A Superior Contiguous Whole Genome Assembly for Shrimp (Penaeus indicus)

Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.

Section: Resultsmentioning

confidence: 99%

Abundance and Diversification of Repetitive Elements in Decapoda Genomes

Rutz

Bonassin

Francesconi

et al. 2023

“…This assembly met the criteria for animal genomes, which require contig N50 and scaffold N50 greater than 1 Mb and 10 Mb, respectively [84]. Compared to other shrimp genomes, the chromosome-scale assemblies provided for F. indicus have fewer gaps [78].…”

Section: Genome Assembly At Chromosome Levelmentioning

confidence: 99%

“…In 2022, a "superior contiguous" genome assembly of F. indicus was published with contig N50 1.4 Mb and scaffold N50 34.4 Mb [78]. This assembly met the criteria for animal genomes, which require contig N50 and scaffold N50 greater than 1 Mb and 10 Mb, respectively [84].…”

Section: Genome Assembly At Chromosome Levelmentioning

confidence: 99%

Penaeid Shrimp Chromosome Studies Entering the Post-Genomic Era

Zhang,

Xiang,

Yuan

et al. 2023

Chromosome studies provide the foundation for comprehending inheritance, variation, systematics, and evolution. Penaeid shrimps are a group of crustaceans with great economic importance. Basic cytogenetic information obtained from these shrimps can be used to study their genome structure, chromosome relationships, chromosome variation, polyploidy manipulation, and breeding. The study of shrimp chromosomes experienced significant growth in the 1990s and has been closely linked to the progress of genome research since the application of next-generation sequencing technology. To date, the genome sequences of five penaeid shrimp species have been published. The availability of these genomes has ushered the study of shrimp chromosomes into the post-genomic era. Currently, research on shrimp cytogenetics not only involves chromosome counting and karyotyping, but also extends to investigating submicroscopic changes; exploring genome structure and regulation during various cell divisions; and contributing to the understanding of mechanisms related to growth, sexual control, stress resistance, and genome evolution. In this article, we provide an overview of the progress made in chromosome research on penaeid shrimp. We emphasize the mutual promotion between studies on chromosome structure and genome research and highlight the impact of chromosome-level assembly on studies of genome structure and function. Additionally, we summarize the emerging trends in post-genomic-era shrimp chromosome research.

“…Katneni et al [44] presented a high-quality genome assembly of P. indicus, which spans 1.93 Gb with a scaffold N50 of 34.4 Mb and contains 28,720 protein-coding genes and 49.31% repeat elements. Notably, the P. indicus assembly exhibits the highest proportion of simple sequence repeats (31.99%) among sequenced animal genomes and demonstrates a superior sequence contiguity compared to other shrimp genomes.…”

Section: Genome Assembly Of Penaeusmentioning

confidence: 99%

Genomics of Shrimp Allergens and Beyond

Li,

Chu,

Wai

2023

Allergy to shellfishes, including mollusks and crustaceans, is a growing health concern worldwide. Crustacean shellfish is one of the “Big Eight” allergens designated by the U.S. Food and Drug Administration and is the major cause of food-induced anaphylaxis. Shrimp is one of the most consumed crustaceans triggering immunoglobulin E (IgE)-mediated allergic reactions. Over the past decades, the allergen repertoire of shrimp has been unveiled based on conventional immunodetection methods. With the availability of genomic data for penaeid shrimp and other technological advancements like transcriptomic approaches, new shrimp allergens have been identified and directed new insights into their expression levels, cross-reactivity, and functional impact. In this review paper, we summarize the current knowledge on shrimp allergens, as well as allergens from other crustaceans and mollusks. Specific emphasis is put on the genomic information of the shrimp allergens, their protein characteristics, and cross-reactivity among shrimp and other organisms.