Progress on genomics and locus of important agronomic traits in Chenopodium quinoa.

Quinoa (Chenopodium quinoa, Willd.) as a new health food in the 20th century, its comprehensive nutritional composition, stress resistance and other characteristics have been paid much of attention, and enjoys the reputation of "nutritional gold", "vegetarian king" and "food in the future" in the world. In recent years, with the rapid development of genomics and high-throughput sequencing technology, the high-quality whole genome sequence of quinoa has been completed, and the omics analysis and functional research of a series of key genes have been gradually carried out. In this review, we summarize the research progress in quinoa genomics, gene family analysis of important transcription factors, genetic map construction, QTL mapping of important traits, and genes for important agronomic and yield traits. Moreover, according to the current status of quinoa breeding, this paper also put forward five key problems in quinoa breeding, and pointed out four important directions of genetic improvement and breeding of quinoa in the future, so as to provide reference for the realization of directional genetic improvement of quinoa in the future.

Oesophagostomum dentatum and Oesophagostomum quadrispinulatum: characterization of the complete mitochondrial genome sequences of the two pig nodule worms.

In the present study, the complete mitochondrial DNA (mtDNA) sequences of the pig nodule worm Oesophagostomum quadrispinulatum were determined for the first time, and the mt genome of Oesophagostomum dentatum from China was also sequenced for comparative analysis of their gene contents and genome organizations. The mtDNA sequences of O. dentatum China isolate and O. quadrispinulatum were 13,752 and 13,681 bp in size, respectively. Each of the two mt genomes comprises 36 genes, including 12 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, but lacks the ATP synthetase subunit 8 gene. All genes are transcribed in the same direction and have a nucleotide composition high in A and T. The contents of A+T are 75.79% and 77.52% for the mt genomes of O. dentatum and O. quadrispinulatum, respectively. Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes, with three different computational algorithms (maximum likelihood, maximum parsimony and Bayesian inference), all revealed that O. dentatum and O. quadrispinulatum represent distinct but closely-related species. These data provide novel and useful markers for studying the systematics, population genetics and molecular diagnosis of the two pig nodule worms.

Electrophoretic detection of genetic variability among Schistosoma japonicum isolates by sequence-related amplified polymorphism.

In the present study, sequence-related amplification polymorphism (SRAP) was utilized to study the genetic variability among Schistosoma japonicum isolates from different provinces in China, using Schistosoma mansoni from Puerto Rico for comparison. Five out of ten tested SRAP primer combinations displayed significant polymorphisms among S. japonicum isolates from China, namely ME2/EM1, ME4/EM1, ME4/EM6, ME5/EM4 and ME5/EM5. Analysis of the 61 S. japonicum samples from China with five SRAP primer combinations identified a total of 83 reproducible polymorphic fragments. The number of fragments using each primer combination ranged from 14 to 19, with an average of 16 polymorphic bands per primer pair, and the size of fragment ranged approximately from 100 to 1000 bp. Representative-specific SRAP fragments were excised from the gels, and confirmed by PCR amplification of genomic DNA using primers designed and based on the sequences of these SRAP fragments. Based on SRAP profiles, unweighted pair-group method with arithmetic averages (UPGMA) dendrogram was constructed. UPGMA clustering algorithm categorized S. japonicum isolates from China into nine clades and two lineages (representing the mountainous and lake/marshland regions). These results indicate the usefulness of the SRAP technique for revealing genetic variability among S. japonicum isolates from China, and the SRAP technique should be applicable to other living organisms.

Genetic characterization of ticks from southwestern Romania by sequences of mitochondrial cox1 and nad5 genes.

In the present study, samples representing three hard tick species and one soft tick species, namely Dermacentor marginatus, Haemaphysalis punctata, Ixodes ricinus and Argas persicus from southwestern Romania, and one hard tick, Haemaphysalis longicornis, from China were characterized genetically by a portion of mitochondrial cytochrome c oxidase subunit 1 gene (pcox1) and a portion of nicotinamide adenine dinucleotide dehydrogenase subunit 5 gene (pnad5). The pcox1 and pnad5 were amplified separately from individual ticks by PCR, sequenced and analyzed. The length of pcox1 and pnad5 sequences of all samples was 732 and 519 bp, respectively. The intra-specific sequence variation in De. marginatus was 0.1-1.0% for pcox1 and 0.2-1.2% for pnad5, whereas in Ha. punctata it was 0.4-1.9% for pcox1 and 0.4-1.0% for pnad5. For the tick species examined in the present study, sequence comparison revealed that the inter-specific sequence differences were higher: 15.9-27.6% for pcox1 and 20.3-42.4% for pnad5. This suggests that the cox1 and nad5 sequences could provide useful genetic markers for the specific identification and genetic characterization of ticks in Romania and elsewhere.

