De novo assembly and annotation of the mangrove cricket genome

Satoh, Ayumi; Takasu, Miwako; Yano, Kentarô; Terai, Yohey

doi:10.1186/s13104-021-05798-z

Cited by 11 publications

(10 citation statements)

References 29 publications

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“…Cricket genomes have been ever studied in various contexts, such as evolutionary biology, developmental and regenerative biology, and even entomophagy (Table 1). Out of the seven Orthoptera genomes registered in the National Center of Biotechnology Information (NCBI) Genome, the cricket genome that is currently sequenced consists of six species, namely Laupala kohalensis (Blankers et al 2018a), Teleogryllus oceanicus (Pascoal et al 2019), T. occipitalis (Kataoka et al 2020, Gryllus bimaculatus (Ylla et al 2021), Acheta domesticus (Gupta et al 2020), and Apteronemobius asahinai (Satoh et al 2021). The assembled size of current version of A. domesticus genomes registered in the NCBI (about 1.0 Gbp, GCA_014858955.1) is far less from Gupta et al 2020).…”

Section: The Most Up-to-date Status Of Cricket Genomics and Transcrip...mentioning

confidence: 99%

“…RNA-seq analysis has detected a few hundreds of significant circatidal cycling transcripts, including genes encoding antioxidants and detoxification enzymes (Satoh and Terai, 2019). The draft genome of this species has been recently sequenced by the hybrid Illumina/ Nanopore sequencing technologies, which will accelerate molecular research in the studies on circatidal rhythm (Satoh et al 2021).…”

Section: Othersmentioning

confidence: 99%

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Dissecting cricket genomes for the advancement of entomology and entomophagy

et al. 2022

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Significant advances in biophysical methods such as next-generation sequencing technologies have now opened the way to conduct evolutionary and applied research based on the genomic information of greatly diverse insects. Crickets belonging to Orthoptera (Insecta: Polyneoptera), one of the most flourishing groups of insects, have contributed to the development of multiple scientific fields including developmental biology and neuroscience and have been attractive targets in evolutionary ecology for their diverse ecological niches. In addition, crickets have recently gained recognition as food and feed. However, the genomic information underlying their biological basis and application research toward breeding is currently underrepresented. In this review, we summarize the progress of genomics of crickets. First, we outline the phylogenetic position of crickets in insects and then introduce recent studies on cricket genomics and transcriptomics in a variety of fields. Furthermore, we present findings from our analysis of polyneopteran genomes, with a particular focus on their large genome sizes, chromosome number, and repetitive sequences. Finally, how the cricket genome can be beneficial to the food industry is discussed. This review is expected to enhance greater recognition of how important the cricket genomes are to the multiple biological fields and how basic research based on cricket genome information can contribute to tackling global food security.

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Section: The Most Up-to-date Status Of Cricket Genomics and Transcrip...mentioning

confidence: 99%

Section: Othersmentioning

confidence: 99%

Dissecting cricket genomes for the advancement of entomology and entomophagy

et al. 2022

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“…However, its protracted development means that genome editing is challenging. Apteronemobius asahinai also shows promise as a tidal model (Satoh and Terai, 2019) and has a recently published draft genome (Satoh et al, 2021). Other models include an intertidal limpet (Schnytzer et al, 2018) and bivalves (Connor and Gracey, 2012; Frontiers in Physiology | 5 February 2022 | Volume 13 | Article 830107 Mat et al, 2012Mat et al, , 2014Mat et al, , 2016Gracey and Connor, 2016;Payton et al, 2017) but for the limpet in particular, individual, entrainable phenotypes are not as easily measured as for more mobile animals that lend themselves to infra-red beam monitoring.…”

Section: How Do We Decipher the Molecular Basis Of Circatidal Clocks?mentioning

confidence: 99%

Towards an Understanding of Circatidal Clocks

2022

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Circadian clocks are an intrinsic element of life that orchestrate appropriately timed daily physiological and behavioural rhythms entrained to the solar cycle, thereby conferring increased fitness. However, it is thought that the first archaic ‘proto-clocks’ evolved in ancient cyanobacteria in a marine environment, where the dominant time cues (zeitgebers) probably would have been lunar-driven and included tidal cycles. To date, non-circadian ‘marine clocks’ have been described with circatidal (~12.4 h), circasemilunar (~14.8 days), and circalunar (~29.5 days) periodicity, mostly studied in accessible but temporally complex intertidal habitats. In contrast to the well-described circadian clock, their molecular machinery is poorly understood, and fundamental mechanisms remain unclear. We propose that a multi-species approach is the most apposite strategy to resolve the divergence that arose from non-circadian clockwork forged in an evolutionary environment with multiple zeitgebers. We review circatidal clock models with a focus on intertidal organisms, for which robust behavioural, physiological, or genetic underpinnings have been explicated, and discuss their relative experimental merits. Developing a comprehensive mechanistic understanding of circatidal clocks should be a priority because it will ultimately contribute to a more holistic understanding of the origins and evolution of chronobiology itself.

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“…Along with the black carpenter ant, several other insect genomes have benefitted greatly from long-read sequencing (13)(14)(15)(16). Single insect sequencing has also been previously performed.…”

Section: Rationalementioning

confidence: 99%

De novosequencing, diploid assembly, and annotation of the black carpenter ant,Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing

Faulk

2022

Preprint

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The black carpenter ant (Camponotus pennsylvanicus) is a pest species found widely throughout North America east of the Rocky Mountains. Its frequent infestation in human buildings justifies close genetic examination and its large size and small genome make it ideal for individual sequencing. From a single individual I used long-read nanopore sequencing to assemble a genome of 306 Mb, with an N50 of 565 Kb, and 60X coverage, with quality assessed by a 97.0% BUSCO score, improving upon related ant assemblies. The reads provided secondary information in the form of parasitic and symbiont genomes, as well as epigenetic information. I assembled a complete Wolbachia bacterial isolate with a genome size of 1.2 Mb and 76X coverage, as well as a commensal bacterium of the carpenter ant tribe, the species-specific symbiont Blochmannia pennsylvanicus, at 791 Kb, 2400X coverage, which matched to within 200 bp of its previously published reference. I also produced a complete mitochondrial genome with over 5000X coverage, revealing minor rearrangements and the first assembly for this species. DNA methylation and hydroxymethylation was measured simultaneously at whole genome, base-pair resolution level from the same nanopore reads and confirmed extremely low levels seen in the Formicidae family of Hymenoptera. A phased diploid assembly was built, revealing a moderate level of heterozygosity, with 0.16% of bases having biallelic SNPs from the two parental haplotypes. Protein prediction yielded 20,209 putative amino acid sequences and annotation identified 86% matched to previously known proteins. All assemblies were derived from a single Minion flow cell generating 20 Gb of sequence for a cost of $1047 including all consumable reagents. Adding fixed costs for required equipment and batch costs for reagents brings the cost to assemble an ant-sized genome to less than $5000. Complete analysis was performed in under 1 week on a commodity computer desktop with 64 Gb memory.

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De novo assembly and annotation of the mangrove cricket genome

Cited by 11 publications

References 29 publications

Dissecting cricket genomes for the advancement of entomology and entomophagy

Dissecting cricket genomes for the advancement of entomology and entomophagy

Towards an Understanding of Circatidal Clocks

De novosequencing, diploid assembly, and annotation of the black carpenter ant,Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing

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