Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca)

Abstract

Crustaceans of the order Notostraca (Branchiopoda) are distributed worldwide and are known for the remarkable morphological stasis between their extant and Permian fossil species. Moreover, these crustaceans show relevant ecological traits and a wide range of reproductive strategies. However, genomic studies on notostracans are fairly limited. Here, we present the genome sequences of two notostracan taxa, Lepidurus arcticus and Lepidurus apus lubbocki. Taking advantage of the small genome sizes (~0.11 pg) of these taxa, genomes were sequenced for one individual per species with one run on the Illumina HiSeq X platform. We finally assembled 73.2 Mbp (L. arcticus) and 90.3 Mbp (L. apus lubbocki) long genomes. Assemblies cover up to 84% of the estimated genome size, with a gene completeness >97% for both genomes. In total, 13%-16% of the assembled genomes consist of repeats, and based on read mapping, L. apus lubbocki shows a significantly lower transposable element content than L. arcticus. The analysis of 2,376 orthologous genes indicates an~7% divergence between the two Lepidurus taxa, with a nucleotide substitution rate significantly lower than that of Daphnia taxa. K a /K s analysis suggests purifying selection in both branchiopod lineages, raising the question of whether the low substitution rate of Lepidurus is correlated with morphological conservation or is linked to specific biological traits. Our analysis demonstrates that, in these organisms, it is possible to obtain high-quality draft genomes from single individuals with a relatively low sequencing effort. This result makes Lepidurus and Notostraca interesting models for genomic studies at taxonomic, ecological and evolutionary levels.

Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea)

“…Interestingly, both Anostraca and Notostraca stem branches show decidedly lower ω values (0.127 and 0.184, respectively), consistent with purifying selection. Overall, the present data do not support any correlation between the observed substitution rates variation and changes in natural selection regime, in agreement with genome-wide data [25].…”

“…These data are in agreement with those from a recent genome-wide survey where the nucleotide substitution rate calculated for L. arcticus and L. apus lubbocki was found to be significantly lower than the one calculated for D. magna and D. pulex . In contrast to this, however, the amino acid substitution rate did not vary significantly, in line with the observed general pattern of negative selection [25]. We therefore checked the extent of selective pressures on mitogenomic sequences calculating the ω ratio across the tree branches.…”

“…Total DNA was extracted from individual specimens using the DNA extraction kit (STRATEC), after dissection for gut removal. Whole genome sequencing has been carried out on Illumina HiSeq2000 (Johns Hopkins University Experimental and Computational Genomics Core, SKCCC, USA) on parthenogenetic T. cancriformis sample (paired end, 2 × 100 bp; insert size = 150 bp; Luchetti, unpublished data), and on HiSeqX platform (Macrogen Inc., South Korea) on bisexual T. cancriformis and Lepidurus taxa (paired end, 2 × 150 bp; insert size = 350 bp) [25]. Mitochondrial genomes were de novo assembled from a random subset of 1 million read pairs per sample using the SPAdes v. 3.11.1 assembler with default parameters [26].…”

Discovery of Novel Crustacean and Cephalopod Flaviviruses: Insights into the Evolution and Circulation of Flaviviruses between Marine Invertebrate and Vertebrate Hosts

“…In a screen of genomes deposited in the NCBI whole-genome contig database, we identified numerous flavivirus EVEs within crustacean genomes but were unable to identify any in deposited cephalopod genomes. Two representative flavivirus EVEs from the tadpole shrimp, Lepidurus arcticus (63), and the planktonic crustacean Daphnia magna are presented ( Fig. 6).…”

Tolerance at the genetic level of the brine shrimp Artemia salina to a wide range of salinity

“…From the predicted ORFs, only homologous pancrustacean proteins were selected for downstream analysis, based on the results of a local BLASTp search (e-value cutoff = 1.e-05). The reference protein database for the BLASTp search was constructed from pancrustacean species as follows: Armadillidium nasatum (NCBI, SEYY00000000.1), Artemia franciscana (https://antagen.kopri.re.kr/), Catajapyx aquilonaris (BCM-HGSC; https://i5k.nal.usda.gov), Daphnia magna (NCBI, QYSF00000000.1), Daphnia pulex (NCBI, FLTH00000000.2), Eulimnadia texana (NCBI, NKDA00000000.1), Eurytemora a nis (NCBI, AZAI00000000.2), Folsomia candida (NCBI, LNIX00000000.1), Lepidurus arcticus (NCBI, RJJB00000000.1), Lepidurus apus lubbocki (RJJA00000000.1), Orchesella cincta (NCBI, LJIJ00000000.1), Penaeus vannamei (NCBI, NIUR000000000.1), Tigriopus californicus (NCBI, VCGU00000000.1), Tribolium castaneum (NCBI, AAJJ00000000.2), and Zootermopsis nevadensis (NCBI, AUST00000000.1) [34][35][36][37][38][39][40][41][42][43][44][45]. The predicted proteins and their coding sequences are available in Additional File 4.…”