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June 1, 2021  |  

SMRT Sequencing of whole mitochondrial genomes and its utility in association studies of metabolic disease.

In this study we demonstrate the utility of Single-Molecule Real Time SMRT sequencing to detect variants and to recapitulate whole mitochondrial genomes in an association study of Metabolic syndrome using samples from a well-studied cohort from Micronesia. The Micronesian island of Kosrae is a rare genetic isolate that offers significant advantages for genetic studies of human disease. Kosrae suffers from one of the highest rates of MetS (41%), obesity (52%), and diabetes (17%) globally and has a homogeneous environment making this an excellent population in which to study these significant health problems. We are conducting family-based association analyses aimed at identifying specific mitochondrial variants that contribute to obesity and other co-morbid conditions. We sequenced whole mitochondrial genomes from 10 Kosraen individuals who represent greater than 25 % of the mitochondrial genetic diversity for the entire Kosraen population. Using Pacific Biosciences C2 chemistry, SMRTbell libraries were constructed from pooled, full-length, unsheared 5 kb PCR amplicons, tiling the entire 16.6 kb mtDNA genome. Average read lengths for each sample were between 2500-3000 bp, with 5% of reads between 6,000-8,000 bases, depending on movie lengths. The data generated in this study serve as proof of principle that SMRT Sequencing data can be utilized for identification of high-quality variants and complete mitochondrial genome sequences. These data will be leveraged to identify causative variants for Metabolic syndrome and associated disorders.

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June 1, 2021  |  

Sequencing and de novo assembly of the 17q21.31 disease associated region using long reads generated by Pacific Biosciences SMRT Sequencing technology.

Assessment of genome-wide variation revealed regions of the genome with complex, structurally diverse haplotypes that are insufficiently represented in the human reference genome. The 17q21.31 region is one of the most dynamic and complex regions of the human genome. Different haplotypes exist, in direct and inverted orientation, showing evidence of positive selection and predisposing to microdeletion associated with mental retardation. Sequencing of different haplotypes is extremely important to characterize the spectrum of structural variation at this locus. However, de novo assembly with second-generation sequencing reads is still problematic. Using PacBio technology we have sequenced and de novo assembled a tiling path of eight BAC clones (~1.6 Mb region) across this medically relevant region from the library of a hydatidiform mole. Complete hydatidiform moles arise from the fertilization of an enucleated egg from a single sperm and therefore carry a haploid complement of the human genome, eliminating allelic variation that may confound mapping and assembly. The PacBio RS system enables single molecule real time sequencing, featuring long reads and fast turnaround times. With deep sequencing, PacBio reads were able to generate a very uniform sequencing coverage with close to 100% coverage of most of the target interval regions covered. Due to long read lengths, the PacBio RS data could be accurately assembled.

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June 1, 2021  |  

Using whole exome sequencing and bacterial pathogen sequencing to investigate the genetic basis of pulmonary non-tuberculous mycobacterial infections.

Pulmonary non-tuberculous mycobacterial (PNTM) infections occur in patients with chronic lung disease, but also in a distinct group of elderly women without lung defects who share a common body morphology: tall and lean with scoliosis, pectus excavatum, and mitral valve prolapse. In order to characterize the human host susceptibility to PNTM, we performed whole exome sequencing (WES) of 44 individuals in extended families of patients with active PNTM as well as 55 additional unrelated individuals with PNTM. This unique collection of familial cohorts in PNTM represents an important opportunity for a high yield search for genes that regulate mucosal immunity. An average of 58 million 100bp paired-end Illumina reads per exome were generated and mapped to the hg19 reference genome. Following variant detection and classification, we identified 58,422 potentially high-impact SNPs, 97.3% of which were missense mutations. Segregating variants using the family pedigrees as well as comparisons to the unrelated individuals identified multiple potential variants associated with PNTM. Validations of these candidate variants in a larger PNTM cohort are underway. In addition to WES, we sequenced the genomes of 52 mycobacterial isolates, including 9 from these PNTM patients, to integrate host PNTM susceptibility with mycobacterial genotypes and gain insights into the key factors involved in this devastating disease. These genomes were sequenced using a combination of 454, Illumina, and PacBio platforms and assembled using multiple genome assemblers. The resulting genome sequences were used to identify mycobacterial genotypes associated with virulence, invasion, and drug resistance.