The complete mitochondrial genomes for three Toxocara species of human and animal health significance.

BACKGROUND: Studying mitochondrial (mt) genomics has important implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. In addition, mt genome sequences have provided useful markers for investigating population genetic structures, systematics and phylogenetics of organisms. Toxocara canis, Toxocara cati and Toxocara malaysiensis cause significant health problems in animals and humans. Although they are of importance in human and animal health, no information on the mt genomes for any of Toxocara species is available. RESULTS: The sizes of the entire mt genome are 14,322 bp for T. canis, 14029 bp for T. cati and 14266 bp for T. malaysiensis, respectively. These circular genomes are amongst the largest reported to date for all secernentean nematodes. Their relatively large sizes relate mainly to an increased length in the AT-rich region. The mt genomes of the three Toxocara species all encode 12 proteins, two ribosomal RNAs and 22 transfer RNA genes, but lack the ATP synthetase subunit 8 gene, which is consistent with all other species of Nematode studied to date, with the exception of Trichinella spiralis. All genes are transcribed in the same direction and have a nucleotide composition high in A and T, but low in G and C. The contents of A+T of the complete genomes are 68.57% for T. canis, 69.95% for T. cati and 68.86% for T. malaysiensis, among which the A+T for T. canis is the lowest among all nematodes studied to date. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. The mt genome structures for three Toxocara species, including genes and non-coding regions, are in the same order as for Ascaris suum and Anisakis simplex, but differ from Ancylostoma duodenale, Necator americanus and Caenorhabditis elegans only in the location of the AT-rich region, whereas there are substantial differences when compared with Onchocerca volvulus,Dirofiliria immitis and Strongyloides stercoralis. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes revealed that the newly described species T. malaysiensis was more closely related to T. cati than to T. canis, consistent with results of a previous study using sequences of nuclear internal transcribed spacers as genetic markers. CONCLUSION: The present study determined the complete mt genome sequences for three roundworms of human and animal health significance, which provides mtDNA evidence for the validity of T. malaysiensis and also provides a foundation for studying the systematics, population genetics and ecology of these and other nematodes of socio-economic importance.

Characterization of the complete mitochondrial genomes of five Eimeria species from domestic chickens.

Chicken coccidiosis caused by members of the genus Eimeria causes significant economic losses worldwide. In the present study we sequenced the complete mitochondrial DNA (mtDNA) sequences of six Eimeria species and analyzed features of their gene contents and genome organizations. The complete mt genomes of E. acervulina, E. brunetti, E. maxima, E. necatrix, E. tenella and E. praecox were 6179bp, 6148bp, 6169bp, 6214bp, 6213bp and 6174bp in size, respectively. All of the mt genomes consist of 3 genes for proteins (cox1, cox3, and cytb), 12 gene fragments for the large subunit (LSU) rRNA, and 7 gene fragments for the small subunit (SSU) rRNA, but no transfer RNA genes. The organization of the mt genomes is similar to that of Plasmodium, but distinct from Babesia and Theileria. The putative direction of translation for 3 genes (cox1, cox3, and cytb) was the same in all six Eimeria species. The contents of A+T of the mt genomes were 65.35% for E. acervulina, 65.43% for E. brunetti, 64.53% for E. maxima, 65.04% for E. necatrix, 64.98% for E. tenella and 65.59% for E. praecox. The AT bias has a significant effect on both the codon usage pattern and amino acid composition of proteins. Phylogenetic analyses using concatenated nucleotide sequences of the 2 protein-coding genes (cytb and cox1), with three different computational algorithms (Bayesian analysis, maximum parsimony and maximum likelihood), all revealed distinct groups with high statistical support, indicating that the six Eimeria spp. represent six distinct but closely-related species. These data provide novel mtDNA markers for studying the molecular epidemiology and population genetics of the six Eimeria spp., and should have implications for the molecular diagnosis, prevention and control of coccidiosis in domestic chickens.

