ABSTRACT _Exopalaemon carinicauda_, a eurythermal and euryhaline shrimp, contributes one third of the total biomass production of polyculture ponds in eastern China and is considered as a

potential ideal experimental animal for research on crustaceans. We conducted a high-quality chromosome-level genome assembly of _E. carinicauda_ combining PacBio HiFi and Hi-C sequencing

data. The total assembly size was 5.86 Gb, with a contig N50 of 235.52 kb and a scaffold N50 of 138.24 Mb. Approximately 95.29% of the assembled sequences were anchored onto 45

pseudochromosomes. BUSCO analysis revealed that 92.89% of 1,013 single-copy genes were highly conserved orthologs. A total of 44, 288 protein-coding genes were predicted, of which 70.53%

ASSEMBLY AND EVOLUTIONARY ANALYSIS OF _COREGONUS USSURIENSIS_ BERG Article Open access 18 July 2024 CHROMOSOME-SCALE ASSEMBLY OF _ARTEMIA TIBETIANA_ GENOME, FIRST AQUATIC INVERTEBRATE GENOME

FROM TIBET PLATEAU Article Open access 12 May 2025 CHROMOSOME-LEVEL ASSEMBLY OF _TRIPLOPHYSA YARKANDENSIS_ GENOME BASED ON THE SINGLE MOLECULE REAL-TIME SEQUENCING Article Open access 05

January 2024 BACKGROUND & SUMMARY The family Palaemonidae, including more than 1400 species in 181 genera, represents the largest family of the order Decapoda1. Animals from this family

are found in marine and freshwater environments in tropical to temperate regions worldwide. It includes several shrimps with high economic value, such as _Macrobrachium rosenbergii_,

_Macrobrachium nipponense_ and _Exopalaemon carinicauda_. The ridgetail white shrimp _E. carinicauda_ is a eurythermal and euryhaline shrimp distributed over a wide geographical area

throughout tropical, subtropical, and temperate coastal waters2,3. It can survive in a multitude of environmental extremes, has a broad salinity tolerance of 2–44 and can survive in

freshwater after domestication4. It is also capable of inhabiting temperatures as low as −3 °C and as high as 39 °C5,6. As one of the most commercially valuable pond-raised species of

shrimp, _E. carinicauda_ contributes to one third of the total production of polyculture ponds in eastern China7. In addition to its important economic value in aquaculture, it is considered

a potential ideal experimental animal for research on crustaceans for its moderate size, transparent body (Fig. 1), short reproductive cycle, large eggs (diameters ranging 0.57–1.08 mm) and

ease of culturing and breeding in captive conditions8. Currently, CRISPR/Cas9-mediated genome editing technology has been successfully used in _E. carinicauda_, which is the first time that

gene editing has been realized in a decapod crustacean9,10. However, the absence of genomic data limits the further application of gene editing in studying the molecular biology,

cytobiology and genetics of crustaceans. Therefore, a high-quality reference genome is essential for understanding the molecular biology, genetics, breeding, ecology and adaptation of _E.

carinicauda_. A fragmented draft genome of _E. carinicauda_ has been assembled using Illumina short reads containing 13,897,062 scaffolds (contig N50, 263 bp)11. Genome survey analysis

indicated that _E. carinicauda_ has a relatively large genome size of 5.73 Gb, which is at least twice as large as that of many decapod shrimps12,13,14. In this study, an improved

chromosome-level genome of _E. carinicauda_ was assembled using the PacBio sequencing platform, Illumina paired-end sequencing, and high-throughput chromatin conformation capture (Hi-C)

technology. Our previous studies suggested that the _E. carinicauda_ karyotype is 2n = 9015, similar to that of other _Exopalaemon_ species16. The final genome size was 5.86 Gb with a contig

N50 length of 235.52 kb and a scaffold N50 length of 138.24 Mb. A total of 44,288 protein-coding genes were predicted in the genome of _E. carinicauda_. This chromosome-level genome

assembly of _E. carinicauda_ provides a valuable genomic resource for further genetic improvement and understanding of the functional genes and molecular mechanisms of _E. carinicauda_.

