•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.
•A full-length transcriptome of Urechis unicinctus was generated by using SMRT Sequencing technology.•A total of 59,371 unigenes with a 2,779 bp average length were obtained.•2,613 lncRNAs, 59,190 ...CDSs, 35,166 SSRs, and 1,733 TFs were identified in the transcriptome.•211 PRRs were identified, including TLRs, CLTs, SRs, PGRPs, and GNBPs.•Numerous transcript variations of immune molecules provide new insights into the innate immune system of Urechis unicinctus.
The Echiura worm Urechis unicinctus refers to a common benthic invertebrate found in the intertidal zone of Huanghai as well as Bohai Bay. U. unicinctus is known to contain various physiologically active substances, making it highly valuable in terms of its edibility, medicinal properties, and economic potential. Nonetheless, the limited study on the immune system of U. unicinctus poses difficulties for its aquaculture and artificial reproduction. Marine invertebrates, including shellfish and U. unicinctus, are thought to primarily depend on their innate immune system for disease protection, owing to the severalinnate immune molecules they possess. Herein, we employed PacBio single-molecule real-time (SMRT) sequencing technology to perform the full-length transcriptome analysis of U. unicinctus individuals under five different conditions (room temperature (RT), low temperature (LT), high temperature (HT), without water (DRY), ultraviolet irradiation (UV)). Concequently, we identified 59,371 unigenes that had a 2,779 bp average length, 2,613 long non-coding RNAs (lncRNAs), 59,190 coding sequences (CDSs), 35,166 simple sequence repeats (SSRs), and 1,733 transcription factors (TFs), successfully annotating 90.58 % (53,778) of the unigenes. Subsequently, key factors associated with immune-related processes, such as non-self-recognition, cellular immune defenses, and humoral immune defenses, were searched. Our study also identified pattern recognition receptors (PRRs) that included 17 peptidoglycan recognition proteins (PGRPs), 13 Gram-negative binding proteins (GNBPs), 18 scavenger receptors (SRs), 74 toll-like receptors (TLRs), and 89 C-type lectins (CLTs). Altogether, the high-quality transcriptome obtained data will offer valuable insights for further investigations into U. unicinctus innate immune response, laying the foundation for subsequent molecular biology studies and aquaculture.
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.
Acipenser dabryanus, also called Yangtze sturgeon or Dabry's sturgeon, is an endemic species restricted to the upper reaches of the Yangtze River in China. In the present study, we conducted the ...first full-length transcriptome analysis of A. dabryanus by the use of SMRT sequencing technology. Transcriptome sequencing generated a total of 155,348 unigenes with a mean length of 2996 bp. A total of 131,711 (84.78%) unigenes were annotated in various databases and comparative analysis was performed between A. dabryanus and its the related species. Based on the sequence information, three members in the tripartite motif (TRIM) family, namely, TRIM32, TRIM36 and TRIM71, were identified. The full-length TRIM genes encoded polypeptides with a typical TRIM structure: a RING domain, one or two B-box domains, and variable domains at the C-terminus. Gene expression profile analysis showed that the three TRIM genes were constitutively expressed in A. dabryanus, and the highest expression levels of TRIM32 and TRIM36 were found in the brain, while TRIM71 was predominantly expressed in the muscle. Upon challenge with the bacterial pathogen Edwardsiella tarda, significant upregulation of TRIMs was observed in both mucosal and systemic-associated immune tissues. Our data revealed the possible functional role of TRIMs in both mucosal and systemic defence of A. dabryanus in the immune response against bacterial infection.
•The first full-length transcriptome sequencing of Acipenser dabryanus was obtained using SMRT technology.•The TRIM32, TRIM36 and TRIM71 were identified from A. dabryanus.•TRIM transcripts were detected in a wide range of tissues.•Upon challenge with bacterial pathogen, significant upregulation of TRIMs was observed in various immune tissues.
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.
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.
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.
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.
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