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Circular karyotype representation of the chromosomes in non-overlapping windows of 100 kb. Tracks from inside to outside are GC content, gene density, Gypsy density, Copia density and DNA transposons density.
Source publication
Despite the rapid advances in sequencing technology, limited genomic resources are currently available for phytophagous spider mites, which include many important agricultural pests. One of these pests is Tetranychus piercei (McGregor), a serious banana pest in East Asia exhibiting remarkable tolerance to high temperature. In this study, we assembl...
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The Caucasian dwarf goby Knipowitschia cf. caucasica is a new invasive alien Gobiidae spreading in the Lower Rhine since 2019. Little is known about the invasion biology of the species and further investigations to reconstruct the invasion history are lacking genomic resources. We assembled a high-quality chromosome-scale reference genome of Knipow...
Citations
Technological advances have propelled DNA sequencing of non-model organisms, making sequencing more accessible and cost effective, which has also increased the availability of raw data in public repositories. However, contamination is a significant concern, and the use and reuse of sequencing data requires quality control and curation. A reference genome for the Australian native rainforest tree Rhodamnia argentea Benth. (malletwood) was assembled from Oxford Nanopore Technologies (ONT) long-reads, 10x Genomics Chromium linked-reads, and Hi-C data (N50 = 32.3 Mbp and BUSCO completeness 98.0%) with 99.0% of the 347 Mbp assembly anchored to 11 chromosomes (2 n = 22). The R . argentea genome will inform conservation efforts for Myrtaceae species threatened by the global spread of the fungal disease myrtle rust. We observed contamination in the sequencing data and further investigation revealed an arthropod source. Here, we demonstrate the feasibility of assembling a high-quality gapless telomere-to-telomere mite genome using contaminated host plant sequencing data. The mite exhibits genome streamlining and has a 35 Mbp genome (68.6% BUSCO completeness) on two chromosomes, capped with a novel TTTGG telomere sequence. Phylogenomic analysis suggests that it is a previously unsequenced eriophyoid mite. Despite its unknown identity, this complete nuclear genome provides a valuable resource to investigate invertebrate genome reduction. This study emphasises the importance of checking sequencing data for contamination, especially when working with non-model organisms. It also enhances our understanding of two species, including a tree that faces substantial conservation challenges, contributing to broader biodiversity initiatives.
Significance
The genomes of Rhodamnia argentea and an associated eriophyoid mite, which contaminated the tree raw sequencing data, were assembled for the first time. We generated valuable chromosome-level genomic resources for the conservation of myrtle rust impacted tree species, pest genomics, and understanding genome streamlining. The research underscores the growing prevalence of sequencing experiments in non-model organisms while emphasising the importance of quality control and curation of sequencing data.