Electrophoretic analysis of sequence variability in three mitochondrial DNA regions for ascaridoid parasites of human and animal health significance.

Sequence variability in three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1), NADH dehydrogenase subunits 1 and 4 (nad1 and nad4), among and within Toxocara canis, T. cati, T. malaysiensis, T. vitulorum and Toxascaris leonina from different geographical origins was examined by a mutation-scanning approach. A portion of the cox1 gene (pcox1), a portion of the nad1 and nad4 genes (pnad1 and pnad4) were amplified separately from individual ascaridoid nematodes by polymerase chain reaction and the amplicons analyzed by single-strand conformation polymorphism (SSCP). Representative samples displaying sequence variation in SSCP profiles were subjected to sequencing in order to define genetic markers for their specific identification and differentiation. While the intra-specific sequence variations within each of the five ascaridoid species were 0.2-3.7% for pcox1, 0-2.8% for pnad1 and 0-2.3% for pnad4, the inter-specific sequence differences were significantly higher, being 7.9-12.9% for pcox1, 10.7-21.1% for pnad1 and 12.9-21.7% for pnad4, respectively. Phylogenetic analyses based on the combined sequences of pcox1, pnad1 and pnad4 revealed that the recently described species T. malaysiensis was more closely related to T. cati than to T. canis. These findings provided mtDNA evidence for the validity of T. malaysiensis and also demonstrated clearly the usefulness and attributes of the mutation-scanning sequencing approach for studying the population genetic structures of these and other nematodes of socio-economic importance.

[Comparison of light characteristics in different size gaps in eastern Liaoning montane secondary forests].

With three different size gaps (G1, 670 m2; G2, 290 m2; and G3, 90 m2) in eastern Liaoning montane secondary forests of China as test objects, and through a continuous measurement of light intensity, the spatiotemporal distribution of photosynthetic photon flux density (PPFD) in the gaps was compared. The results showed that the diurnal variation of PPFD in the gaps was greater at northern than at southern position. The larger the forest gap, the broader the higher PPFD value area, and the more obvious the heterogeneity. As for the monthly variation of PPFD, the maximum PPFD at each position of the gaps appeared at the beginning of growth season (i.e., in April and May), while the minimum PPFD occurred in different months. The maximum PPFD at the eastern and western positions of each gap was basically appeared in the same months, and the PPFD was significantly higher in spring than in summer and autumn (P < 0.05). The mean monthly PPFD at the centers of G1, G2, and G3 was 66.59%, 49.05%, and 30.37% of full sunlight, respectively, and in growth season, the PPFD at gap center was 37.8, 27.9 and 10.3 times higher than that at understory. It was suggested that owing to the different size and shape of forest gap and the effects of landform, the light intensity and its distribution in forest gap were different, being the key factors leading to the heterogeneity of regeneration pattern and the variation of species composition in forest gap.

[Effects of ectomycorrhizal fungi on alleviating the decline of Pinus sylvestris var. mongolica plantations on Keerqin sandy land].

Based on the observations of air temperature, soil temperature, and root systems of Pinus sylvestris var. mongolica plantations on southeastern Keerqin sandy land, the decline mechanisms of the plantations were analyzed from the aspect of the effects of temperature on the growth and survival of ectomycorrhizal fungi (ECM). The results indicated that ECM could hardly survive with in 0-5 cm soil layer because of its high temperature environment, but the temperature condition in 20-40 cm soil layer was suitable for the survival and growth of ECM. 78% of the roots of 13-42 years old P. sylvestris var. mongolica tress were distributed in 20-40 cm soil layer, which suggested that the existence of ECM in this soil layer inhibited or alleviated the decline of the P. sylvestris var. mongolica plantations, and was not the inducing factor of the plantations' top withering, low growth rate, and tree death. The lack of ECM in surface soil layer (0-5 cm) could be one of the main reasons leading to the death of seedlings root systems, and thus, the failure of P. sylvestris var. mongolica plantations' regeneration.

The evaluation for generic-level monophyly of Ancyrocephalinae (Monogenea, Dactylogyridae) using ribosomal DNA sequence data.

