Journal: BMC Genomics

Article Title: Illuminating the dark side of the human transcriptome with long read transcript sequencing

doi: 10.1186/s12864-020-07123-7

Figure Lengend Snippet: Long transcript assembly benchmarking. Sensitivity and precision of guided and unguided long read transcriptome assembly methods. a Gene loci level for simulated PacBio reads. b Gene loci level for simulated Nanopore reads. c Transcript level for simulated PacBio reads. d Transcript level for simulated Nanopore reads. e Transcript level for PacBio Sequel II Iso-Seq SIRV reads. f Example of erroneous transcript prediction by guided Talon where supporting reads are from another transcript model. These supporting reads are from 5′ degraded RNA resulting in the confusion

Article Snippet: We benchmarked the long read based transcriptome assembly of TAMA, Stringtie2 [ ], TALON [ ], and Cupcake [ ] using three different datasets: simulated PacBio data, simulated Nanopore data, and PacBio Sequel II Iso-Seq data from Lexogen’s Spike-in RNA Variant (SIRV) control mix.

Techniques:

Journal: Frontiers in Fungal Biology

Article Title: What lies behind the large genome of Colletotrichum lindemuthianum

doi: 10.3389/ffunb.2024.1459229

Figure Lengend Snippet: Comparing the C. lindemuthianum genome assembly using different approaches.

Article Snippet: The C. lindemuthianum isolate genomic DNA was sequenced using the PacBio Sequel platform (CD Genomics, New York, United States).

Techniques:

Journal: iScience

Article Title: Organisation and evolution of the major histocompatibility complex class I genes in cetaceans

doi: 10.1016/j.isci.2024.109590

Figure Lengend Snippet: Genomes used and assembly information, including number of BLAST hits obtained from NCBI

Article Snippet: Eubalaena glacialis , North Atlantic right whale , Eugl , Balaenidae , USA: Amelia Island, Florida , mEubGla1.hap1 , GCA_028571275.1 , 9/02/2023 , 32.0x , Hifiasm + Hi-C phasing v. 0.16.1 + galaxy2; Bionano Solve v. 3.7.0 + galaxy0; salsa v. 2.3 + galaxy3 , PacBio Sequel II HiFi; Bionano DLS; 3D DNA Hi-C , 28.

Techniques: Sequencing, Northern Blot

Journal: IMA Fungus

Article Title: IMA Genome - F15

doi: 10.1186/s43008-021-00077-9

Figure Lengend Snippet: Bayesian six loci phylogeny including the genome sequence of Niebla homalea (highlighted in bold as Niebla genome ). Posterior probability values above 0.95 are indicated below the branches. Ramalina farinacea and Vermilacinia procera were used as outgroup

Article Snippet: Extracted DNA was submitted to Inqaba Biotec (Pretoria, South Africa) for low coverage sequencing on the PacBio Sequel II System and to Macrogen (Seoul, Korea) for sequencing on the Illumina HiSeq 2500 platform.

Techniques: Sequencing

Journal: PLOS ONE

Article Title: Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca

doi: 10.1371/journal.pone.0303408

Figure Lengend Snippet: State of the art of reference genome availability for chelonians. Species and subspecies are classified and divided into the main ecotypes (freshwater, marine, or terrestrial species). Estimated genome size is represented as Gb for all species. Assembly level represents the highest level for any object in the assembly (i.e., the sequence organization or connection among them). Sequencing technology is defined for every species jointly with N50, which indicates if the genome was sequenced using long-read (expressed on Mb) or short-read methods (expressed on kb).

Article Snippet: , Malaclemys terrapin pileata , 2.21 , Chromosome , PacBio Sequel II HiFi; Bionano Genomics DLS; Arima Hi-C v2 , 75.6 Mb , GCA_027887155.1.

Techniques: Sequencing

Journal: PLOS ONE

Article Title: Taking advantage of reference-guided assembly in a slowly-evolving lineage: Application to Testudo graeca

doi: 10.1371/journal.pone.0303408

Figure Lengend Snippet: (A) BUSCO completeness comparison with the five assembled Testudinidae genomes. (B) Number of genes annotated for the five Testudinidae genomes and for T . graeca . (C) Circos plot of the mitogenome, with the position of the annotated genes and depth of coverage (inner circle). (D) Demographic reconstruction of the large annotated chromosomes for T . graeca .

Article Snippet: , Malaclemys terrapin pileata , 2.21 , Chromosome , PacBio Sequel II HiFi; Bionano Genomics DLS; Arima Hi-C v2 , 75.6 Mb , GCA_027887155.1.

Techniques: Comparison