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June 1, 2021  |  

Integrative biology of a fungus: Using PacBio SMRT Sequencing to interrogate the genome, epigenome, and transcriptome of Neurospora crassa.

PacBio SMRT Sequencing has the unique ability to directly detect base modifications in addition to the nucleotide sequence of DNA. Because eukaryotes use base modifications to regulate gene expression, the absence or presence of epigenetic events relative to the location of genes is critical to elucidate the function of the modification. Therefore an integrated approach that combines multiple omic-scale assays is necessary to study complex organisms. Here, we present an integrated analysis of three sequencing experiments: 1) DNA sequencing, 2) base-modification detection, and 3) Iso-seq analysis, in Neurospora crassa, a filamentous fungus that has been used to make many landmark discoveries in biochemistry and genetics. We show that de novo assembly of a new strain yields complete assemblies of entire chromosomes, and additionally contains entire centromeric sequences. Base-modification analyses reveal candidate sites of increased interpulse duration (IPD) ratio, that may signify regions of 5mC, 5hmC, or 6mA base modifications. Iso-seq method provides full-length transcript evidence for comprehensive gene annotation, as well as context to the base-modifications in the newly assembled genome. Projects that integrate multiple genome-wide assays could become common practice for identifying genomic elements and understanding their function in new strains and organisms.

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June 1, 2021  |  

A novel analytical pipeline for de novo haplotype phasing and amplicon analysis using SMRT Sequencing technology.

While the identification of individual SNPs has been readily available for some time, the ability to accurately phase SNPs and structural variation across a haplotype has been a challenge. With individual reads of an average length of 9 kb (P5-C3), and individual reads beyond 30 kb in length, SMRT Sequencing technology allows the identification of mutation combinations such as microdeletions, insertions, and substitutions without any predetermined reference sequence. Long- amplicon analysis is a novel protocol that identifies and reports the abundance of differing clusters of sequencing reads within a single library. Graphs generated via hierarchical clustering of individual sequencing reads are used to generate Markov models representing the consensus sequence of individual clusters found to be significantly different. Long-amplicon analysis is capable of differentiating between underlying sequences that are 99.9% similar, which is suitable for haplotyping and differentiating pseudogenes from coding transcripts. This protocol allows for the identification of structural variation in the MUC5AC gene sequence, despite the presence of a gap in the current genome assembly, and can also be used for HLA haplotyping. Clustering can also been applied to identify full length transcripts for the purpose of estimating consensus sequences and enumerating isoform types. Long-amplicon analysis allows for the elucidation of complex regions otherwise missed by other sequencing technologies, which may contribute to the diagnosis and understanding of otherwise complex diseases.

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June 1, 2021  |  

High-throughput analysis of full-length proviral HIV-1 genomes from PBMCs.

Background: HIV-1 proviruses in peripheral blood mononuclear cells (PBMCs) are felt to be an important reservoir of HIV-1 infection. Given that this pool represents an archival library, it can be used to study virus evolution and CD4+ T cell survival. Accurate study of this pool is burdened by difficulties encountered in sequencing a full-length proviral genome, typically accomplished by assembling overlapping pieces and imputing the full genome. Methodology: Cryopreserved PBMCs collected from a total of 8 HIV+ patients from 1997-2001 were used for genomic DNA extraction. Patients had been receiving cART for 2-8 years at the time samples were obtained. 7 patients had pVL >50 copies/mL (mean: 312,282, range: 18,372-683,400) and 1 had pVL <50. Genomic DNA was subjected to limiting dilution prior to amplification of near-full-length genomes by a newly developed nested PCR. The predicted size of the PCR product was 9.0 kb, spanning from the 5’ LTR through the 3’ LTR. Single molecules were sequenced as near-full-length amplicons directly from PCR products without shearing using commercially available P4-C2 reagents and standard protocols on a PacBio RS II instrument. Quality of the genomes was validated by clonal positive controls and synthetic mixtures. Results: Near-full-length provirus genome sequences were successfully obtained from all 8 patients as continuous long reads from single molecules. PacBio sequencing required approximately 10% of the PCR product needed for Sanger sequencing and generated 325 MB per 3-hour run including 1,800 full-length intact genome reads on average. One patient’s sample was not at a limiting dilution and analysis revealed multiple subspecies. For 8 near-fulllength provirus genomes derived from the other 7 patients, large internal deletions were noted in 2 proviruses; APOBEC-mediated hypermutations were seen in 2 proviruses; and 4 proviruses appeared to be intact genomes. All of the defective proviruses showed a complete absence of resistance mutations in either RT or protease, even after 2-8 years of cART. On the contrary, all of the intact proviruses contained evidence of ART-resistance associated mutations suggesting that they represented relatively recent variants. Conclusions: Combining a novel protocol for full-length limiting dilution amplification of proviruses with PacBio SMRT sequencing allowed for the generation of near-full-length genomes with good quality and an ability to detect minor variants at the 1-10% level. Preliminary data analyses suggest that defective proviruses may represent archival variants that persist long-term in host cells, while intact proviruses within the PBMC pool showing evidence of active virus replication may represent more recent variants.

