Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea

Chromosome-level genome assembly and annotation of the black sea urchin Arbacia lixula (Linnaeus, 1758)

The black sea urchin (Arbacia lixula) is a keystone species inhabiting the coastal shallow waters of the Mediterranean Sea, which is a key driver of littoral communities' structure. Here, we present the first genome assembly and annotation of this species, standing as the first Arbacioida genome, including both nuclear and mitochondrial genomes. To obtain a chromosome-level assembly, we used a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). In addition, we generated a high-quality nuclear annotation of both coding and non-coding genes, by using published RNA-Seq data from several individuals of A. lixula and gene models from closely related species. The nuclear genome assembly has a total span of 607.91 Mb, being consistent with its experimentally estimated genome size. The assembly contains 22 chromosome-scale scaffolds (96.52% of the total length), which coincides with its known karyotype. A total of 72,767 transcripts were predicted from the nuclear genome, 24,171 coding, and 48,596 non-coding that included lncRNA, snoRNA, and tRNAs. The circularized mitochondrial genome had 15,740 bp comprising 13 protein-coding genes, 2 rRNA, and 22 tRNA. This reference genome will enhance ongoing A. lixula studies and benefit the wider sea urchin scientific community.

A novel deep-benthic sea cucumber species of Benthodytes (Holothuroidea, Elasipodida, Psychropotidae) and its comprehensive mitochondrial genome sequencing and evolutionary analysis

BACKGROUND

The holothurians, commonly known as sea cucumbers, are marine organisms that possess significant dietary, nutritional, and medicinal value. However, the National Center for Biotechnology Information (NCBI) currently possesses only approximately 70 complete mitochondrial genome datasets of Holothurioidea, which poses limitations on conducting comprehensive research on their genetic resources and evolutionary patterns. In this study, a novel species of sea cucumber belonging to the genus Benthodytes, was discovered in the western Pacific Ocean. The genomic DNA of the novel sea cucumber was extracted, sequenced, assembled and subjected to thorough analysis.

RESULTS

The mtDNA of Benthodytes sp. Gxx-2023 (GenBank No. OR992091) exhibits a circular structure spanning 17,386 bp, comprising of 13 protein-coding genes (PCGs), 24 non-coding RNAs (2 rRNA genes and 22 tRNA genes), along with two putative control regions measuring 882 bp and 1153 bp, respectively. It exhibits a high AT% content and negative AT-skew, which distinguishing it from the majority of sea cucumbers in terms of environmental adaptability evolution. The mitochondrial gene homology between Gxx-2023 and other sea cucumbers is significantly low, with less than 91% similarity to Benthodytes marianensis, which exhibits the highest level of homology. Additionally, its homology with other sea cucumbers is below 80%. The mitogenome of this species exhibits a unique pattern in terms of start and stop codons, featuring only two types of start codons (ATG and ATT) and three types of stop codons including the incomplete T. Notably, the abundance of AT in the Second position of the codons surpasses that of the First and Third position. The gene arrangement of PCGs exhibits a relatively conserved pattern, while there exists substantial variability in tRNA. Evolutionary analysis revealed that it formed a distinct cluster with B. marianensis and exhibited relatively distant phylogenetic relationships with other sea cucumbers.

CONCLUSIONS

These findings contribute to the taxonomic diversity of sea cucumbers in the Elasipodida order, thereby holding significant implications for the conservation of biological genetic resources, evolutionary advancements, and the exploration of novel sea cucumber resources.

The mitochondrial genome of the deep-sea pyramid urchin Echinocrepis rostrata (Echinoidea: Holasteroida: Pourtalesiidae)

We present the mitochondrial genome of the deep-sea, epibenthic, irregular echinoid Echinocrepis rostrata, representing the first sequenced mitogenome of the order Holasteroida. The length of the complete E. rostrata mitochondrial genome is 15,716 base pairs, and its GC content is 34.87%. It contains 13 protein-coding genes, two rRNA genes, and 22 tRNA genes, whose order is identical to that of all other available echinoid mitogenomes. Phylogenetic analysis of available mitochondrial genomes, based on all coding loci, places E. rostrata as the sister group to spatangoids (heart urchins).

A 104-Ma record of deep-sea Atelostomata (Holasterioda, Spatangoida, irregular echinoids) - a story of persistence, food availability and a big bang

Deep-sea macrobenthic body fossils are scarce due to the lack of deep-sea sedimentary archives in onshore settings. Therefore, hypothesized migrations of shallow shelf taxa into the deep-sea after phases of mass extinction (onshore-offshore pattern in the literature) due to anoxic events is not constrained by the fossil record. To resolve this conundrum, we investigated 1,475 deep-sea sediment samples from the Atlantic, Pacific and Southern oceans (water depth ranging from 200 to 4,700 m), providing 41,460 spine fragments of the crown group Atelostomata (Holasteroida, Spatangoida). We show that the scarce fossil record of deep-sea echinoids is in fact a methodological artefact because it is limited by the almost exclusive use of onshore fossil archives. Our data advocate for a continuous record of deep-sea Atelostomata back to at least 104 Ma (late early Cretaceous), and literature records suggest even an older age (115 Ma). A gradual increase of different spine tip morphologies from the Albian to the Maastrichtian is observed. A subsequent, abrupt reduction in spine size and the loss of morphological inventory in the lowermost Paleogene is interpreted to be an expression of the "Lilliput Effect", related to nourishment depletion on the sea floor in the course of the Cretaceous-Paleogene (K-Pg) Boundary Event. The recovery from this event lasted at least 5 Ma, and post-K-Pg Boundary Event assemblages progress-without any further morphological breaks-towards the assemblages observed in modern deep-sea environments. Because atelostomate spine morphology is often species-specific, the variations in spine tip morphology trough time would indicate species changes taking place in the deep-sea. This observation is, therefore, interpreted to result from in-situ evolution in the deep-sea and not from onshore-offshore migrations. The calculation of the "atelostomate spine accumulation rate" (ASAR) reveals low values in pre-Campanian times, possibly related to high remineralization rates of organic matter in the water column in the course of the mid-Cretaceous Thermal Maximum and its aftermath. A Maastrichtian cooling pulse marks the irreversible onset of fluctuating but generally higher atelostomate biomass that continues throughout the Cenozoic.