bims-sevkro 2018-07-08 papers

on Sex chromosome evolution

Issue of 2018–07–08
seven papers selected by
Vladimir Trifonov, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences

Transcriptome Profiling of Single Mouse Oocytes.
Evolutionary dynamics of transposable elements during silkworm domestication.
Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes.
The evolutionary history of human populations in Europe.
Analysis of the conserved NER helicases (XPB and XPD) and UV-induced. DNA damage in Hydra.
Characterization of four new mitogenomes from Ocypodoidea & Grapsoidea, and phylomitogenomic insights into thoracotreme evolution.
Comparison of two complete mitochondrial genomes from Perlodidae (Plecoptera: Perloidea) and the family-level phylogenetic implications of Perloidea.

Methods Mol Biol. 2018 ;1818 51-65

Transcriptome Profiling of Single Mouse Oocytes.

Maud Borensztein, Laurène Syx, Nicolas Servant, Edith Heard.

  Single-cell RNA-sequencing (scRNAseq) enables the detection and quantification of mature RNAs in an individual cell. Assessing single cell transcriptomes can circumvent the limited amount of starting material obtained in oocytes or embryos, in particular when working with mutant mice. Here we outline our scRNAseq protocol to study mouse oocyte transcriptomes, derived from Tang et al., Nat Methods 6(5):377-382, 2009 . The method describes the different steps from single cell isolation and cDNA amplification to high-throughput sequencing. The bioinformatics pipeline used to analyze and compare genome-wide gene expression between individual oocytes is then described.

Keywords:  Gene expression; Maternal pool; Single-cell RNA-sequencing; Single-cell bioinformatics pipeline

DOI:  https://doi.org/10.1007/978-1-4939-8603-3_7
Genes Genomics. 2018 Jun 30.

Evolutionary dynamics of transposable elements during silkworm domestication.

Min-Jin Han, Hong-En Xu, Xiao-Min Xiong, Hua-Hao Zhang.

  Although there are some documented examples on population dynamics of transposable elements (TEs) in model organisms, the evolutionary dynamics of TEs in domesticated species has not been systematically investigated. The objective of this study is to understand population dynamics of TEs during silkworm domestication. In this work, using transposon-display we examined the polymorphism of seven TE families [they represent about 59% of silkworm (Bombyx mori) total TE content] in four domesticated silkworm populations and one wild silkworm population. Maximum likelihood (ML) was used to estimate selection pressure. Population differentiation and structure were performed by using AMOVA analysis and program DISTRUCT, respectively. The results of transposon-display showed that significant differentiation occurred between the domesticated silkworm and wild silkworm. These TEs have experienced expansions and fixation in the domesticated silkworm but not in wild silkworm. Furthermore, the ML results indicated that purifying selection of TEs in the domesticated silkworm were significantly weaker than that in the wild silkworm. Interestingly, an adaptation insertion induced by BmMITE-2 was found, and this insertion can reduce the polymorphism of the flanking regions of its neighboring COQ7 gene. Our results suggested that TEs expanded and were fixed in the domesticated silkworm might result from demographic effects and artificial selection during domestication. We concluded that the data presented in this study have general implication in animal and crop improvements as well as in domestication of new species.

Keywords:  Domestication; Evolutionary dynamics; Silkworm; Transposable elements; Weak selection

DOI:  https://doi.org/10.1007/s13258-018-0713-1
Mol Phylogenet Evol. 2018 Jun 28. pii: S1055-7903(18)30055-1. [Epub ahead of print]

Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes.

Juan E Uribe, Rafael Zardoya, Nicolas Puillandre.

