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.
ABSTRACT
Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal.
Subject(s)
Cattle/genetics , Genome , Molecular Sequence Annotation , Animals , Cattle/classification , Phylogeny , Whole Genome SequencingABSTRACT
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.
Subject(s)
Columbidae/classification , Columbidae/genetics , Genome, Mitochondrial , Animals , Base Composition , Codon , Genes, Mitochondrial , Genome Size , Open Reading Frames , Sequence Analysis, DNA , Whole Genome SequencingABSTRACT
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.
Subject(s)
Foxes/genetics , Genome, Mitochondrial/genetics , Animals , Base Composition/genetics , Genes, rRNA/genetics , RNA, Transfer/genetics , Tandem Repeat Sequences/geneticsABSTRACT
The Common redpoll (Carduelis flammea) is one species of family Fringillidae. In the present study, we determined the complete mitochondrial DNA sequences of this species. The mitochondrial genome of Common redpoll is a circular molecule of 16 820 bp in size and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The total base composition is 31.35% for C, 14.14% for G, 30.57% for A and 23.94% for T, respectively. The phylogenetic tree of Common redpoll and 12 other closely related Fringillidae species was built. These data will be useful for studying the genetic diversity within the species of Common redpoll and phylogenetic relationships among different Fringillidae species.
Subject(s)
Birds/classification , Birds/genetics , Genome, Mitochondrial , Genomics , Animals , Base Composition , Genes, Mitochondrial , Genome Size , Genomics/methods , Open Reading Frames , Phylogeny , Sequence Analysis, DNA , Whole Genome SequencingABSTRACT
Genomic DNAs from Arctic fox were cleaved with restriction enzymes. The prominent ethidium-bromide stanined bands were cloned and sequenced after separation of DNA fragments by agarose gel electrophoresis. Forty-two satellite sequences were obtained by sequencing. Sequence analyses revealed that the satellite monomer in length was 737 bp, with an average G+C content of 51.9%. There were 91%-97% homology among the monomers, and the monomer consisted of three subrepeats of approximately 245 bp in length with 51%-54% homology. The satellite DNAs were specific for canidae, and had 74% homology to the dog centromere-associated nucleotide sequences. In order to distinguish from another satellite DNAs of canidae genome, the satellite was designated as alpha satellite DNA.