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June 1, 2021  |  

Long-read, single-molecule applications for protein engineering.

The long read lengths of PacBio’s SMRT Sequencing enable detection of linked mutations across multiple kilobases of sequence. This feature is particularly useful in the context of protein engineering, where large numbers of similar constructs are generated routinely to explore the effects of mutations on function and stability. We have developed a PCR-based barcoded sequencing method to generate high quality, full-length sequence data for batches of constructs generated in a common backbone. Individual barcodes are coupled to primers targeting a common region of the vector of interest. The amplified products are pooled into a single DNA library, and sequencing data are clustered by barcode to generate multi-molecule consensus sequences for each construct present in the pool. As a proof-of-concept dataset, we have generated a library of 384 randomly mutated variants of the Phi29 DNA polymerase, a 575 amino acid protein encoded by a 1.7 kb gene. These variants were amplified with a set of barcoded primers, and the resulting library was sequenced on a single SMRT Cell. The data produced sequences that were completely concordant with independent Sanger sequencing, for a 100% accurate reconstruction of the set of clones.

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June 1, 2021  |  

An interactive workflow for the analysis of contigs from the metagenomic shotgun assembly of SMRT Sequencing data.

The data throughput of next-generation sequencing allows whole microbial communities to be analyzed using a shotgun sequencing approach. Because a key task in taking advantage of these data is the ability to cluster reads that belong to the same member in a community, single-molecule long reads of up to 30 kb from SMRT Sequencing provide a unique capability in identifying those relationships and pave the way towards finished assemblies of community members. Long reads become even more valuable as samples get more complex with lower intra-species variation, a larger number of closely related species, or high intra-species variation. Here we present a collection of tools tailored for PacBio data for the analysis of these fragmented metagenomic assembles, allowing improvements in the assembly results, and greater insight into the communities themselves. Supervised classification is applied to a large set of sequence characteristics, e.g., GC content, raw-read coverage, k-mer frequency, and gene prediction information, allowing the clustering of contigs from single or highly related species. A unique feature of SMRT Sequencing data is the availability of base modification / methylation information, which can be used to further analyze clustered contigs expected to be comprised of single or very closely related species. Here we show base modification information can be used to further study variation, based on differences in the methylated DNA motifs involved in the restriction modification system. Application of these techniques is demonstrated on a monkey intestinal microbiome sample and an in silico mix of real sequencing data from distinct bacterial samples.

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June 1, 2021  |  

SMRT Sequencing solutions for plant genomes and transcriptomes

Single Molecule, Real-Time (SMRT) Sequencing provides efficient, streamlined solutions to address new frontiers in plant genomes and transcriptomes. Inherent challenges presented by highly repetitive, low-complexity regions and duplication events are directly addressed with multi- kilobase read lengths exceeding 8.5 kb on average, with many exceeding 20 kb. Differentiating between transcript isoforms that are difficult to resolve with short-read technologies is also now possible. We present solutions available for both reference genome and transcriptome research that best leverage long reads in several plant projects including algae, Arabidopsis, rice, and spinach using only the PacBio platform. Benefits for these applications are further realized with consistent use of size-selection of input sample using the BluePippin™ device from Sage Science. We will share highlights from our genome projects using the latest P5- C3 chemistry to generate high-quality reference genomes with the highest contiguity, contig N50 exceeding 1 Mb, and average base quality of QV50. Additionally, the value of long, intact reads to provide a no-assembly approach to investigate transcript isoforms using our Iso-Seq protocol will be presented for full transcriptome characterization and targeted surveys of genes with complex structures. PacBio provides the most comprehensive assembly with annotation when combining offerings for both genome and transcriptome research efforts. For more focused investigation, PacBio also offers researchers opportunities to easily investigate and survey genes with complex structures.