METHODS ANIMAL MATERIALS AND GENOME SEQUENCING A female shrimp was collected from Rizhao Haichen Aquatic Co., Ltd. The muscle tissue was collected for DNA extraction and library

construction. Total genomic DNA was extracted using a cetyltrimethylammonium bromide method. For the genome survey, a 350 bp paired-end library was constructed according to the

manufacturer’s instructions (Illumina, San Diego, CA, USA) and sequenced on an Illumina NovaSeq 6000 platform. A total of 276.18 Gb of raw data were obtained, which covered approximately 54 

× of the estimated genome (Table 1). For PacBio sequencing, a 15 kb library was constructed using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences, Menlo Park, CA, USA) and

sequenced with circular consensus sequencing mode using a single 8 M SMRT Cell on the PacBio Sequel II platform (Pacific Biosciences). After filtering out the low-quality reads and sequence

adapters, 3636.91 Gb subreads of PacBio Data were obtained, representing approximately 708 × sequence coverage based on the estimated genome size (Table 1). Finally, 203.27 Gb of CCS reads

were generated using SMRTLink 9.0 which covered approximately 40 × of the estimated genome. For the construction of the Hi-C library, DNA was fixed with 4% formaldehyde solution and digested

with the 4-cutter restriction enzyme MboI. The digested fragments were labeled with biotin-14-dCTP, then the cross-linked fragments were subjected to blunt-end ligation. The library was

sequenced on the Illumina NovaSeq 6000 platform, and approximately 552.65 Gb of Hi-C clean reads were generated, covering approximately 108 × of the estimated genome (Table 1). GENOME SURVEY

The genome size and heterozygosity were estimated using the k-mer method before genome assembly17. The k-mer distribution was calculated from Illumina short reads using Jellyfish based on

k-mer (k = 17)18. The heterozygosity ratio was estimated by the online tool of GenomeScope19 (https://github.com/schatzlab/genomescope). Finally, the estimated genome size of _E.

carinicauda_ was predicted to be approximately 5.12 Gb, with 84.74% repetitive sequences, and the genome heterozygosity was 2.62% using a 17-mer analysis (Fig. 2), suggesting a complex

genome of _E. carinicauda_. CHROMOSOME-LEVEL GENOME ASSEMBLY The initial genome was assembled with HiFi reads using the Peregrine (v0.1.6.1) (https://github.com/cschin/peregrine). A modified

“best overlap graph” strategy was used to get the contig assembly based on the overlap graph. Contig overlaps were removed from the assembled contig sequences using Purge_dups

(https://github.com/dfguan/purge_dups). _De novo_ assembly of PacBio sequences yielded a preliminary assembly of 5.86 Gb, containing 47,421 contigs with a contig N50 length of 235.28 kb, a

maximum length of 3,038,493 bp and a GC content of 34.79% (Table 1). Chromosome-level assembly of _E. carinicauda_ was conducted using Hi-C technology. Juicer (v1.6.2)20 and 3D-DNA

(v180922)21 software were implemented to obtain the chromosome-level whole genome assembly. The filtered Hi-C reads were aligned to the initial draft genome using Juicer (v1.6.2). Only

uniquely mapped and valid paired-end reads were used for the assembly using 3D-DNA. Juicebox (v1.9.8) was used to manually order the scaffolds to generate more precise chromosome-level

genome of _E. carinicauda_ according to the chromosomal interaction heatmap22. Contact maps were visualized using HiCExplorer (v3.3)23. The number of chromosomes was 90, which was determined

based on karyological observations of _E. carinicauda_ chromosomes in our previous study15. The contigs were ultimately clustered into 45 pseudochromosomes for _E. carinicauda_, with a

scaffold N50 length of 138.24 Mb. The total length of the 45 pseudochromosomes was 5.58 Gb (covered 95.29%) (Fig. 3a,b), of which the length ranged from 46.25 Mb to 338.48 Mb. The length of

the un-placed scaffolds was 275.86 Mb (Table 2). The quality of the final chromosome-level genome assembly was assessed using the following three methods. First, we aligned the Illumina DNA