To overcome the limited regional and taxonomic coverage in previous studies of the Ancyrocephalinae (Monogenea, Dactylogyridae), we present further findings on the molecular systematics and phylogeny of a broader selection of specimens, aiming to build a molecular phylogeny of the Ancyrocephalinae, and to assess the monophyly of each available genus, using D1-D2 domain of LSU rDNA and the combined LSU and partial sequence of SSU rDNA data sets. Our studies showed that 18 Haliotrema species were highly dispersive to form several clades with species from ten closely related genera. The host range of Euryhaliotrematoides species was not only restricted in butterfly fishes (Chaetodontidae), but widen to include the Lutjanidae. Euryhaliotrema was phylogenetically more closely related to Aliatrema than to Euryhaliotrematoides. Given that the species Haliotrema kurodai, Haliotrema spirotubiforum and Haliotrema anguiformis had a funnel-shaped base of the coiled male copulatory organ (MCO) lacking an accessory piece, and our molecular evidence, we proposed to transfer the three species to the Aliatrema as new combinations. We proposed to combine Bravohollisia and Caballeria into one genus, mainly based on molecular evidence and their similar MCO characters. Using SSU+ITS1 data set, Scutogyrus was robustly resolved as a polyphyletic group and its status should be questioned. Based on the present molecular evidence and their similar MCO characters, we proposed to combine Cichlidogyrus and Scutogyrus into one genus, Cichlidogyrus, by treating Scutogyrus as the synonym of Cichlidogyrus. Generally, the present study indicated that the vagina can make little contribution for understanding the generic-level monophyly, due to its high variability even among phylogenetically very closely related species, but it was useful for species determination. Given that phylogenetically closely related species from the same or closely related host species may have similar MCO characters but distinct haptoral characters, we consider that it is dangerous to erect a genus mainly based on different haptoral characters, particularly those separated from existing genera. The resultant phylogenetic reconstructions indicated that the radiation of some Haliotrema species has correlated with their hosts, because species from closely related fishes have correspondingly shown close relationships. Though the present study can not provide the comparison of host-parasite associations, phylogenetically closely related Haliotrema species which have similar morphological characters (both MCOs and haptors) but distinct/distantly related host species may indicate a speciation model of host-switching.

PCR-based identification and delineation of members within the Pseudorhabdosynochus lantauensis complex (Monogenea: Diplectanidae).

Molecular methods using genetic markers in the nuclear ribosomal DNA (rDNA) were established to identify and distinguish between two members within the Pseudorhabdosynochus lantauensis complex and two morphologically distinct congeners, Pseudorhabdosynochus epinepheli and Pseudorhabdosynochus coioidesis, from different marine fish species and various geographical origins. Supported by selective DNA sequencing, it was demonstrated that the polymerase chain reaction (PCR)-coupled single-strand conformation polymorphism analysis of the first internal transcribed spacer and restriction fragment length polymorphism analysis of a variable region (representing the D1-D3 domains) in the large subunit of rDNA achieved the identification and delineation of all four taxa examined. These PCR-based approaches provide useful complementary tools to traditional methods for the accurate identification of species within the genus Pseudorhabdosynochus (irrespective of developmental stage) and have major implications for studying the ecology, transmission, and population genetic structures of these and other related parasites and for the prevention and control of the diseases they cause.

PCR-SSCP as a molecular tool for the identification of Benedeniinae (Monogenea: Capsalidae) from marine fish.

PCR-based single strand conformation polymorphism (SSCP) analysis was used to characterize monogenean specimens of the subfamily Benedeniinae of morphologically uncertain specific status from different marine fish species, using Neobenedenia melleni, N. girellae and Entobdella corona for comparison. The first internal transcribed spacer (ITS-1) and the 5' terminal variable region (D1-D3 domains) of the large subunit ribosomal DNA (lsrDNA) were amplified separately from individual monogeneans, and the amplicons were subjected to PCR-SSCP analyses, followed by direct sequencing. Both SSCP patterns and the ITS-1 sequences data allowed specimens representing Entobdella spp. from the host Taeniura melanospilos to be unequivocally distinguished from those representing Neobenedenia spp. and those representing Benedenia spp. Neobenedenia girellae, a morphologically controversial species, had identical SSCP banding pattern and ITS-1 sequence to that of N. melleni, supporting the proposal that N. girellae is a synonym of N. melleni. Neobenedenia spp. and Benedenia spp. had identical SSCP patterns and ITS-1 sequences. These findings and the PCR-SSCP approach taken should have implications for the accurate identification and assessment of taxonomic validity of other important monogenean groups of the marine fish.