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Limonius californicus, Limonius canus, Limonius infuscatus, Hadromorphus glaucus, Selatosomus aeripennis

ABSTRACT: Population genomic and phylogenetic analysis of three wireworm (Coleoptera: Elateridae) species

PROVIDER: PRJNA595620 | ENA |

REPOSITORIES: ENA

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Project description:Population genomic and phylogenetic analysis of three wireworm (Coleoptera: Elateridae) species

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RNA-Seq Based Reconstruction of the Phylogenetic Tree of the Genus Flaveria (Asteraceae)

Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.

2015-01-08 | E-GEOD-54339 | biostudies-arrayexpress

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Sphyracephala beccarii

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Sphyracephala beccarii. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.

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Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Teleopsis quinqueguttata. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes.

2015-12-11 | GSE75872 | GEO

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Sphyracephala beccarii

2015-12-11 | E-GEOD-75873 | biostudies-arrayexpress

Comparative Genomic Hybridization (CGH) reveals sex chromosome location and gene movement in stalk-eyed flies (family Diopsidae), Teleopsis quinqueguttata

Project description:We utilized Comparative Genomic Hybridization (CGH), using probes designed from de novo assembly of a testes transcriptome, to identify genes located on the sex chromosomes and autosomes of a stalk-eyed fly, Teleopsis quinqueguttata. Analysis of X chromosome gene content revealed the evolution of a neo-X chromosome that originated prior to the diversification of the family. Comparison of X-linkage across three species spanning the phylogenetic breadth of the family indicates abundant chromosomal gene movement, particularly for genes expressed exclusively in the testes. Two-condition experiment, female vs. male DNA, for one species with 3 biological replicates

2015-12-11 | E-GEOD-75872 | biostudies-arrayexpress

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