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June 1, 2021  |  

Evaluation of multiplexing strategies for HLA genotyping using PacBio Sequencing technology.

Fully phased allele-level sequencing of highly polymorphic HLA genes is greatly facilitated by SMRT Sequencing technology. In the present work, we have evaluated multiple DNA barcoding strategies for multiplexing several loci from multiple individuals, using three different tagging methods. Specifically MHC class I genes HLA-A, -B, and –C were indexed via DNA Barcodes by either tailed primers or barcoded SMRTbell adapters. Eight different 16-bp barcode sequences were used in symmetric & asymmetric pairing. Eight DNA barcoded adapters in symmetric pairing were independently ligated to a pool of HLA-A, -B and –C for eight different individuals, one at a time and pooled for sequencing on a single SMRT Cell. Amplicons generated from barcoded primers were pooled upfront for library generation. Eight symmetric barcoded primers were generated for HLA class I genes. These primers facilitated multiplexing of 8 samples and also allowed generation of unique asymmetric pairings for simultaneous amplification from 28 reference genomic DNA samples. The data generated from all 3 methods was analyzed using LAA protocol in SMRT analysis V2.3. Consensus sequences generated were typed using GenDx NGS engine HLA-typing software.

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June 1, 2021  |  

Complex alternative splicing patterns in hematopoietic cell subpopulations revealed by third-generation long reads.

Background: Alternative splicing expands the repertoire of gene functions and is a signature for different cell populations. Here we characterize the transcriptome of human bone marrow subpopulations including progenitor cells to understand their contribution to homeostasis and pathological conditions such as atherosclerosis and tumor metastasis. To obtain full-length transcript structures, we utilized long reads in addition to RNA-seq for estimating isoform diversity and abundance. Method: Freshly harvested, viable human bone marrow tissues were extracted from discarded harvesting equipment and separated into total bone marrow (total), lineage-negative (lin-) progenitor cells and differentiated cells (lin+) by magnetic bead sorting with antibodies to surface markers of hematopoietic cell lineages. Sequencing was done with SOLiD, Illumina HiSeq (100bp paired-end reads), and PacBio RS II (full-length cDNA library protocol for 1 – 6 kb libraries). Short reads were assembled using both Trinity for de novo assembly and Cufflinks for genome-guided assembly. Full-length transcript consensus sequences were obtained for the PacBio data using the RS_IsoSeq protocol from PacBios SMRTAnalysis software. Quantitation for each sample was done independently for each sequencing platform using Sailfish to obtain the TPM (transcripts per million) using k-mer matching. Results: PacBios long read sequencing technology is capable of sequencing full-length transcripts up to 10 kb and reveals heretofore-unseen isoform diversity and complexity within the hematopoietic cell populations. A comparison of sequencing depth and de novo transcript assembly with short read, second-generation sequencing reveals that, while short reads provide precision in determining portions of isoform structure and supporting larger 5 and 3 UTR regions, it fails in providing a complete structure especially when multiple isoforms are present at the same locus. Increased breadth of isoform complexity is revealed by long reads that permits further elaboration of full isoform diversity and specific isoform abundance within each separate cell population. Sorting the distribution of major and minor isoforms reveals a cell population-specific balance focused on distinct genome loci and shows how tissue specificity and diversity are modulated by alternative splicing.

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June 1, 2021  |  

Rapid full-length Iso-Seq cDNA sequencing of rice mRNA to facilitate annotation and identify splice-site variation.

PacBio’s new Iso-Seq technology allows for rapid generation of full-length cDNA sequences without the need for assembly steps. The technology was tested on leaf mRNA from two model O. sativa ssp. indica cultivars – Minghui 63 and Zhenshan 97. Even though each transcriptome was not exhaustively sequenced, several thousand isoforms described genes over a wide size range, most of which are not present in any currently available FL cDNA collection. In addition, the lack of an assembly requirement provides direct and immediate access to complete mRNA sequences and rapid unraveling of biological novelties.

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June 1, 2021  |  

A genome assembly of the domestic goat from 70x coverage of single molecule, real-time sequence.

