TSEBRA: transcript selector for BRAKER

Gabriel, Lars; Hoff, Katharina J.; Brůna, Tomáš; Borodovsky, Mark; Stanke, Mario

doi:10.1186/s12859-021-04482-0

Cited by 163 publications

(146 citation statements)

References 45 publications

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“…2013) , after which we aligned the processed RNAseq reads to the chromosome-level genome assembly using . Final annotation of protein-coding genes was done using TSEBRA (Gabriel et al . 2021), which selects curated transcripts generated by the BRAKER annotation pipeline (Hoff et al .…”

Section: Methodsmentioning

confidence: 99%

Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish

Rivera‐Colón¹,

Rayamajhi²,

Minhas³

et al. 2022

Preprint

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White-blooded Antarctic icefishes are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation of C. esox, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Our study presents the first whole genome characterization of a secondarily temperate notothenioid to date, providing a key resource and platform for understanding the adaptive potential of the highly vulnerable icefishes, and of cryonotothenioids in general, in face of a warming Antarctic environment.

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Section: Methodsmentioning

confidence: 99%

Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish

Rivera‐Colón¹,

Rayamajhi²,

Minhas³

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…2.1.5; RRID: SCR_018964; Bruna et al 2020 ) and TSEBRA (ver. 1.0.3; Gabriel et al 2021 ). For accurate gene prediction, we aligned the RNA-sequencing reads using STAR aligner (ver.…”

Section: Methodsmentioning

confidence: 99%

Chromosome-Level Genome Assembly of the Butter Clam Saxidomus purpuratus

Kim

Choi

et al. 2022

Genome Biology and Evolution

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Herein, we provide the first whole-genome sequence of the purple butter clam (Saxidomus purpuratus), an economically important bivalve shellfish. Specifically, we sequenced and de novo assembled the genome of S. purpuratus based on PromethION long reads and Hi-C data. The 978-Mb genome of S. purpuratus comprises 19 chromosomes with 36,591 predicted protein-coding genes. The N50 length of S. purpuratus genome is 52 Mb, showing the highest continuous assembly among bivalve genomes. The Benchmarking by Universal Single-Copy Orthologs (BUSCO) assessment indicated that 95.07% of complete metazoan universal single-copy orthologs (n = 954) were present in the assembly. Approximately 51% of S. purpuratus genome comprises repetitive sequences. Based on the high-quality S. purpuratus genome, we resolved half of the immune-associated genes, namely, scavenger receptor (SR) proteins, which are collinear to those in the closely related Cyclina sinensis genome. This finding suggested a high degree of conservation among immune-associated genes. Twenty-two (19%) SR proteins are tandemly duplicated in S. purpuratus genome, suggesting putative convergence evolution. Overall, S. purpuratus genome provides a new resource for the discovery of economically important traits and immune-response genes.

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“…4.64 ( 13 ). The resulting BRAKER2 gtf file was parsed using TSEBRA ( 14 ) and AGAT ver. 0.8.0 ( 15 ).…”

Section: Announcementmentioning

confidence: 99%