial genome of Pallas’s Leaf Warbler (Phylloscopus proregulus)

Abstract In the present study, the complete mitochondrial DNA sequence of Pallas’s Leaf Warbler (Phylloscopus proregulus) was determined for the first time. The mitochondrial genome of Pallas’s Leaf Warbler is a circular molecule of 16,880 bp in size and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 2 control regions. The base composition is 32.7% for C, 14.3% for G, 30.0% for A and 23.0% for T. These data will be useful for studying the genetic diversity within the species of Pallas’s Leaf Warbler and phylogenetic relationships among different Phylloscopidae species.

The complete sequence of mitochondrial genome of Siberian accentor (Prunella montanella).

Abstract The Siberian accentor, Prunella montanella (Passeriformes, Prunellidae), is a small passerine bird. In this study, the complete mitochondrial genome sequence of Siberian accentor was determined. It has a total length of 16 832 bp, and contains 13 protein coding genes, 22 tRNA genes, two ribosome RNA genes, and one control region. The nucleotide composition is 30.1% for A, 31.0% for C, 15.0% for G and 23.9% for T, respectively. The overall GC content is lower than AT. The phylogenetic tree of Siberian accentor and 10 other species belonging to order Passeriformes was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of Siberian accentors.

The complete sequence of the mitochondrial genome of Arctic fox (Alopex lagopus)

Abstract In the present study, the complete mitochondrial genome sequence of Arctic fox (Alopex lagopus) was determined for the first time. It has a total length of 16,656 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 1 control region. The nucleotide composition is 31.3% for A, 26.2% for C, 14.8% for G and 27.7% for T, respectively. The D-loop region located between tRNAPro and tRNAPhe contains a (ACACGTACACGCAT)18 tandem repeat array. The data will be useful for the investigation of the genetic structure and diversity in the natural and farmed population of Arctic foxes.

Identification and characterization of the cDNA sequence encoding amelogenin in rabbit (Oryctolagus cuniculus).

Amelogenins, the most abundant proteins in tooth enamel extracellular matrix (ECM), are essential for tooth amelogenesis. The nucleotide sequence of amelogenin gene (AMEL) for rabbit, as an important member of mammals and good continuously growing incisor model, is important for comparative and evolutional study. Previous studies about rabbit amelogenin proteins got no consensus yet even as to their existence or size. In this study, with combined usage of in silico and molecular cloning technologies, we identified sequences of two transcripts of rabbit amelogenin, resulting from the alternative splicing of the 45-bp exon 4. The coding regions of the two transcripts are of 567- and 522-bp, encoding 188 and 173 amino acids including a 17-residue signal peptide, respectively. Sequence analysis revealed that rabbit amelogenin features in extremely high GC-content in nucleotide sequence and Alanine content in protein sequence. Detailed comparison of amino acid sequence with other mammals showed that the rabbit amelogenin protein is conserved in the sites and regions important for protein functions. Overall, our results uncovered the mysteries about rabbit amelogenin and revealed its sequence peculiarities.