Project description:The northern white rhinoceros (Ceratotherium simum cottoni) genome and annotation were previously published, but the annotation contained few genes, with many annotation misalignments, and nomenclature not matching HGNC/VGNC naming conventions, making transcriptional studies very difficult. We used in vivo collected granulosa cells for RNA sequencing and de novo transcript assembly through StringTie to identify all nucleotide gene sequences in our samples. Through extensive manual curation we were able to generate a greatly improved genome annotation increasing gene numbers by 81%. This will greatly enable researchers in this field to utilize the genome and annotation to complete transcriptional studies with this species.
Project description:This data contributes to a telomere-to-telomere genome assembly and annotation of the naked mole-rat, Heterocephalus glaber. To epigenetically annotate centromeres, we performed CENPA ChIP-seq experiments in the male subordinate NMR livers. These experiments included an Input control, and a H3K27Ac ChIP-seq experiment to annotate active enhancers and ensure hat the ChIP-seq experiment with antibodies performed as expected.
Project description:This data contributes to a telomere-to-telomere genome assembly and annotation of the naked mole-rat, Heterocephalus glaber. To epigenetically annotate centromeres, we performed CENPA ChIP-seq experiments in the male subordinate NMR livers. To ensure antibody quality, as this was the first time CENPA ChIP-seq was performed in the NMR, we performed H3K27Ac and CENPA ChIP-seq experiments on a TeloHAOEC cell line.
Project description:This project encompasses a de novo genome assembly of the cochineal bug, Dactylopius opuntiae, incorporating RNA-seq and MS/MS mass spectrometry proteomics as evidence for gene calling and protein annotation.
Project description:The incomplete genome annotation of non-model organisms hampers molecular and proteomic studies. Proteomics informed by transcriptomics (PIT) is suited to non-model organisms because peptides are identified using transcriptomic, not genomic, data. Aedes aegypti is the mosquito vector for the (re-)emerging dengue, chikungunya, yellow fever and Zika viruses. An Ae. aegypti genome sequence is available, however experimental evidence for >90% of the Ae. aegypti proteome or the activity of transposable elements (TEs) that constitute 50% of the Ae. aegypti genome is lacking. We used PIT to characterise the proteome of the Aedes aegypti derived cell line Aag2. Hotspots of incomplete genome annotation were identified which are not explained by poor sequence and assembly quality. We developed criteria for the characterisation of proteomically active TEs and demonstrate that protein expression does not correlate with a TE’s genomic abundance. Finally, we identify Phasi Charoen-like virus as an unrecognised contaminant of Aag2 cells. We therefore present the first proteomic characterisation of mobile genetic elements, and provide proof-of-principle that PIT can evaluate a genome’s annotation to guide annotation efforts.
Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
Project description:This dataset includes RNAseq data of 7 tissues/developmental stages of Lathyrus sativus genotype LSWT11 and 2 tissues with drought- and well-watered treatments of Lathyrus sativus genotypes LS007 and Mahateora. These data were used in the functional annotation pipeline of the Rbp1.0 genome assembly of LS007. The multi-tissue transcriptome was also used to support gene candidate identification by mRNA abundance. Also included is Hi-C sequencing data used to scaffold the assembly into pseudochromosomes
Project description:Species within the Drosophila quinaria group are models for ecological genetic studies on topics that include morphological diversity, color pattern development, and feeding behavior. Here, we performed bulk RNA-seq of mixed male and female adult flies to provide evidence for annotation of our hybrid assembly of the Drosophila subpalustris genome.