Goat is an important source of milk, meat, and fiber, especially in developing countries. An advantage of goats as livestock is the low maintenance requirements and high adaptability compared to other milk producers. The global population of domestic goats exceeds 800 million. In Africa, goat production is characterized by low productivity levels, and attempts to introduce more productive breeds have met with poor success due in part to nutritional constraints. It has been suggested that incorporation of selective breeding within the herds adapted for survival could represent one approach to improving food security across Africa. A recently produced genome assembly of a Chinese Yunnan breed goat, based on 192 Gb of short reads across a range of insert sizes from 180 bp to 20 kb, reported a contig N50 of 18.7 kb. The scaffold N50 was improved from 2.2 Mb to 3.1 Mb by addition of fosmid end sequence, with an estimated 140 million Ns in gaps and 91% coverage. The assembly has proven somewhat problematic for pursuing genome-wide association analysis with SNP arrays, apparently due in part to errors in ordering of markers using the draft genome. In order to provide a higher quality assembly, we sequenced a highly inbred, San Clemente breed goat genome using 458 SMRT cells on the Pacific Biosciences platform. These cells generated 193.5 Gbases of sequence after processing into subreads, with mean 5110 bases and max subread length of 40.5 kb. This sequence data generated an assembly using the recently reported MHAP error correction approach and Celera Assembler v8.2. The contig N50 was 2.5 Mb, with the largest contig spanning 19.5 Mb. Additional characteristics of the assembly will be presented.

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June 1, 2021  |  

De novo assembly of a complex panicoid grass genome using ultra-long PacBio reads with P6C4 chemistry

Drought is responsible for much of the global losses in crop yields and understanding how plants naturally cope with drought stress is essential for breeding and engineering crops for the changing climate. Resurrection plants desiccate to complete dryness during times of drought, then “come back to life” once water is available making them an excellent model for studying drought tolerance. Understanding the molecular networks governing how resurrection plants handle desiccation will provide targets for crop engineering. Oropetium thomaeum (Oro) is a resurrection plant that also has the smallest known grass genome at 250 Mb compared to Brachypodium distachyon (300 Mb) and rice (350 Mb). Plant genomes, especially grasses, have complex repeat structures such as telomeres, centromeres, and ribosomal gene cassettes, and high heterozygosity, which makes them difficult to assembly using short read next generation sequencing technologies. Ultra-long PacBio reads using the new P6C4 chemistry and the latest 15kb Blue Pippin size-selection protocol to generate 20kb insert libraries that yielded an average read length of 12kb providing ~72X coverage, and 10X coverage with reads over 20kb. The HGAP assembly covers 98% of the genome with a contig N50 of 2.4 Mb, which makes it one of the highest quality and most complete plant genomes assembled to date. Oro has a compact genome structure compared to other grasses with only 16% repeat sequences but has very good collinearity with other grasses. Understanding the genomic mechanisms of extreme desiccation tolerance in resurrection plants like Oro will provide insights for engineering and intelligent breeding of improved food, fuel, and fiber crops.

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June 1, 2021  |  

A workflow for the analysis of contigs from the metagenomic shotgun assembly of SMRT Sequencing data

The throughput of SMRT Sequencing and long reads allows microbial communities to be analyzed using a shotgun sequencing approach. Key to leveraging this data is the ability to cluster sequences belonging to the same member of a community. Long reads of up to 40 kb provide a unique capability in identifying those relationships, and pave the way towards finished assemblies of community members. Long reads are highly valuable when samples are more complex and containing lower intra-species variation, such as a larger number of closely related species, or high intra-species variation. Here, we present a collection of tools tailored for the analysis of PacBio metagenomic assemblies. These tools allow for improvements in the assembly results, and greater insight into the complexity of the study communities. Supervised classification is applied to a large set of sequence characteristics (e.g. GC content, raw read coverage, k-mer frequency, and gene prediction information) and to cluster contigs from single or highly related species. Assembly in isolation of the raw data associated with these contigs is shown to improve assembly statistics. A unique feature of SMRT Sequencing is the availability to leverage simultaneously collected base modification / methylation data to aid the clustering of contigs expected to comprise a single or very closely related species. We demonstrate the added value of base modification information to distinguish and study variation within metagenomic samples based on differences in the methylated DNA motifs involved in the restriction modification system. Application of these techniques is demonstrated on a mock community and monkey intestinal microbiome sample.

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