Genome survey sequencing of the Caribbean spiny lobster Panulirus argus: Genome size, nuclear rRNA operon, repetitive elements, and microsatellite discovery

Background Panulirus argus is an ecologically relevant species in shallow water hard-bottom environments and coral reefs and target of the most lucrative fishery in the greater Caribbean region. Methods This study reports, for the first time, the genome size and nuclear repetitive elements, including the 45S ribosomal DNA operon, 5S unit, and microsatellites, of P. argus. Results Using a k-mer approach, the average haploid genome size estimated for P. argus was 2.17 Gbp. Repetitive elements comprised 69.02% of the nuclear genome. In turn, 30.98% of the genome represented low- or single-copy sequences. A considerable proportion of repetitive sequences could not be assigned to known repeat element families. Taking into account only annotated repetitive elements, the most frequent belonged to Class I-LINE which were noticeably more abundant than Class I-LTR-Ty- 3/Gypsy, Class I-LTR-Penelope, and Class I-LTR-Ty-3/Bel-Pao elements. Satellite DNA was also abundant. The ribosomal operon in P. argus comprises, in the following order, a 5′ ETS (length = 707 bp), ssrDNA (1,875 bp), ITS1 (736 bp), 5.8S rDNA (162 bp), ITS2 (1,314 bp), lsrDNA (5,387 bp), and 3′ ETS (287 bp). A total of 1,281 SSRs were identified.

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Genome Survey Sequencing of an Iconic ‘Trophy’ Sportfish, the Roosterfish Nematistius pectoralis: Genome Size, Repetitive Elements, Nuclear RNA Gene Operon, and Microsatellite Discovery

Genes ◽

10.3390/genes12111710 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1710

Author(s):

J. Antonio Baeza ◽

José Luis Molina-Quirós ◽

Sebastián Hernández-Muñoz

Keyword(s):

Genome Size ◽

Repetitive Sequences ◽

Repetitive Elements ◽

Class I ◽

5.8S Rdna ◽

Genome Survey ◽

Genome Content ◽

Data Deficient ◽

Conservation Plans ◽

Low Coverage

The ‘Pez Gallo’ or the Roosterfish, Nematistius pectoralis, is an ecologically relevant species in the shallow water soft-bottom environments and a target of a most lucrative recreational sport fishery in the Central Eastern Pacific Ocean. According to the International Union for Conservation of Nature, N. pectoralis is assessed globally as Data Deficient. Using low-coverage short Illumina 300 bp pair-end reads sequencing, this study reports, for the first time, the genome size, single/low-copy genome content, and nuclear repetitive elements, including the 45S rRNA DNA operon and microsatellites, in N. pectoralis. The haploid genome size estimated using a k-mer approach was 816.04 Mbp, which is within the range previously reported for other representatives of the Carangiformes order. Single/low-copy genome content (63%) was relatively high. A large portion of repetitive sequences could not be assigned to the known repeat element families. Considering only annotated repetitive elements, the most common were classified as Satellite DNA which were considerably more abundant than Class I-Long Interspersed Nuclear Elements and Class I-LTR Retroviral elements. The nuclear ribosomal operon in N. pectoralis consists of, in the following order: a 5′ ETS (length = 948 bp), ssrDNA (1835 bp), ITS1 (724 bp), a 5.8S rDNA (158 bp), ITS2 (508 bp), lsrDNA (3924 bp), and a 3′ ETS (32 bp). A total of 44 SSRs were identified. These newly developed genomic resources are most relevant for improving the understanding of biology, developing conservation plans, and managing the fishery of the iconic N. pectoralis.

