Contributors: Kumar Saurabh Singh, MD Sharma
... 1. Whole-genome GFF file (raw and filtered for min. gene length) [Maniola.jurtina.gff3, Maniola_jurtina_filtered.gff3] 2. List of M. jurtina proteins [Mjurtina_proteins.fa]. 3. Results of spot pattern genes BLAST against M. jurtina proteome [Lepidoptera_MJ_protein_matches.xlsx].
A nemertean excitatory peptide/CCHamide regulates ciliary swimming in the larvae of Lineus longissimus
Contributors: Thiel, Daniel, Bauknecht, Philipp, Jékely, Gáspár, Hejnol, Andreas
... Background: The trochozoan excitatory peptide (EP) and its ortholog, the arthropod CCHamide, are neuropeptides that are only investigated in very few animal species. Previous studies on different trochozoan species focused on their physiological effect in adult specimens, demonstrating a myo-excitatory effect, often on tissues of the digestive system. The function of EP in the planktonic larvae of trochozoans has not yet been studied.Results: We surveyed transcriptomes from species of various spiralian (Orthonectida, Nemertea, Brachiopoda, Entoprocta, Rotifera) and ecdysozoan taxa (Tardigrada, Onychophora, Priapulida, Loricifera, Nematomorpha) to investigate the evolution of EPs/CCHamides in protostomes. We found that the EPs of several pilidiophoran nemerteans show a characteristic difference in their C-terminus. Deorphanization of a pilidiophoran EP receptor showed, that the two splice variants of the nemertean Lineus longissimus EP activate a single receptor. We investigated the expression of EP in L. longissimus larvae and juveniles with customized antibodies and found that EP positive nerves in larvae project from the apical organ to the ciliary band and that EP is expressed more broadly in juveniles in the neuropil and the prominent longitudinal nerve cords. While exposing juvenile L. longissimus specimens to synthetic excitatory peptides did not show any obvious effect, exposure of larvae to either of the two EPs increased the beat frequency of their locomotory cilia and shifted their vertical swimming distribution in a water column upwards.Conclusion: Our results show that EP/CCHamide peptides are broadly conserved in protostomes. We show that the EP increases the ciliary beat frequency of L. longissimus larvae, which shifts their vertical distribution in a water column upwards. Endogenous EP may be released at the ciliary band from the projections of apical organ EP positive neurons to regulate ciliary beating. This locomotory function of EP in L. longissimus larvae stands in contrast to the repeated association of EP/CCHamides with its myo-excitatory effect in adult trochozoans and the general association with the digestive system in many protostomes.
Contributors: Thompson, Luke Richard
... The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the ocean; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, II) and 5 Prochlorococcus (ecotype HLII) cells from the Red Sea and combined them with globally-sourced reference genomes to cluster genes into ortholog groups (OGs) using the program OrthoMCL (version 2.0). OrthoMCL configuration settings were as follows: percentMatchCutoff=50, evalueExponentCutoff=–5. This yielded 5272 SAR11 OGs and 10439 Prochlorococcus OGs. This archive contains four files: the protein identifiers associated with each OG (proch_ortholog_groups.txt, sar11_ortholog_groups.txt) and the protein sequences for each protein identifier (proch_protein_sequences.fasta, sar11_protein_sequences.fasta).
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Contributors: Myrthe Jager, Francis Blokzijl
... NERdeficiency vcfs VAF < 0.3
Contributors: Myrthe Jager, Francis Blokzijl
... NER-deficiency filtered VCF files
Contributors: Winter, Graeme
... Useful small (488 frame) Eiger data set recorded during routine testing, useful for software testing as it is small. Data recorded from a thaumatin crystal (unfortunate naming on my part)
Contributors: Melissa Jordan, Richard Newcomb
... Olfactory receptor genes identified from the genome assembly of tuatara (Sphenodon punctatus). File 1: List of intact OR genes File 2: alignment file used to infer phylogenetic relationship between intact tuatara ORs and other species of terrestrial squamates and two species of bird. File 3: Excel spreadsheet listing OR identification from scaffolds (includes data on pseudogenes and partials)
Supplementary material 2 from: Zhao Y, Liu X-z, Bai F-y (2019) Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data. MycoKeys 47: 75-95. https://doi.org/10.3897/mycokeys.47.29180
Contributors: Zhao, Ying, Liu, Xin-zhan, Bai, Feng-yan
... Supplementary material 2 from: Zhao Y, Liu X-z, Bai F-y (2019) Four new species of Tremella (Tremellales, Basidiomycota) based on morphology and DNA sequence data. MycoKeys 47: 75-95. https://doi.org/10.3897/mycokeys.47.29180
Contributors: Hala, Sharif; Antony, Chakkiath Paul; Alshehri, Mohammed; Alsaedi, Asim; Al Thaqafi, Abdulhakeem O.; Mufti, Areej; Kaaki, Mai; Alhaj-Hussein, Baraa T.; Zowawi, Hosam Mamoon; Al-Amri, Abdulfattah; Pain, A.
... Fasta and gff files for the assemblies that were obtained from the study "Emergence of Klebsiella quasipneumoniae harboring blaKPC-2 in Saudi Arabia"
Contributors: Velikova, Gergana V., Schuster-Böckler, Benjamin
... The test dataset for asTair, which is a little tool developed for the analysis of bisulfite-free and base-resolution sequencing data generated with TET Assisted Pyridine borane Sequencing (TAPS) or other modified cytosine to thymine conversion methods (mCtoT), but it also has some tricks for bisulfite sequencing data (unmodified cytosine to thymine conversion methods, CtoT). More about the tool may be found here: https://bitbucket.org/bsblabludwig/astair/ More about the TAPS method can be found here: https://www.nature.com/articles/s41587-019-0041-2