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First annotated draft genomes of nonmarine ostracods (Ostracoda, Crustacea) with different reproductive modes.

ABSTRACT: Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources for this class are still lacking. We have successfully assembled and annotated the first reference genomes for three species of nonmarine ostracods; two with obligate sexual reproduction (Cyprideis torosa and Notodromas monacha) and the putative ancient asexual Darwinula stevensoni. This kind of genomic research has so far been impeded by the small size of most ostracods and the absence of genetic resources such as linkage maps or BAC libraries that were available for other crustaceans. For genome assembly, we used an Illumina-based sequencing technology, resulting in assemblies of similar sizes for the three species (335-382 Mb) and with scaffold numbers and their N50 (19-56 kb) in the same orders of magnitude. Gene annotations were guided by transcriptome data from each species. The three assemblies are relatively complete with BUSCO scores of 92-96. The number of predicted genes (13,771-17,776) is in the same range as Branchiopoda genomes but lower than in most malacostracan genomes. These three reference genomes from nonmarine ostracods provide the urgently needed basis to further develop ostracods as models for evolutionary and ecological research.

SUBMITTER: Tran Van P

PROVIDER: S-EPMC8049415 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Ostracods genomes

Project description:Genome evolution under sexual and asexual reproduction (Ostracods genomes)

| PRJEB38362 | ENA

Cryptic species in putative ancient asexual darwinulids (Crustacea, Ostracoda).

Project description:Fully asexually reproducing taxa lack outcrossing. Hence, the classic Biological Species Concept cannot be applied.We used DNA sequences from the mitochondrial COI gene and the nuclear ITS2 region to check species boundaries according to the evolutionary genetic (EG) species concept in five morphospecies in the putative ancient asexual ostracod genera, Penthesilenula and Darwinula, from different continents. We applied two methods for detecting cryptic species, namely the K/? method and the General Mixed Yule Coalescent model (GMYC). We could confirm the existence of species in all five darwinulid morphospecies and additional cryptic diversity in three morphospecies, namely in Penthesilenula brasiliensis, Darwinula stevensoni and in P. aotearoa. The number of cryptic species within one morphospecies varied between seven (P. brasiliensis), five to six (D. stevensoni) and two (P. aotearoa), respectively, depending on the method used. Cryptic species mainly followed continental distributions. We also found evidence for coexistence at the local scale for Brazilian cryptic species of P. brasiliensis and P. aotearoa. Our ITS2 data confirmed that species exist in darwinulids but detected far less EG species, namely two to three cryptic species in P. brasiliensis and no cryptic species at all in the other darwinulid morphospecies.Our results clearly demonstrate that both species and cryptic diversity can be recognized in putative ancient asexual ostracods using the EG species concept, and that COI data are more suitable than ITS2 for this purpose. The discovery of up to eight cryptic species within a single morphospecies will significantly increase estimates of biodiversity in this asexual ostracod group. Which factors, other than long-term geographic isolation, are important for speciation processes in these ancient asexuals remains to be investigated.

| S-EPMC3389007 | biostudies-literature

Two new Cypridopsinae Kaufmann, 1900 (Crustacea, Ostracoda) from southern Africa.

Project description:Two new Cypridopsinae ostracods, Potamocyprismeissneri sp. nov. and Sarscypridopsisharundineti sp. nov. are described. Both were found only as asexual (all-female) populations in temporary waters of southern Africa. Potamocyprismeissneri was collected from a small pan in the North-West Province of South Africa. It is approximately 0.5 mm long and belongs to the species group with long swimming setae on the second antennae. However, the species has a somewhat isolated position in the genus owing to the conspicuously reticulated carapace, which is furthermore densely covered by prominent conuli with normal pores carrying long sensilla, as well as to the wide anterior and posterior flanges on the left valve. To allow identification of the new species in relation to its closest congeners, a key to the species of the genus Potamocypris Brady, 1870 from southern Africa is provided. The genus Sarscypridopsis McKenzie, 1977 mostly has an Afrotropical distribution with only few species occurring in other regions. Sarscypridopsisharundineti was collected from floodplains of the outskirts of the Okavango Delta in Botswana. It is approximately 0.4 mm long and can be distinguished from congeners mainly by the smaller and more oval-shaped valves. We conclude that southern African Cypridopsinae urgently need integrated taxonomic revision, by means of both morphological characters and DNA-sequence data.

| S-EPMC8677703 | biostudies-literature

Barcoding of ancient lake ostracods (crustacea) reveals cryptic speciation with extremely low distances.