With more than 5,000 species, Conoidea is one of the most diversified superfamilies of Gastropoda. Recently, the family-level classification of these venomous predator snails has undergone substantial changes, on the basis of a phylogenetic tree reconstructed combining partial mitochondrial and nuclear gene sequences, and up to 16 families are now recognized. However, phylogenetic relationships among these families remain largely unresolved. Here, we sequenced 20 complete or nearly complete mitochondrial (mt) genomes, which were combined with mt genomes available in GenBank to construct a dataset that included representatives of 80% of the known families, although for some we had only one species or genus as representative. Most of the sequenced conoidean mt genomes shared a constant genome organization, and observed rearrangements were limited exclusively to tRNA genes in a few lineages. Phylogenetic trees were reconstructed using probabilistic methods. Two main monophyletic groups, termed "Clade A" and "Clade B", were recovered with strong support within a monophyletic Conoidea. Clade A (including families Clavatulidae, Horaiclavidae, Turridae s.s., Terebridae, Drilliidae, Pseudomelatomidae, and Cochlespiridae) was composed of four main lineages, one of which was additionally supported by a rearrangement in the gene order. Clade B (including families Conidae, Borsoniidae, Clathurellidae, Mangeliidae, Raphitomidae, and Mitromorphidae) was composed of five main lineages. The reconstructed phylogeny rejected the monophyly of Clavatulidae, Horaiclavidae, Turridae, Pseudomelatomidae, and Conidae, indicating that several of the currently accepted families may be ill-defined. The reconstructed tree also revealed new phylogenetic positions for genera characterized as tentative (Gemmuloborsonia, Lucerapex, and Leucosyrinx), enigmatic (Marshallena) or challenging to place (Fusiturris), which will potentially impact the classification of the Conoidea.

DOI: https://doi.org/10.1016/j.ympev.2018.06.037
Curr Opin Genet Dev. 2018 Jun 27. pii: S0959-437X(18)30058-3. [Epub ahead of print]53 21-27

The evolutionary history of human populations in Europe.

Iosif Lazaridis.

I review the evolutionary history of human populations in Europe with an emphasis on what has been learned in recent years through the study of ancient DNA. Human populations in Europe ∼430-39kya (archaic Europeans) included Neandertals and their ancestors, who were genetically differentiated from other archaic Eurasians (such as the Denisovans of Siberia), as well as modern humans. Modern humans arrived to Europe by ∼45kya, and are first genetically attested by ∼39kya when they were still mixing with Neandertals. The first Europeans who were recognizably genetically related to modern ones appeared in the genetic record shortly thereafter at ∼37kya. At ∼15kya a largely homogeneous set of hunter-gatherers became dominant in most of Europe, but with some admixture from Siberian hunter-gatherers in the eastern part of the continent. These hunter-gatherers were joined by migrants from the Near East beginning at ∼8-9kya: Anatolian farmers settled most of mainland Europe, and migrants from the Caucasus reached eastern Europe, forming steppe populations. After ∼5kya there was migration from the steppe into mainland Europe and vice versa. Present-day Europeans (ignoring the long-distance migrations of the modern era) are largely the product of this Bronze Age collision of steppe pastoralists with Neolithic farmers.

DOI: https://doi.org/10.1016/j.gde.2018.06.007
Biochim Biophys Acta. 2018 Jun 27. pii: S0304-4165(18)30181-8. [Epub ahead of print]

Analysis of the conserved NER helicases (XPB and XPD) and UV-induced. DNA damage in Hydra.

Alisha A Galande, Nusrat Perween, Masafumi Saijo, Saroj S Ghaskadbi, Surendra Ghaskadbi.

   BACKGROUND: Nucleotide excision repair (NER) pathway is an evolutionarily conserved mechanism of genome maintenance. It detects and repairs distortions in DNA double helix. Xeroderma Pigmentosum group B (XPB) and group D (XPD) are important helicases in NER and are also critical subunits of TFIIH complex. We have studied XPB and XPD for the first time from the basal metazoan Hydra which exhibits lack of organismal senescence.
METHODS: In silico analysis of proteins was performed using MEGA 6.0, Clustal Omega, Swiss Model, etc. Gene expression was studied by in situ hybridization and qRT-PCR. Repair of CPDs was studied by DNA blot assay. Interactions between proteins were determined by co- immunoprecipitation. HyXPB and HyXPD were cloned in pET28b, overexpressed and helicase activity of purified proteins was checked.
RESULTS: In silico analysis revealed presence of seven classical helicase motifs in HyXPB and HyXPD. Both proteins revealed polarity-dependent helicase activity. Hydra repairs most of the thymine dimers induced by UVC (500 J/m2) by 72 h post-UV exposure. HyXPB and HyXPD transcripts, localized all over the body column, remained unaltered post-UV exposure indicating their constitutively expression. In spite of high levels of sequence conservation, XPB and XPD failed to rescue defects in human XPB- and XPD-deficient cell lines. This was due to their inability to get incorporated into the TFIIH multiprotein complex.
CONCLUSIONS: Present results along with our earlier work on DNA repair proteins in Hydra bring out the utility of Hydra as model system to study evolution of DNA repair mechanisms in metazoans.

