scholarly journals Discovery of a New TLR Gene and Gene Expansion Event through Improved Desert Tortoise Genome Assembly with Chromosome-Scale Scaffolds

2020 ◽  
Vol 12 (2) ◽  
pp. 3917-3925
Author(s):  
Greer A Dolby ◽  
Matheo Morales ◽  
Timothy H Webster ◽  
Dale F DeNardo ◽  
Melissa A Wilson ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Mojave Desert ◽  
De Novo ◽  
Stop Codon ◽  
Draft Genome ◽  
Gene Families ◽  
Sea Turtle ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Gene Expansion

Abstract Toll-like receptors (TLRs) are a complex family of innate immune genes that are well characterized in mammals and birds but less well understood in nonavian sauropsids (reptiles). The advent of highly contiguous draft genomes of nonmodel organisms enables study of such gene families through analysis of synteny and sequence identity. Here, we analyze TLR genes from the genomes of 22 tetrapod species. Findings reveal a TLR8 gene expansion in crocodilians and turtles (TLR8B), and a second duplication (TLR8C) specifically within turtles, followed by pseudogenization of that gene in the nonfreshwater species (desert tortoise and green sea turtle). Additionally, the Mojave desert tortoise (Gopherus agassizii) has a stop codon in TLR8B (TLR8-1) that is polymorphic among conspecifics. Revised orthology further reveals a new TLR homolog, TLR21-like, which is exclusive to lizards, snakes, turtles, and crocodilians. These analyses were made possible by a new draft genome assembly of the desert tortoise (gopAga2.0), which used chromatin-based assembly to yield draft chromosomal scaffolds (L50 = 26 scaffolds, N50 = 28.36 Mb, longest scaffold = 107 Mb) and an enhanced de novo genome annotation with 25,469 genes. Our three-step approach to orthology curation and comparative analysis of TLR genes shows what new insights are possible using genome assemblies with chromosome-scale scaffolds that permit integration of synteny conservation data.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2017 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A. Dolby ◽  
Melissa Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2018 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A Dolby ◽  
Melissa A Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 kb, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis

2018 ◽  
Vol 6 (16) ◽  
pp. e00265-18 ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Kathryn Bartley ◽  
Edward J. Marr ◽  
Harry W. Wright ◽  
Robert J. Weaver ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Psoroptes Ovis ◽  
Protein Coding ◽  
Content Type ◽  
Sheep Scab ◽  
Draft Genome Assembly ◽  
Intense Pruritus

ABSTRACT Sheep scab, caused by infestation with Psoroptes ovis, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene prediction of P. ovis based on PacBio de novo sequencing. The ∼63.2-Mb genome encodes 12,041 protein-coding genes.

scholarly journals First draft genome assembly of the Argane tree (Argania spinosa)

F1000Research ◽  
2020 ◽  
Vol 7 ◽  
pp. 1310
Author(s):  
Slimane Khayi ◽  
Nour Elhouda Azza ◽  
Fatima Gaboun ◽  
Stacy Pirro ◽  
Oussama Badad ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Environmental Changes ◽  
De Novo ◽  
Arid Zone ◽  
Draft Genome ◽  
Illumina Hiseq ◽  
Argania Spinosa ◽  
Draft Genome Assembly ◽  
Food And Feed ◽  
Tree Genetics

Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of  A. spinosa was created using a hybrid  de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.6 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2018 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A Dolby ◽  
Melissa A Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 kb, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2017 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A. Dolby ◽  
Melissa Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

scholarly journals De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)

2021 ◽  
Author(s):  
Luis J Chueca ◽  
Tilman Schell ◽  
Markus Pfenninger
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Land Snail ◽  
Land Snails ◽  
Agricultural Pests ◽  
De Novo Genome Assembly ◽  
Draft Genome Assembly ◽  
Western Palearctic ◽  
A Genome

Abstract Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.

scholarly journals Genome Report: De novo genome assembly and annotation for the Taita white-eye (Zosterops silvanus)

