An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (<i>Knightia excelsa</i>) genome

Cartney, Ann Mc; Hilario, Elena; Choi, Seung-Sub; Guhlin, Joseph; Prebble, Jessica M.; Houliston, Gary J.; Buckley, Thomas R.; Chagné, David

doi:10.1111/1755-0998.13406

Cited by 8 publications

(4 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, based on de novo assembly, we obtained a genome size of 1.71 Gb for the whitespot parrotfish. This variation in genome size may be due to changes in the quality and depth of sequencing data or assembly strategies [68,69]. Among them, we found that the whitespot parrotfish exhibited higher heterozygosity compared to C. undulatus [70].…”

Section: Genome Assembly and Annotationmentioning

confidence: 89%

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

Liang,

Xian,

Pan

et al. 2024

Genes

View full text Add to dashboard Cite

Scarus forsteni, a whitespot parrotfish from the Scaridae family, is a herbivorous fish inhabiting coral reef ecosystems. The deterioration of coral reefs has highly affected the habitats of the parrotfish. The decline in genetic diversity of parrotfish emphasizes the critical importance of conserving their genetic variability to ensure the resilience and sustainability of marine ecosystems for future generations. In this study, a genome of S. forsteni was assembled de novo through using Illumina and Nanopore sequencing. The 1.71-Gb genome of S. forsteni, was assembled into 544 contigs (assembly level: contig). It exhibited an N50 length of 17.97 Mb and a GC content percentage of 39.32%. Our BUSCO analysis revealed that the complete protein of the S. forsteni genome had 98.10% integrity. Combined with structure annotation data, 34,140 (74.81%) genes were functionally annotated out of 45,638 predicted protein-coding genes. Upon comparing the genome size and TE content of teleost fishes, a roughly linear relationship was observed between these two parameters. However, TE content is not a decisive factor in determining the genome size of S. forsteni. Population history analysis results indicate that S. forsteni experienced two major population expansions, both of which occurred before the last interglacial period. In addition, through a comparative genomic analysis of the evolutionary relationship of other species, it was found that S. forsteni had the closest relationship with Cheilinus undulatus, another member of the Labridae family. Our expansion and contraction analysis of the gene family showed that the expansion genes were mainly associated with immune diseases, organismal systems, and cellular processes. At the same time, cell transcription and translation, sex hormone regulation, and other related pathways were also more prominent in the positive selection genes. The genomic sequence of S. forsteni offers valuable resources for future investigations on the conservation, evolution, and behavior of fish species.

show abstract

Section: Genome Assembly and Annotationmentioning

confidence: 89%

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

Liang,

Xian,

Pan

et al. 2024

Genes

View full text Add to dashboard Cite

show abstract

“…69 Genomics of other members of the Proteaceae is progressing with the sequencing of the Waratah (Telopea speciosissima) supported by the Genomics of Australian Plants Program of Bioplatforms Australia (https:// www.genomicsforaustralianplants.com/) and the Nightcap Oak (Eidothea hardenianna) supported by the Threatened Species Initiative and Rewarewa (Knightia excelsa) in New Zealand. 70 These species are of value as ornamentals or for timber and the analysis of their genomes will advance knowledge of the evolution and biology of the Proteaceae. Other Proteaceae species with seeds that have been considered food sources include Hicksbeachia pinnatifolia and Athertonia diversifolia.…”

Section: Macadamiamentioning

confidence: 99%

Genomic characterization supporting the development of new food and crop options from the Australian flora

Henry

2023

Sustainable Food Technol.

View full text Add to dashboard Cite

show abstract

“…In addition, the chromosomal assembly pipelines is inconsistent in different studies 27,28 and lack a well-tested, standardized workflow. Moreover, some critical steps such as removing haplotig, organelle DNA contamination and gap closing are prone to being overlooked 32,33,34 . Given that only 0.17% of the eukaryotic species have undergone genome assembly 5 , there is a great need for a standardized and user-friendly automated tool for accurate chromosome-level genome assembly.…”

mentioning

confidence: 99%

Chrom-pro: A User-Friendly Toolkit for De-novo Chromosome Assembly and Genomic Analysis

Song,

Ye,

Liu

et al. 2024

Preprint

View full text Add to dashboard Cite

Chromosome-level genome assembly is fundamental to current genomic and post- genomic research, however, the process remains complicated and challenging due to the lack of a standardized automatic workflow. The frequently-used method for high-quality genome assembly generally employs second-generation sequencing (SGS) low error reads, third-generation sequencing (TGS) long reads and Hi-C reads. In this study, we developed a multifunctional toolkit called Chrom-pro that integrated commonly-used algorithms for de novo chromosome-level genome assembly with above three data sets into a user-friendly, automatic workflow. Besides chromosome assembly, Chrom-pro also encompasses multiple functionalities for genome quality assessment, comparative genomic analysis, and structural variant detection, which offers substantial support for downstream research. To evaluate the performance of Chrom-pro software, we tested the software with publicly available sequencing data of mango, pufferfish, and plum, and the excellence was confirmed by achieving a BUSCO completeness score of over 95% as well as high collinearity with the reference genome. Furthermore, we applied Chrom-pro to investigating the impact of different internal algorithm options on the accuracy of chromosome assembly, providing guidance for advancing relevant research in the future. Overall, the development of Chrom-pro will significantly improve the efficiency and quality of chromosome assembly and contributing to the advancement of genomic research.

show abstract

An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

Cited by 8 publications

References 54 publications

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

Genomic characterization supporting the development of new food and crop options from the Australian flora

Chrom-pro: A User-Friendly Toolkit for De-novo Chromosome Assembly and Genomic Analysis

Contact Info

Product

Resources

About