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Yes, we can use it: a formal test on the accuracy of low-pass nanopore long-read sequencing for mitophylogenomics and barcoding research using the Caribbean spiny lobster Panulirus argus

BMC Genomics ◽

10.1186/s12864-020-07292-5 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

J. Antonio Baeza

Keyword(s):

Low Income ◽

Fishery Management ◽

De Novo ◽

Spiny Lobster ◽

Population Connectivity ◽

Panulirus Argus ◽

Low Income Countries ◽

Caribbean Region ◽

Long Read ◽

The Caribbean

Abstract Background Whole mitogenomes or short fragments (i.e., 300–700 bp of the cox1 gene) are the markers of choice for revealing within- and among-species genealogies. Protocols for sequencing and assembling mitogenomes include ‘primer walking’ or ‘long PCR’ followed by Sanger sequencing or Illumina short-read low-coverage whole genome (LC-WGS) sequencing with or without prior enrichment of mitochondrial DNA. The aforementioned strategies assemble complete and accurate mitochondrial genomes but are time consuming and/or expensive. In this study, I first tested whether mitogenomes can be sequenced from long-read nanopore sequencing data exclusively. Second, I explored the accuracy of the long-read assembled genomes by comparing them to a ‘gold’ standard reference mitogenome retrieved from the same individual using Illumina sequencing. Third and lastly, I tested if the long-read assemblies are useful for mitophylogenomics and barcoding research. To accomplish these goals, I used the Caribbean spiny lobster Panulirus argus, an ecologically relevant species in shallow water coral reefs and target of the most lucrative fishery in the greater Caribbean region. Results LC-WGS using a MinION ONT device and various de-novo and reference-based assembly pipelines retrieved a complete and highly accurate mitogenome for the Caribbean spiny lobster Panulirus argus. Discordance between each of the long-read assemblies and the reference mitogenome was mostly due to indels at the flanks of homopolymer regions. Although not ‘perfect’, phylogenetic analyses using entire mitogenomes or a fragment of the cox1 gene demonstrated that mitogenomes assembled using long reads reliably identify the sequenced specimen as belonging to P. argus and distinguish it from other related species in the same genus, family, and superorder. Conclusions This study serves as a proof-of-concept for the future implementation of in-situ surveillance protocols using the MinION to detect mislabeling in P. argus across its supply chain. Mislabeling detection will improve fishery management in this overexploited lobster. This study will additionally aid in decreasing costs for exploring meta-population connectivity in the Caribbean spiny lobster and will aid with the transfer of genomics technology to low-income countries.

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Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales

Genome ◽

10.1139/gen-2013-0042 ◽

2013 ◽

Vol 56 (9) ◽

pp. 487-494 ◽

Cited By ~ 14

Author(s):

Kate L. Hertweck

Keyword(s):

Genome Size ◽

De Novo ◽

Genomic Sequence ◽

Sequence Data ◽

Repetitive Sequences ◽

Nuclear Genome ◽

Research Field ◽

Holistic View ◽

Illumina Data ◽

Low Coverage

The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a nonmodel system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from 11 exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that although some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources.

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Origin of the Eukaryotic Cell

Molecular Frontiers Journal ◽

10.1142/s2529732517400120 ◽

2017 ◽

Vol 01 (02) ◽

pp. 108-120 ◽

Cited By ~ 2

Author(s):

Nick Lane

Keyword(s):

Protein Synthesis ◽

Host Cell ◽

Genome Size ◽

Energy Savings ◽

Nuclear Genome ◽

Eukaryotic Cell ◽

Eukaryotic Cells ◽

Bacterial Genomes ◽

Complex Cells ◽

Life On Earth

All complex life on Earth is composed of ‘eukaryotic’ cells. Eukaryotes arose just once in 4 billion years, via an endosymbiosis — bacteria entered a simple host cell, evolving into mitochondria, the ‘powerhouses’ of complex cells. Mitochondria lost most of their genes, retaining only those needed for respiration, giving eukaryotes ‘multi-bacterial’ power without the costs of maintaining thousands of complete bacterial genomes. These energy savings supported a substantial expansion in nuclear genome size, and far more protein synthesis from each gene.