Project description:Ostracods are drastically reduced crustaceans, with never more than eight appendages enclosed between two valves, leaving only a limited number of morphological characters for species delineation. Conservative morphology of characters used to define genera, along with high variability of characters used to define species are creating problems in applying a morphospecies concept. A high intraspecific variability in a Lake Biwa (Japan) endemic, Physocypria biwaensis (Okubo, 1990), has been observed previously but was never studied in detail. Two sympatric forms, differing in pigmentation and size, suggest a presence of reproductive isolation. The aim of this study is to employ molecular and morphometric tools to aid in species delineation within P. biwaensis complex and reconstruct their phylogenetic relationships. A fragment of the mtCOI gene was amplified from 30 specimens, and an additional 37 specimens were studied for morphological characters. Resulting phylogenies showed that each morphologically distinct form is associated with a distinct phylogenetic group based on mtDNA. The average pairwise distance is very low (5%), indicating a recent divergence time. I speculate that there is a possibility that one of them originated in the lake, while the other probably colonized it afterwards. This seems to be supported with an apparent niche partitioning at different depths. In spite of the fact that traditionally used sexual characters are highly variable in these two species, the morphometric analysis of shell and soft part related characters clearly delineates them and suggests that such characters may be useful for future detection of seemingly cryptic ostracod species.

| S-EPMC4374928 | biostudies-literature

Ostracods (Crustacea) and their palaeoenvironmental implication for the Solimoes Formation (Late Miocene; Western Amazonia/Brazil).

Project description:Western Amazonia's landscape and biota were shaped by an enormous wetland during the Miocene epoch. Among the most discussed topics of this ecosystem range the question on the transitory influx of marine waters. Inter alia the occurrence of typically brackish water associated ostracods is repeatedly consulted to infer elevated salinities or even marine ingressions. The taxonomical investigation of ostracod faunas derived from the upper part of the Solimões Formation (Eirunepé; W-Brazil) documents a moderately diverse assemblage (19 species). A wealth of freshwater ostracods (mainly Cytheridella, Penthesilenula) was found co-occurring with taxa (chiefly Cyprideis) usually related to marginal marine settings today. The observed faunal compositions as well as constantly very light δ18O- and δ13C-values obtained by measuring both, the freshwater and brackish water ostracod group, refer to entirely freshwater conditions. These results corroborate with previous sedimentological and palaeontological observations, which proposed a fluvial depositional system for this part of western Amazonia during the Late Miocene. We demonstrate that some endemic, "brackish" water ostracods (i.e., Cyprideis) have been effectively adapted to freshwater conditions. Thus, their occurrence is no univocal evidence for the influence of brackish or marine waters in western Amazonia during the Miocene.

| S-EPMC4599595 | biostudies-literature

Exceptional preservation of reproductive organs and giant sperm in Cretaceous ostracods.

Project description:The bivalved crustacean ostracods have the richest fossil record of any arthropod group and display complex reproductive strategies contributing to their evolutionary success. Sexual reproduction involving giant sperm, shared by three superfamilies of living ostracod crustaceans, is among the most fascinating behaviours. However, the origin and evolution of this reproductive mechanism has remained largely unexplored because fossil preservation of such features is extremely rare. Here, we report exceptionally preserved ostracods with soft parts (appendages and reproductive organs) in a single piece of mid-Cretaceous Kachin amber (approximately 100 Myr old). The ostracod assemblage is composed of 39 individuals. Thirty-one individuals belong to a new species and genus, Myanmarcypris hui gen. et sp. nov., exhibiting an ontogenetic sequence from juveniles to adults (male and female). Seven individuals are assigned to Thalassocypria sp. (Cypridoidea, Candonidae, Paracypridinae) and one to Sanyuania sp. (Cytheroidea, Loxoconchidae). Our micro-CT reconstruction provides direct evidence of the male clasper, sperm pumps (Zenker organs), hemipenes, eggs and female seminal receptacles with giant sperm. Our results reveal that the reproduction behavioural repertoire, which is associated with considerable morphological adaptations, has remained unchanged over at least 100 million years-a paramount example of evolutionary stasis. These results also double the age of the oldest unequivocal fossil animal sperm. This discovery highlights the capacity of amber to document invertebrate soft parts that are rarely recorded by other depositional environments.

| S-EPMC7542813 | biostudies-literature

Annotated Draft Genomes of Two Caddisfly Species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera).

