Donkey genomes provide new insights into domestication and selection for coat color.

Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition.

Variation among 532 genomes unveils the origin and evolutionary history of a global insect herbivore.

The diamondback moth, Plutella xylostella is a cosmopolitan pest that has evolved resistance to all classes of insecticide, and costs the world economy an estimated US $4-5 billion annually. We analyse patterns of variation among 532 P. xylostella genomes, representing a worldwide sample of 114 populations. We find evidence that suggests South America is the geographical area of origin of this species, challenging earlier hypotheses of an Old-World origin. Our analysis indicates that Plutella xylostella has experienced three major expansions across the world, mainly facilitated by European colonization and global trade. We identify genomic signatures of selection in genes related to metabolic and signaling pathways that could be evidence of environmental adaptation. This evolutionary history of P. xylostella provides insights into transoceanic movements that have enabled it to become a worldwide pest.

Novel genotypes and multilocus genotypes of Enterocytozoon bieneusi in two wild rat species in China: potential for zoonotic transmission.

Enterocytozoon bieneusi is an opportunistic pathogen in immunodeficient patients. Although this pathogen has been reported in many domestic animals, few data are available about the occurrence of E. bieneusi in wild rats. In the current study, a total of 228 fecal samples from two wild rat species (Leopoldamys edwardsi and Berylmys bowersi) in China were examined by a nested PCR-based sequencing approach employing the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The overall prevalence of E. bieneusi in wild rats was 33.3% (76/228), with 35.1% (39/111) in L. edwardsi and 31.6% (37/117) in B. bowersi. Ten E. bieneusi genotypes (including four known and six novel genotypes) were identified, with the novel CQR-2 (n = 15) as the predominant genotype. Phylogenetic analysis indicated that ten genotypes in the present study belong to zoonotic group 1, which contains many genotypes in humans. Furthermore, multilocus sequence typing (MLST) analysis showed that 19 ITS-positive samples were successfully amplified at three microsatellites and one minisatellite, forming 18 multilocus genotypes (MLGs). This is the first report of E. bieneusi infection in the wild rats L. edwardsi and B. bowersi. Our findings suggest that wild rats could be a significant source of human infection, including contaminated food and water.

The Complete Mitochondrial Genome of the Caecal Fluke of Poultry, Postharmostomum commutatum, as the First Representative from the Superfamily Brachylaimoidea.

Postharmostomum commutatum (Platyhelminthes: Brachylaimoidea), a parasite of the caeca of poultry, has been frequently reported from many countries and regions, including China. However, the molecular epidemiology, population genetics and phylogenetics of this parasite are poorly understood. In the present study, we determined and characterized the complete mitochondrial (mt) genome of P. commutatum, as the first representative from the superfamily Brachylaimoidea. The mt genome of P. commutatum is a circular DNA molecule of 13,799 bp in size and encodes the complete set of 36 genes (12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) as well as a typical control region. The mt genome of P. commutatum presents a clear bias in nucleotide composition with a negative AT-skew on average (-0.306) and a positive GC-skew on average (0.466). Phylogenetic analyses showed that P. commutatum (superfamily Brachylaimoidea) and other ten members of the order Diplostomida were recovered as sister groups of the order Plagiorchiida, indicating that the order Diplostomida is paraphyletic. This is the first mt genome of any member of the superfamily Brachylaimoidea and should represent a rich source of genetic markers for molecular epidemiological, population genetic and phylogenetic studies of parasitic flukes of socio-economic importance in poultry.

Characterization of the complete mitochondrial genome of the echinostome Echinostoma miyagawai and phylogenetic implications.

Echinostomes are important intestinal foodborne parasites. Despite their significance as pathogens, characterization of the molecular biology and phylogenetics of these parasites are limited. In the present study, we determined the entire mitochondrial (mt) genome of the echinostome Echinostoma miyagawai (Hunan isolate) and examined the phylogenetic relationship with selected members of the suborder Echinostomata. The complete mt genome of E. miyagawai (Hunan isolate) was 14,468 bp in size. This circular mt genome contained 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one non-coding region. The gene order and genomic content were identical with its congeners. Phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) based on the concatenated amino acid sequences of 12 protein-coding genes strongly supported monophyly for the genus Echinostoma; however, they rejected monophyly for the family Echinostomatidae and the genus Fasciola. The mt genomic data described in this study provides useful genetic markers for studying the population genetics, molecular biology, and phylogenetics of these echinostomes.

Comparative analysis of mitochondrial DNA datasets indicates that Toxascaris leonina represents a species complex.