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Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds

Scientific Reports ◽

10.1038/s41598-019-56383-1 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Rahman Ebrahimzadegan ◽

Andreas Houben ◽

Ghader Mirzaghaderi

Keyword(s):

Repetitive Sequences ◽

Nuclear Genome ◽

B Chromosome ◽

B Chromosomes ◽

Festuca Pratensis ◽

Ltr Retrotransposons ◽

Chromosome Identification ◽

Satellite Repeats ◽

Low Pass ◽

Illumina Sequence

AbstractHere, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (−B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.

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Directly ageing the Caribbean spiny lobster, Panulirus argus with validated band counts from gastric mill ossicles

ICES Journal of Marine Science ◽

10.1093/icesjms/fsy177 ◽

2018 ◽

Vol 76 (2) ◽

pp. 442-451 ◽

Cited By ~ 7

Author(s):

Gaya Gnanalingam ◽

Mark J Butler ◽

Thomas R Matthews ◽

Emily Hutchinson ◽

Raouf Kilada

Keyword(s):

Spiny Lobster ◽

Age Determination ◽

Florida Keys ◽

Panulirus Argus ◽

Gastric Mill ◽

Coefficients Of Variation ◽

The Caribbean ◽

First Time ◽

Reader Experience

Abstract In crustaceans, ecdysis was long believed to result in the loss and replacement of all calcified structures, precluding the use of conventional ageing methods. However, the discovery of bands in the gastric ossicles of several crustaceans with some correlation with age suggests that direct age estimation may be possible. We applied this method to a tropical spiny lobster, Panulirus argus, one of the most iconic and economically valuable species in the Caribbean. The presence of growth bands was investigated using wild lobsters of unknown age and was validated with captive reared lobsters of known age (1.5–10 years) from the Florida Keys, Florida (USA). Bands were consistently identified in ptero- and zygo-cardiac ossicles of the gastric mill and did not appear to be associated with moulting. Validation with known age animals confirms that bands form annually. Counts between independent readers were reproducible with coefficients of variation ranging from 11% to 26% depending on reader experience and the structure used. This study demonstrates, for the first time, that direct age determination of P. argus is possible.

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Estimation of abundance and spatial distribution of Panulirus argus using different methodologies in artificial shelter, trap and coral reef fisheries

Crustaceana ◽

10.1163/15685403-00003159 ◽

2013 ◽

Vol 86 (2) ◽

pp. 158-181 ◽

Cited By ~ 2

Author(s):

Raúl Cruz ◽

Carlos A. Borda

Keyword(s):

Spatial Distribution ◽

Spiny Lobster ◽

Panulirus Argus ◽

Fishing Gear ◽

Productive Capacity ◽

Fishing Pressure ◽

The West ◽

Effective Measure ◽

Protection Area ◽

Marine Protection

Estimates of spiny lobster stocks (Panulirus argus Latreille, 1804) represent a fundamental input for population assessment models and are, therefore, indispensable for proper management. In this study we analysed methodologies employed in the Gulf of Batabanó (Cuba) and Providencia and Santa Catalina (Colombian Caribbean) to estimate abundance (N) and stock productivity. We found evidence that the relative abundance (CPUE) for trap-like jaulones and skin diving in natural shelters was likely to remain high despite the decline in abundance (hyperstability). In contrast, the proportionality between CPUE and N was satisfactory in artificial shelters (Cuban pesqueros). Stock productivity was greater for jaulones (22 288 kg/km2) than for pesqueros (1309 kg/km2) or natural shelters (15.25 kg/km2), reflecting differences in the productive capacity of each type of fishing gear. In natural shelters the exploitable biomass is under great fishing pressure and the reproductive stock is likely to decrease. Thus, the West zone of Providencia and Santa Catalina, characterized by high-density seagrass and mangrove, should be designated a marine protection area to prevent a lobster fishing collapse. The most effective measure to revert the lobster fishing collapse in Cuba would be to ban the use of jaulones and liftable pesqueros, thereby reducing fishing intensity.

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