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Sunday, October 25, 2020

PAG PacBio Workshop: Resolving the complexity of genomic and epigenomic variations in arabidopsis

Chongyuan Luo from the Salk Institute for Biological Studies describes sequencing three strains of Arabidopsis thaliana using PacBio technology. The goal: uncover structural variants that have been missed by short-read and other sequencers. Luo notes that PacBio sequencing provides highly accurate SNP detection and also extends the mappability of reads beyond what is possible with short-read data, producing better and more accurate assemblies.

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Tuesday, April 21, 2020

Whole-genome sequence of the oriental lung fluke Paragonimus westermani.

Foodborne infections caused by lung flukes of the genus Paragonimus are a significant and widespread public health problem in tropical areas. Approximately 50 Paragonimus species have been reported to infect animals and humans, but Paragonimus westermani is responsible for the bulk of human disease. Despite their medical and economic importance, no genome sequence for any Paragonimus species is available.We sequenced and assembled the genome of P. westermani, which is among the largest of the known pathogen genomes with an estimated size of 1.1 Gb. A 922.8 Mb genome assembly was generated from Illumina and Pacific Biosciences (PacBio) sequence data, covering 84% of…

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Tuesday, April 21, 2020

Long-read amplicon denoising.

Long-read next-generation amplicon sequencing shows promise for studying complete genes or genomes from complex and diverse populations. Current long-read sequencing technologies have challenging error profiles, hindering data processing and incorporation into downstream analyses. Here we consider the problem of how to reconstruct, free of sequencing error, the true sequence variants and their associated frequencies from PacBio reads. Called ‘amplicon denoising’, this problem has been extensively studied for short-read sequencing technologies, but current solutions do not always successfully generalize to long reads with high indel error rates. We introduce two methods: one that runs nearly instantly and is very accurate for…

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Tuesday, April 21, 2020

Complete Genome Sequence of Lactococcus lactis subsp. cremoris 3107, Host for the Model Lactococcal P335 Bacteriophage TP901-1.

The complete genome sequence of Lactococcus lactis subsp. cremoris 3107, a dairy starter strain and a host for the model lactococcal P335 bacteriophage TP901-1, is reported here. The circular chromosome of L. lactis subsp. cremoris 3107 is among the smallest genomes of currently sequenced lactococcal strains. L. lactis subsp. cremoris 3107 harbors a complement of six plasmids, which appears to be a reflection of its adaptation to the nutrient-rich dairy environment.

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Tuesday, April 21, 2020

Single-Molecule Sequencing: Towards Clinical Applications.

In the past several years, single-molecule sequencing platforms, such as those by Pacific Biosciences and Oxford Nanopore Technologies, have become available to researchers and are currently being tested for clinical applications. They offer exceptionally long reads that permit direct sequencing through regions of the genome inaccessible or difficult to analyze by short-read platforms. This includes disease-causing long repetitive elements, extreme GC content regions, and complex gene loci. Similarly, these platforms enable structural variation characterization at previously unparalleled resolution and direct detection of epigenetic marks in native DNA. Here, we review how these technologies are opening up new clinical avenues that…

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Tuesday, April 21, 2020

A full-length transcriptome of Sepia esculenta using a combination of single-molecule long-read (SMRT) and Illumina sequencing

As an economically important cephalopods species, wild-caught Sepia esculenta fishery has suffered a server decline due to over-fishing and ocean environmental damage. To restore this seriously declining fishery resource, we should understand the genetic foundation and molecular mechanism of spawning, reproduction and mortal of golden cuttlefish. In this study, we generated the full-length transcriptome of S. esculenta based on the total RNA of tissue samples (brain, optic gland, nidamental gland, ovary and muscle at different developmental stages) using a combination of single-molecule real-time (SMRT) and Illumina RNA-seq technology. A total of 14.16 Gb SMRT sequencing data were assembled into 94,635…

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Tuesday, April 21, 2020

Microsatellite marker set for genetic diversity assessment of primitive Chitala chitala (Hamilton, 1822) derived through SMRT sequencing technology.