2020 ◽  
Author(s):  
Jan O. Engler ◽  
Yvonne Lawrie ◽  
Yannick Gansemans ◽  
Filip Van Nieuwerburgh ◽  
Alexander Suh ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Draft Genome ◽  
Wild Female ◽  
De Novo Genome Assembly ◽  
Small Areas ◽  
Fragmented Forest ◽  
Draft Genome Assembly ◽  
Taita Hills ◽  
Genomic Resource

AbstractThe Taita White-eye (Zosterops silvanus) is an endangered songbird endemic to the Taita Hills of Southern Kenya, where it is confined to small areas of fragmented forest. With diversification rates exceeding those reported in most other vertebrates, White-eyes are a prime example of a ‘great speciator’. Nevertheless, we still know surprisingly little about the genomic underpinnings leading to this extraordinary fast radiation. Here, we present a draft genome assembly (ZSil_MB_1.0) for the Taita White-eye generated from a blood sample of a wild, female bird captured in the Taita Hills, Kenya. By performing a de novo assembly with linked-reads and annotation of the assembly with the MAKER pipeline, we generated a 1.069 Gb assembly with a scaffold N50 of 1.105 Mb and an L50 of 244. After quality evaluation of the assembly, we identified 92.1% of BUSCOs complete or fragmented, indicating that our de novo assembly is of high quality. This new assembly provides a genomic resource for future studies into the evolutionary and comparative genomics of this rapidly diversifying group of birds.

scholarly journals Draft Genome Assembly of the Poultry Red Mite, Dermanyssus gallinae

2018 ◽  
Vol 7 (18) ◽  
Author(s):  
Stewart T. G. Burgess ◽  
Kathryn Bartley ◽  
Francesca Nunn ◽  
Harry W. Wright ◽  
Margaret Hughes ◽  
...  
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Gene Prediction ◽  
Draft Genome ◽  
Egg Laying ◽  
Dermanyssus Gallinae ◽  
Poultry Red Mite ◽  
Draft Genome Assembly ◽  
Long Read

The poultry red mite, Dermanyssus gallinae, is a major worldwide concern in the egg-laying industry. Here, we report the first draft genome assembly and gene prediction of Dermanyssus gallinae, based on combined PacBio and MinION long-read de novo sequencing.

scholarly journals Improved draft of the Mojave Desert tortoise genome, Gopherus agassizii, version 1.1

2017 ◽  
Author(s):  
Timothy H Webster ◽  
Greer A. Dolby ◽  
Melissa Wilson Sayres ◽  
Kenro Kusumi
Keyword(s):  
Threatened Species ◽  
Mojave Desert ◽  
Gene Annotation ◽  
Draft Genome ◽  
Gopherus Agassizii ◽  
Desert Tortoise ◽  
Draft Genome Assembly ◽  
Initial Release ◽  
Exogenous Sequence ◽  
Mojave Desert Tortoise

Exogenous sequence contamination presents a challenge in first-draft genomes because it can lead to non-contiguous, chimeric assembled sequences. This can mislead downstream analyses reliant on synteny, such as linkage-based analyses. Recently, the Mojave Desert Tortoise (Gopherus agassizii) draft genome was published as a resource to advance conservation efforts for the threatened species and discover more about chelonian biology and evolution. Here, we illustrate steps taken to improve the desert tortoise draft genome by removing contaminating sequences—actions that are typically carried out after the initial release of a draft genome assembly. We used information from NCBI’s Vecscreen output to remove intra-scaffold contamination and trim heading and trailing Ns. We then reordered and renamed scaffolds, and transferred the gene annotation onto this assembly. Finally, we describe the tools developed for this pipeline, freely available on Github (https://github.com/thw17/G_agassizii_reference_update), which facilitate post-assembly processing of other draft genomes. The new gopAga1.1 genome has an N50 of 251 KB, L50 of 2592 scaffolds, and its annotation retains 17,201 of the original 20,172 genes that were unaffected by the scaffold processing.

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