Project description:Members of the speciose insect order Trichoptera (caddisflies) provide important ecosystem services, for example, nutrient cycling through breaking down of organic matter. They are also of industrial interest due to their larval silk secretions. These form the basis for their diverse case-making behavior that allows them to exploit a wide range of ecological niches. Only five genomes of this order have been published thus far, with variable qualities regarding contiguity and completeness. A low-cost sequencing strategy, that is, using a single Oxford Nanopore flow cell per individual along with Illumina sequence reads was successfully used to generate high-quality genomes of two Trichoptera species, Plectrocnemia conspersa and Hydropsyche tenuis. Of the de novo assembly methods compared, assembly of low coverage Nanopore reads (∼18×) and subsequent polishing with long reads followed by Illumina short reads (∼80-170× coverage) yielded the highest genome quality both in terms of contiguity and BUSCO completeness. The presented genomes are the shortest to date and extend our knowledge of genome size across caddisfly families. The genomic region that encodes for light (L)-chain fibroin, a protein component of larval caddisfly silk was identified and compared with existing L-fibroin gene clusters. The new genomic resources presented in this paper are among the highest quality Trichoptera genomes and will increase the knowledge of this important insect order by serving as the basis for phylogenomic and comparative genomic studies.

| S-EPMC6916706 | biostudies-literature

A new species of Elpidium (Crustacea, Ostracoda) from bromeliads in Cusuco National Park, Honduras.

Project description:Passively dispersing aquatic invertebrates such as Ostracoda in restricted aquatic habitats such as bromeliads remain an intriguing observation considering the highly specialised dispersal vectors needed for efficient colonisation. Here we describe a new species of Elpidium, Elpidium merendonense sp. n., collected from bromeliads in the cloud forest from Cusuco National Park, Honduras. Elpidium merendonense sp. n. is a small to medium-sized species that can be easily distinguished from its congeners by its unique outgrowth at the posterior end of the left valve, visible especially in females. The species was common all through the park occurring at a wide range of altitudes and in different species of bromeliads. This finding is the first freshwater ostracod species described from Honduras and is in agreement with the prediction that the genus Elpidium contains a large number of species with small geographic distributions. We update the list of described species of Elpidium and present a key to species.

| S-EPMC3701230 | biostudies-literature

<i>Pontopolycope orientalis</i> sp. nov. (Crustacea: Ostracoda: Polycopidae), the First Report of a Living Species of the Genus from the Indo-Pacific Region.

Project description:The present study describes Pontopolycope orientalis sp. nov. (Polycopidae), which was collected from the shallow sandy bottom off of Nagannu Island, Okinawa Prefecture, southwestern Japan. This new species is the first living representative of Pontopolycope from the Indo-Pacific region. We also provided a key to identifying five living congeners throughout the world's oceans. Since Pontopolycope is defined by the morphological characteristics of the carapace, the following five fossil and subfossil (empty valve) species of Polycope (Polycopidae) are moved to Pontopolycope: Pontopolycope luxuriosa (Herrig, 1964) comb. nov., P. sanctacatherinae (Whatley and Downing, 1983) comb. nov., P. krauseae (Herrig, 1994) comb. nov., P. proboscidea (Herrig, 1994) comb. nov., and P. isolata (Whatley, Jones and Wouters, 2000) comb. nov. Finally, the nucleotide sequence data of three genes (18S rRNA, 28S rRNA, and mitochondrial cytochrome c oxidase subunit 1) of the new species are provided for future systematic and phylogenetic studies.

| S-EPMC7396926 | biostudies-literature

Sub-decadal resolution in sediments of Late Miocene Lake Pannon reveals speciation of Cyprideis (Crustacea, Ostracoda).

Project description:Late Miocene "Lake Pannon" (~11.3 Ma) was a remnant of the Central Paratethyan Sea. Successive freshening and constantly changing environmental conditions, like oxygenation, nutrition and substrate led to a well-documented radiation in molluscs and ostracods. Among ostracods (small crustaceans), Cyprideis is one of the most common genera in "Lake Pannon", as well as in several other ancient lakes, showing numerous adaptations and speciations. Here, we present high-resolution data from an early transgression of "Lake Pannon" in the Eastern Styrian Basin (SE Austria). Mataschen clay pit is in the focus of geologic and paleontologic research since 20 years and its geologic and paleoecologic evolution is well-documented. We drilled five cores covering a ~2.3 m long section and completely sampled it in 5-mm thick intervals to reconstruct minute changes in the ostracod fauna over a transgression of a brackish water body. The dominant genus, Cyprideis, is represented by three species C. mataschensis, C. kapfensteinensis and C. ex gr. pannonica. Through morphometric analyses we highlight the variance of each taxon and suggest that there is no direct ecologic control on size or shape. Furthermore, we found a second, co-occurring morphotype of C. kapfensteinensis which is directly related to an elevation of salinities above 13 psu. The presence of two intermediate specimens between the two morphotypes in the sample directly below the first appearance of C. kapfensteinensis B leads us to the conclusion that we are facing a speciation event leading to four sympatric species of Cyprideis.

| S-EPMC4406499 | biostudies-literature

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