In present study, single molecule-real time sequencing technology was used to obtain a validated set of microsatellite markers for application in population genetics of the primitive fish, Chitala chitala. Assembly of circular consensus sequencing reads resulted into 1164 sequences which contained 2005 repetitive motifs. A total of 100 sequences were used for primer designing and amplification yielded a set of 28 validated polymorphic markers. These loci were used to genotype n?=?72 samples from three distant riverine populations of India, namely Son, Satluj and Brahmaputra, for determining intraspecific genetic variation. The microsatellite loci exhibited high level of polymorphism with PIC values…

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Tuesday, April 21, 2020

The red bayberry genome and genetic basis of sex determination.

Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high-quality genome for both a female and a male individual of red bayberry. The genome size was 313-Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole-genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59-Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them…

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Tuesday, April 21, 2020

Hybrid sequencing-based personal full-length transcriptomic analysis implicates proteostatic stress in metastatic ovarian cancer.

Comprehensive molecular characterization of myriad somatic alterations and aberrant gene expressions at personal level is key to precision cancer therapy, yet limited by current short-read sequencing technology, individualized catalog of complete genomic and transcriptomic features is thus far elusive. Here, we integrated second- and third-generation sequencing platforms to generate a multidimensional dataset on a patient affected by metastatic epithelial ovarian cancer. Whole-genome and hybrid transcriptome dissection captured global genetic and transcriptional variants at previously unparalleled resolution. Particularly, single-molecule mRNA sequencing identified a vast array of unannotated transcripts, novel long noncoding RNAs and gene chimeras, permitting accurate determination of transcription start,…

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Tuesday, April 21, 2020

Genome sequencing and CRISPR/Cas9 gene editing of an early flowering Mini-Citrus (Fortunella hindsii).

Hongkong kumquat (Fortunella hindsii) is a wild citrus species characterized by dwarf plant height and early flowering. Here, we identified the monoembryonic F. hindsii (designated as ‘Mini-Citrus’) for the first time and constructed its selfing lines. This germplasm constitutes an ideal model for the genetic and functional genomics studies of citrus, which have been severely hindered by the long juvenility and inherent apomixes of citrus. F. hindsii showed a very short juvenile period (~8 months) and stable monoembryonic phenotype under cultivation. We report the first de novo assembled 373.6 Mb genome sequences (Contig-N50 2.2 Mb and Scaffold-N50 5.2 Mb) for F. hindsii. In total, 32 257 protein-coding genes…

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Tuesday, April 21, 2020

Computational aspects underlying genome to phenome analysis in plants.

Recent advances in genomics technologies have greatly accelerated the progress in both fundamental plant science and applied breeding research. Concurrently, high-throughput plant phenotyping is becoming widely adopted in the plant community, promising to alleviate the phenotypic bottleneck. While these technological breakthroughs are significantly accelerating quantitative trait locus (QTL) and causal gene identification, challenges to enable even more sophisticated analyses remain. In particular, care needs to be taken to standardize, describe and conduct experiments robustly while relying on plant physiology expertise. In this article, we review the state of the art regarding genome assembly and the future potential of pangenomics in…

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Tuesday, April 21, 2020

A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana.

Infectious disease is both a major force of selection in nature and a prime cause of yield loss in agriculture. In plants, disease resistance is often conferred by nucleotide-binding leucine-rich repeat (NLR) proteins, intracellular immune receptors that recognize pathogen proteins and their effects on the host. Consistent with extensive balancing and positive selection, NLRs are encoded by one of the most variable gene families in plants, but the true extent of intraspecific NLR diversity has been unclear. Here, we define a nearly complete species-wide pan-NLRome in Arabidopsis thaliana based on sequence enrichment and long-read sequencing. The pan-NLRome largely saturates with…

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