•We inoculated eight corn fields with an arbuscular mycorrhizal fungus.•Abundance of native mycorrhizal fungi was negatively related to soil nutrient contents.•Competitive effects to native fungal ...communities determined establishment success of the inoculant.•Phosphorous modulated the competitive effects between native and introduced fungi.•Crop growth response to inoculation was negatively correlated to fertilized amounts of P.
A major strategy to increase the sustainability of agricultural systems consists of enhancing internal ecosystem processes that support crop production and reduce external resource inputs. However, specific approaches to achieve this goal still need to be identified. Here, we investigated whether inoculation with a high dose of a well-characterized strain of a plant symbiotic arbuscular mycorrhizal (AM) fungus into Swiss corn fields leads to successful establishment of the fungus in plant roots and can generate agronomic benefits for maize production.
We used single-molecule real-time (SMRT) DNA sequencing to assess community composition of native AM fungi and identified environmental management and biological factors affecting AM fungal abundance, establishment success of the introduced fungus and effects of AMF inoculation on corn yield.
While native AM fungal abundance was negatively related to soil P contents, we found significantly positive relationships between soil P contents and establishment success of the inoculated fungus. There was a significantly negative relationship between inoculum establishment and abundance of native AM fungi. Although molecular quantification using strain-specific qPCR indicated that the inoculated strain strongly increased in abundance in roots from most soils investigated, total AM fungal root colonization was only significantly increased in one soil, indicating successful competition of the inoculant for root niche space against native AM fungi. Positive effects on corn yield were only observed when inoculation increased root colonization and were negatively correlated to P fertilization levels.
The results imply that phosphorus plays a major role in defining the abundance of native AM fungi and the composition of their communities and that these effects can determine establishment success of the inoculant. The results further indicate that positive effects on crop yield may only be expected when potentially achievable root colonization levels are not yet reached and AMF communities are not well developed.
Silage quality remains an important issue in farming, as do limitations in the range of products suitable for animal fodder. We therefore explored the microorganisms that are critical for the ...fermentation quality of paper mulberry silage. Low (unwilted) and high (wilted) dry matter (DM) paper mulberry were harvested at two cutting times. These were ensiled for 0, 3, 7, 14, and 56 days, respectively. Compared with unwilted silages, wilting significantly decreased (p < 0.05) silage pH value, ammonia‐N concentration, and yeast counts but increased (p < 0.05) lactic acid content. In addition, higher (p < 0.05) crude protein (CP) contents were also observed in wilted silages. Next‐generation sequencing (NGS) analysis revealed that wilting reduced the abundance of Enterobacter, while increasing that of Lactobacillus. Single‐molecule real‐time sequencing (SMRT) revealed that the silage was enriched in the lactic acid bacteria (LAB), Lactobacillus rhamnosus after wilting, which showed a positive correlation with CP and lactic acid content. We conclude that wilting may help preserve paper mulberry silage, facilitating its use as a new fodder resource. Moreover, L. rhamnosus has the potential to be developed as a new inoculant for the modulation in wilted silages, particularly paper mulberry silage.
Bacterial community was analyzed by combination of NGS and SMRT sequencing. Wilting enriched the abundance of Lactobacillus rhamnosus. Lactobacillus rhamnosus was the critical species showing the most positively correlation with wilted silage quality, and have the potential to be developed as new silage inoculant.
The underlying high-temperature oxidation mechanisms of the heat-resistant austenitic stainless steel with gradient nanostructured surface layer is revealed through systematic analysis of the ...microstructure and composition. Nanoscale oxide grains and high-density grain boundaries promoted the formation of pronounced spinel oxides, which suppressed elemental diffusion and CrO3 volatilization. High level of residual stress in the GNS layer facilitated the formation of high-density precipitates at the oxide/matrix interface and grain boundaries, which hindered the growth of oxide scale and reactive elements diffusion. The enhanced high-temperature oxidation resistance resulted from the synergistic combination of spinel oxides, precipitates, and high-density grain boundaries.
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•Improved oxidation resistance was the synergy result of spinel oxides, precipitates, and grain boundaries.•Extremely fine oxide grains promoted outward diffusion of Mn and forming thick spinel oxide layer.•Gradient strain induced high-density precipitates formation in the gradient nanostructured layer.•Outward diffusion of reactive elements reduced the thermal stability of nanograins.
The Great Himalayan Leaf-nosed bat (
) is one of the most representative species of all echolocating bats and is an ideal model for studying the echolocation system of bats. An incomplete reference ...genome and limited availability of full-length cDNAs have hindered the identification of alternatively spliced transcripts, which slowed down related basic studies on bats' echolocation and evolution. In this study, we analyzed five organs from
for the first time using PacBio single-molecule real-time sequencing (SMRT). There were 120 GB of subreads generated, including 1,472,058 full-length non-chimeric (FLNC) sequences. A total of 34,611 alternative splicing (AS) events and 66,010 Alternative Polyadenylation (APA) sites were detected by transcriptome structural analysis. Moreover, a total of 110,611 isoforms were identified, consisting of 52% new isoforms of known genes and 5% of novel gene loci, as well as 2112 novel genes that have not been annotated before in the current reference genome of
. Furthermore, several key novel genes, including
,
,
, and
, were identified as being associated with nervous, signal transduction, and immune system processes, which may be involved in regulating the auditory nervous perception and immune system that helps bats to regulate in echolocation. In conclusion, the full-length transcriptome results optimized and replenished existing
genome annotation in multiple ways and offer advantages for newly discovered or previously unrecognized protein-coding genes and isoforms, which can be used as a reference resource.
Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in ...2011: Ion Torrent's PGM, Pacific Biosciences' RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy.
Sequence generated by Ion Torrent, MiSeq and Pacific Biosciences technologies displays near perfect coverage behaviour on GC-rich, neutral and moderately AT-rich genomes, but a profound bias was observed upon sequencing the extremely AT-rich genome of Plasmodium falciparum on the PGM, resulting in no coverage for approximately 30% of the genome. We analysed the ability to call variants from each platform and found that we could call slightly more variants from Ion Torrent data compared to MiSeq data, but at the expense of a higher false positive rate. Variant calling from Pacific Biosciences data was possible but higher coverage depth was required. Context specific errors were observed in both PGM and MiSeq data, but not in that from the Pacific Biosciences platform.
All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support.
•This is the first report on metabolic gene clusters in paper mulberry silage.•Ensiling causes a shift in dominant bacteria from Gram-negative to Gram-positive.•Enterobacter and Lactobacillus species ...determine silage fermentation quality.•PacBio sequencing reveals microbial dynamics during silage fermentation.•Paper mulberry can be used to prepare high-quality nutrient-rich silage.
To develop a new high-protein woody forage resource for livestock to alleviate feed shortages in the tropics, we applied PacBio single-molecule, real-time (SMRT) sequencing to explore the community structure, species diversity and metabolic gene clusters of natural microorganisms associated with paper mulberry (PM) silage fermentation. High levels of microbial diversity and abundance were observed in PM raw material, and these levels decreased with the progression of silage fermentation. During woody ensiling, the dominant bacteria shifted from pathogenic Gram-negative Proteobacteria to beneficial Gram-positive Firmicutes. Lactic acid bacteria became the most dominant bacteria that affected fermentation quality in terminal silages. Global and overview maps, carbohydrate metabolism and amino-acid metabolism were the important microbial metabolic pathways that impacted the final fermentation product of silage. PacBio SMRT sequencing revealed specific microbial-related information concerning silage. PM is rich in nutrients and macro mineral contents, which are preserved well during ensiling, indicating that PM silage can serve as a new woody resource suitable for ruminants.
The ability to generate long sequencing reads and access long-range linkage information is revolutionizing the quality and completeness of genome assemblies. Here we use a hybrid approach that ...combines data from four genome sequencing and mapping technologies to generate a new genome assembly of the honeybee Apis mellifera. We first generated contigs based on PacBio sequencing libraries, which were then merged with linked-read 10x Chromium data followed by scaffolding using a BioNano optical genome map and a Hi-C chromatin interaction map, complemented by a genetic linkage map.
Each of the assembly steps reduced the number of gaps and incorporated a substantial amount of additional sequence into scaffolds. The new assembly (Amel_HAv3) is significantly more contiguous and complete than the previous one (Amel_4.5), based mainly on Sanger sequencing reads. N50 of contigs is 120-fold higher (5.381 Mbp compared to 0.053 Mbp) and we anchor > 98% of the sequence to chromosomes. All of the 16 chromosomes are represented as single scaffolds with an average of three sequence gaps per chromosome. The improvements are largely due to the inclusion of repetitive sequence that was unplaced in previous assemblies. In particular, our assembly is highly contiguous across centromeres and telomeres and includes hundreds of AvaI and AluI repeats associated with these features.
The improved assembly will be of utility for refining gene models, studying genome function, mapping functional genetic variation, identification of structural variants, and comparative genomics.
We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing ...platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. The draft genome was improved through Chicago sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the
family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality.
•Obtain a high-quality Ginkgo seed development-related transcript data set.•Reveals the diversity of TTLs regulation modes in ginkgo seed development.•Further optimized the structure and function ...annotations of the ginkgo genome.
Full-length transcriptome sequencing based on the PacBio sequencing platform could significantly optimize the annotation of gene structures. As an ancient relic gymnosperm in the monotypic order Ginkgoales, Ginkgo biloba L. contains rich terpenoids that are medicinally valuable. The seeds have abundant edible endosperm, which is delicious and of high nutritional value. However, existing molecular studies on the developmental process of ginkgo seeds are relatively weak, and the biosynthesis of terpenoids in seeds has received little attention. Therefore, single-molecule real-time (SMRT) technology and Illumina sequencing were combined to sequence six tissues related to the reproductive growth and development of ginkgo in order to generate a high-quality full-length transcription database. In total, 20.98 Gb of clean reads containing 178,548 full-length non-chimeric (FLNC) sequences were obtained. From these data, 4019 novel genes and 22,845 novel isoforms were predicted, 52.32 % of the novel genes were annotated, and three novel isoforms were annotated in terpene synthesis related pathways. The enrichment analysis of differentially expressed genes (DEGs) showed that, 95 genes were enriched into 21 categories related to seed development, and 47 DEGs were enriched in the skeletal pathway of terpene synthesis. Combined with the real-time quantitative reverse transcription PCR (qRT-PCR), the phosphosynthase family members synthesizing terpene precursors have diverse and complex expression trends during seed development. Our findings confirm the advantages of SMRT, which facilitated the construction a rich transcript data-set for research on the development of ginkgo seeds, enriching the annotation of the ginkgo genome, and enhancing our understanding of gene regulation of terpene biosynthesis in ginkgo seeds.
Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these ...fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species.
A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidate de novo assemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previous O. niloticus genome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number of genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recent vasa gene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both a ~9Mbp XY sex determination region on LG1 in O. niloticus, and a ~50Mbp WZ sex determination region on LG3 in the related species O. aureus.
This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome. The study serves as an example of the need for high quality genome assemblies and provides a framework for identifying sex determining genes in tilapia and related fish species.
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