Keywords:  Hydra; XPB; XPD.; cyclobutane pyrimidine dimers; nucleotide excision repair; ultraviolet light

DOI:  https://doi.org/10.1016/j.bbagen.2018.06.017
Gene. 2018 Jun 27. pii: S0378-1119(18)30749-2. [Epub ahead of print]

Characterization of four new mitogenomes from Ocypodoidea & Grapsoidea, and phylomitogenomic insights into thoracotreme evolution.

Jianqin Chen, Yuhui Xing, Wenjia Yao, Chenling Zhang, Zhenhua Zhang, Gongcheng Jiang, Zhengfeng Ding.

  Four new complete mitochondrial genomes (mitogenomes) from the two superfamilies Ocypodoidea and Grapsoidea were sequenced, which represented Uca (Gelasimus) borealis (Ocypodidae: Ucinae), Dotilla wichmani (Dotillidae), Metopograpsus quadridentatus (Grapsidae: Grapsinae), and Gaetice depressus (Varunidae: Gaeticinae). All of the mitogenomes shared the complete set of 37 mitochondrial genes. Mitogenome lengths were 15,659, 15,600, 15,517, and 16,288 bp, respectively, with A + T contents of 69.41%, 68.46%, 70.30%, and 72.96%, respectively. Comparative genomic analyses suggested that they exhibited different genomic rearrangements. In particular, G. depressus shared a major rearrangement pattern present in Eriocheir crabs, while the remainder shared the brachyuran ground genomic rearrangement patterns. Phylomitogenomic inferences provided new evidence for the strongly supported nesting of Thoracotremata within Heterotremata clades. A close phylogenetic relationship was observed between Varunidae and Macrophthalmidae crabs, and between Dotillidae and Grapsidae crabs, which was consistent with mitochondrial genomic rearrangement similarities. Altogether, these results suggest the presence of reciprocal paraphyly for Ocypodoidea and Grapsoidea.

Keywords:  Genomic rearrangement; Grapsoidea; Mitochondrial genome; Ocypodoidea; Phylogenetic relationship; Thoracotremata

DOI:  https://doi.org/10.1016/j.gene.2018.06.088
Gene. 2018 Jun 27. pii: S0378-1119(18)30754-6. [Epub ahead of print]

Comparison of two complete mitochondrial genomes from Perlodidae (Plecoptera: Perloidea) and the family-level phylogenetic implications of Perloidea.

Ying Wang, Jinjun Cao, Dávid Murányi, Weihai Li.

  To obtain a better understanding of the mitochondrial genome in Perlodidae and the phylogeny of Perloidea, we sequenced two perlodid mitochondrial genomes and present comparative analyses in the family Perlodidae. Our results show that genome organization, base composition, codon usage and non-coding and overlapping regions, the sequences of mitochondrial transcription termination factor (DmTTF) and structural elements in control region were conserved in Perlodidae. The unique non-coding regions in COI-trnL2 and trnL2-COII were present in Perlodidae but were incomplete or absent from other stoneflies, and we also discuss the conservative property of the sequences between trnE and trnF, trnS1 and ND1. The secondary structure of tRNAs showed that the trnK, trnP, trnS1 and trnW were identical and the trnS1 could not be folded into typical secondary structure due to its absence of DHU arm. Phylogenetic implications supported that Chloroperlidae is a sister group to Perlodidae and the Perlidae is a sister group to the clade Chloroperlidae + Perlodidae. This study contributes to understanding the comparative mitogenomic analysis of Perlodidae and phylogenetic relationships within the Perloidea.

Keywords:  Mitochondrial genome; Perlodidae; Perloidea; Phylogeny; Stem-loop structure

DOI:  https://doi.org/10.1016/j.gene.2018.06.093