BACKGROUND: Toxascaris leonina is one of the most common intestinal parasites of canids and felids. In this study, we characterised the entire mitochondrial (mt) genome sequence of T. leonina from the cheetah and compared it with that of T. leonina from the dog. RESULTS: The entire mt genome sequence of T. leonina from the cheetah is 14,685 bp in size, which is 375 bp longer than that from the dog, and it is 408 bp longer than that from the South China tiger. The overall nucleotide sequence (except for the non-coding region) identity was 92.8% between the two mt genomes of T. leonina from the cheetah and the dog. For the 12 protein-coding genes, sequence difference between T. leonina from the cheetah and the dog was 5.0-9.7% at the nucleotide level and 1.0-7.2% at the amino acid level. Moreover, comparison of mt cox1 sequences among T. leonina isolates (n = 23) from different hosts revealed substantial nucleotide differences (10.6%). Phylogenetic analysis showed the separation of T. leonina from canid and felid hosts into three distinct clades. CONCLUSIONS: Taken together, these mtDNA datasets indicate that T. leonina from canid and felid hosts represents a species complex. Our results have implications for further studies of the molecular epidemiology, systematics and population genetics of this nematode.

Molecular Prevalence and Genetic Characterization of Toxoplasma gondii in Wild Birds in Hunan Province, China.

Toxoplasma gondii is a ubiquitous apicomplexan parasite of warm-blooded animals and humans. However, limited information is available about T. gondii infection in wild birds. In this study, 239 wild birds were collected from Hunan province of China, including 38 chestnut bunting, 44 olive-backed pipit, 26 yellow-breasted bunting, and 131 tree sparrows. Genomic DNA of brain tissues were extracted and assayed by B1 gene, and the positive samples were genotyped at 10 genetic markers [SAG1, SAG2 (5'+3' SAG2, alter. SAG2), SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico] using multilocus nested-PCR-restriction fragment length polymorphism technology. The results showed that 13 (5.51%) of the 239 wild birds were positive for T. gondii. Among them, three samples have completely genotyped at all loci, and were identified as ToxoDB #10. Our results have indicated that wild birds can carry and potentially disseminate the T. gondii. This is the first report of the molecular prevalence and genetic characterization of T. gondii in wild birds in Hunan province, China. Further research should be investigated to understand weather T. gondii can be transmitted from wild birds to other animals or humans.

Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics.

Longan (Dimocarpus longan Lour.), an important subtropical fruit in the family Sapindaceae, is grown in more than 10 countries. Longan is an edible drupe fruit and a source of traditional medicine with polyphenol-rich traits. Tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled. The draft genome (about 471.88 Mb) of a Chinese longan cultivar, "Honghezi," was estimated to contain 31 007 genes and 261.88 Mb of repetitive sequences. No recent whole-genome-wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3΄H, ANR, and UFGT) and contracted (PAL, CHS, and F3΄5΄H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, as well as the recent expansion and contraction of the NBS-LRR family, suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen resistance characteristics.

NUCLEAR MONOPLOIDY AND ASEXUAL PROPAGATION OF NANNOCHLOROPSIS OCEANICA (EUSTIGMATOPHYCEAE) AS REVEALED BY ITS GENOME SEQUENCE(1).

Species in genus Nannochloropsis are promising candidates for both biofuel and biomass production due to their ability to accumulate rich fatty acids and grow fast; however, their sexual reproduction has not been studied. It is clear that the construction of their metabolic pathways, such as that of polyunsaturated fatty acid (PUFA) biosynthesis, and understanding of their biological characteristics, such as nuclear ploidy and reproductive strategy, will certainly facilitate their genetic improvement through gene engineering and mutation and clonal expansion. In this study, the genome of N. oceanica S. Suda et Miyashita was sequenced with the next-generation Illumina GA sequencing technologies. The genome was ∼30 Mb in size, which contained 11,129 protein-encoding genes. Of them, 59.65% were annotated by aligning with those in diverse protein databases, and 29.68% were assigned at least one function described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Less frequent polymorphic nucleotides (one in 22.06 kb) and the obvious deviation from 1:1 (major:minor, minor ≥10) expectation indicated the nuclear monoploidy of N. oceanica. The lack of the majority of meiosis-specific proteins implied the asexual reproduction of this alga. In combination, the nuclear monoploidy and asexual propagation led us to favor the hypothesis that N. oceanica was a premeiotic or ameiotic alga. In addition, sequence similarity-based searching identified the elongase- and desaturase-encoding genes involved in the biosynthesis of long-chain PUFAs, which provided the genetic basis of its rich content of eicosapentaenoic acid (EPA). The functional genes and their metabolic pathways profiled against its genome sequence will facilitate its integrative investigations.