short reads obtained from our previous study to the assembled genome and found that approximately 99.00% of the DNA short reads could be mapped to our assembly using BWA (v0.7.15)24. Second,

read depth and GC content with 10 kb windows were used to evaluate the assembly results and determine whether there was a significant GC bias or sample contamination, showing that the

assembled genome was clean without contamination (Fig. 4). Finally, genome assembly and completeness were further evaluated using conserved genes in benchmarking universal single-copy

orthologs (BUSCO, v5.2.2) with the arthropoda_odb10 database25. The results showed that 92.89% of the 1013 single-copy genes were highly conserved orthologs (88.75% complete, 4.15%

fragmented, and 7.11% missing) (Table 3). Compared to the published genome of _E. carinicauda_11, our assembled genome is of significantly improved quality and integrity. The contig N50

increased from 263 bp to 235,277 bp, with an increase of nearly 900-fold, and scaffold N50 increased from 816 bp to 138,242,434 bp. Meanwhile, the assembled complete orthologue proportion

enhanced from 43.44% to 88.75% according to the BUSCO assessment. REPETITIVE AND NON-CODING GENE PREDICTION To detect repeat elements in _E. carinicauda_ genome, _de novo_ and homology-based

strategies were combined using multiple methods. Mini-inverted repeat transposable elements (MITEs) were identified using MITE-Hunter (v1.0)26 for _de novo_ annotations. Long terminal

repeat sequences (LTRs) were detected using LTRharvest27 and LTR_Finder (v1.07)28, and the prediction results of these two software programs were integrated using LTR_retriever (v2.8.2)29.

RepeatMasker (v4.1.0)30 was used in the homology-based alignment to search _E. carinicauda_ genome sequence in the RepBase database (http://www.girinst.org/repbase). RepeatMasker was used to

mask the repetitive sequences obtained by the above method, and RepeatModeler (v2.0)31 was used to perform the _de novo_ identification of other repetitive sequences with the repeat-masked

genome. Ultimately, we identified approximately 4.19 Gb of repetitive sequences, accounting for approximately 71.49% of the assembled genome, among which 9.97% were tandem repeat sequences.

Among these repetitive sequences, LTRs (42.52%) accounted for the highest proportion of the assembly, followed by DNA (10.81%) and LINE (3.33%) (Table 4). Five types of noncoding RNA (ncRNA)

were identified in the genome of _E. carinicauda_, including microRNAs (miRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNA), small nuclear RNAs (snRNAs) and small nucleolar RNAs

(snoRNAs). The tRNA was predicted using tRNAscan-SE (v2.0)32. Other types of ncRNAs were detected by alignment to Rfam database33 using infernal (v1.1.3) software34. In total, 10249

non-coding RNAs (ncRNAs) were annotated, including 3,702 rRNAs, 386 miRNAs, 5,811 tRNAs, 269 snRNAs, and 81 snoRNAs (Table 5). GENE PREDICTION AND ANNOTATION We detected the protein-coding

genes in the _E. carinicauda genome_ assembly by a comprehensive strategy that combined _ab initio_ prediction, protein-based homology searches, and RNA sequencing data predictions. For _ab

initio_ prediction, augustus (v3.2.2)35, SNAP (v6.0)36, Glimmer hmm (v3.0.4)37 and GeneMark-ET38 were used to predict the repeat-masked genome structure. For protein-based homology

prediction, the protein sequences of homologous species including _Daphnia pulex_ (GCA_021134715.1), _Procambarus virginalis_ (GCA_020271785.1), _Fenneropenaeus chinensis_ (GCA_019202785.2),

_Penaeus japonicus_ (GCA_017312705.1), _Penaeus monodon_ (GCA_015228065.1), _Litopenaeus vannamei_ (GCA_003789085.1), _Portunus trituberculatus_ (GCA_017591435.1) and _M. nipponense_

(GCA_015104395.1) were downloaded from the NCBI database and aligned against the _E. carinicauda_ genome using GeMoMa (v1.7.1)39 to perform homology prediction. Furthermore, the RNA-seq data

from different tissues and embryonic development stages (PRJNA594425, PRJNA746617, PRJNA756619, PRJNA881755, and PRJNA881756) were mapped to the genome by HISAT2 (v2.1.0)40. The full-length

transcripts (PRJNA594425) from our previous study41 were assembled using Cufflinks (v2.1.1)42, then the open reading frame was predicted using PASA (v20140417)43. The EVidenceModeler44 was

employed to consolidate the results from these three methods, enabling the merging and integration of gene predictions. Finally, 44,288 high-quality protein-coding genes were predicted.

These predicted genes displayed an average gene length of 28,448 bp, an average coding length of 1,424 bp and 6.09 coding exons per gene. These genes were functionally annotated using BLAST

against NR, SwissProt, eggNOG, InterPro, GO and KEGG45. The protein-coding gene functional annotation results were merged using the aforementioned methods. Finally, 70.53% of the total

predicted genes were successfully assigned with at least one functional annotation (Table 6). DATA RECORDS All sequencing data have been uploaded to the NCBI SRA database. The Illumina

sequencing data for genomic survey has been deposited in the NCBI Sequence Read Archive with accession number SRR2788058946 under BioProject accession number PRJNA1070324. The genomic PacBio

sequencing data has been deposited in the NCBI Sequence Read Archive with accession number SRR2775680047, SRR2775680148, SRR2786204449 and SRR2786204550 under BioProject accession number

PRJNA1070324. The Hi-C sequencing data has been deposited in the NCBI Sequence Read Archive with accession number SRR2788053551, SRR2788053652, SRR2788053753, SRR2788053854, SRR2788053955

and SRR2788054056 under BioProject accession number PRJNA1073006. The final chromosome-level assembled genome file has been uploaded to the GenBank database under the accession

JAZBEV00000000057. TECHNICAL VALIDATION To evaluate the integrity and accuracy of the genome assembly, the completeness of the final genome assembly was assessed using BUSCO (v5.2.2) and the

arthropoda_odb10 database25. It was shown that 92.89% of the 1013 single-copy genes were highly conserved orthologs (88.75% complete, 4.15% fragmented, and 7.11% missing). By aligning the

Illumina sequencing reads (PRJNA471201)3 to the genome using BWA (v0.7.15)24, the read-mapping rate was 99.00%. This indicates a high mapping efficiency. Thus, the above results indicated

that we obtained a high-quality genome of the _E. carinicauda_. CODE AVAILABILITY No specific code was used in this study. The data analyses used standard bioinformatic tools specified in

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https://identifiers.org/ncbi/insdc:JAZBEV000000000 (2024). Download references ACKNOWLEDGEMENTS This research was funded by National Key Research and Development Program of China (No.

2023YFD2401001), National Natural Science Foundation of China (32072974), China Agriculture Research System of MOF and MARA (CARS-48) and the Central Public-interest Scientific Institution

Basal Research Fund, CAFS (2023TD50). AUTHOR INFORMATION Author notes * These authors contributed equally: Jiajia Wang, Jianjian Lv, Miao Shi. AUTHORS AND AFFILIATIONS * State Key Laboratory

of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China Jiajia Wang, Jianjian Lv, 

Qiong Wang, Yuying He, Jian Li & Jitao Li * Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, Shandong,

266237, China Jiajia Wang, Jianjian Lv, Qianqian Ge, Qiong Wang, Yuying He, Jian Li & Jitao Li * Berry Genomics Co., Ltd., Beijing, China Miao Shi Authors * Jiajia Wang View author

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CONTRIBUTIONS J.W., J.L. and J.L. (Jitao Li) conceived and designed the study. Q.G. and Q.W. prepared the material. J.W., J.L. (Jianjian Lv) and M.S. analyzed the data. J.W. and Y.H.

prepared the results. J.W. drafted the manuscript. J.L. (Jianjian Lv) and J.L. (Jitao Li) edited and improved the manuscript. All authors read and approved the final manuscript.

CORRESPONDING AUTHOR Correspondence to Jitao Li. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing interests. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature

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white shrimp _Exopalaemon carinicauda_. _Sci Data_ 11, 576 (2024). https://doi.org/10.1038/s41597-024-03423-9 Download citation * Received: 04 March 2024 * Accepted: 24 May 2024 * Published:

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