ZNF280BY and ZNF280AY: autosome derived Y-chromosome gene families in Bovidae

<p>Abstract</p> <p>Background</p> <p>Recent progress in exploring the Y-chromosome gene content in humans, mice and cats have suggested that "autosome-to-Y" transposition of the male fertility genes is a recurrent theme during the mammalian Y-chromosome evolution. These transpositions are lineage-dependent. The purpose of this study is to investigate the lineage-specific Y-chromosome genes in bovid.</p> <p>Results</p> <p>We took a direct testis cDNA selection strategy and discovered two novel gene families, <it>ZNF280BY </it>and <it>ZNF280AY</it>, on the bovine (<it>Bos taurus</it>) Y-chromosome (BTAY), which originated from the transposition of a gene block on the bovine chromosome 17 (BTA17) and subsequently amplified. Approximately 130 active <it>ZNF280BY </it>loci (and ~240 pseudogenes) and ~130 pseudogenized <it>ZNF280AY </it>copies are present over the majority of the male-specific region (MSY). Phylogenetic analysis indicated that both gene families fit with the "birth-and-death" model of evolution. The active <it>ZNF280BY </it>loci share high sequence similarity and comprise three major genomic structures, resulted from insertions/deletions (indels). Assembly of a 1.2 Mb BTAY sequence in the MSY ampliconic region demonstrated that <it>ZNF280BY </it>and <it>ZNF280AY</it>, together with <it>HSFY </it>and <it>TSPY </it>families, constitute the major elements within the repeat units. The <it>ZNF280BY </it>gene family was found to express in different developmental stages of testis with sense RNA detected in all cell types of the seminiferous tubules while the antisense RNA detected only in the spermatids. Deep sequencing of the selected cDNAs revealed that different loci of <it>ZNF280BY </it>were differentially expressed up to 60-fold. Interestingly, different copies of the <it>ZNF280AY </it>pseudogenes were also found to differentially express up to 10-fold. However, expression level of the <it>ZNF280AY </it>pseudogenes was almost 6-fold lower than that of the <it>ZNF280BY </it>genes. <it>ZNF280BY </it>and <it>ZNF280AY </it>gene families are present in bovid, but absent in other mammalian lineages.</p> <p>Conclusions</p> <p><it>ZNF280BY </it>and <it>ZNF280AY </it>are lineage-specific, multi-copy Y-gene families specific to <it>Bovidae</it>, and are derived from the transposition of an autosomal gene block. The temporal and spatial expression patterns of <it>ZNF280BY</it>s in testis suggest a role in spermatogenesis. This study offers insights into the genomic organization of the bovine MSY and gene regulation in spermatogenesis, and provides a model for studying evolution of multi-copy gene families in mammals.</p

Sequencing technologies and genome sequencing

The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research

Palaeocene–Eocene miospores from the Chicxulub impact crater, Mexico. Part 1:spores and gymnosperm pollen

In the summer of 2016, the International Ocean Discovery Program (IODP) Expedition 364 coredthrough the post-impact strata of the end-Cretaceous Chicxulub impact crater, Mexico. Core sampleswere collected from the post-impact successions for terrestrial palynological analysis, yielding a rareDanian to Ypresian high-resolution palynological assemblage. This record constitutes one of the firstPalaeocene and Ypresian palynological assemblages from Central America or Mexico, representing amore coastal lowland palaeoenvironment than previous studies from mainland Mexico. Although theabundance of pollen and spores is very low in the Palaeocene carbonates, abundance increases in themore organic-rich shale layers representing the Palaeocene–Eocene Thermal Maximum (PETM) andlater Ypresian. The spores and gymnosperm pollen identified from IODP 364, although rare comparedto the angiosperm pollen, are a diverse mix of cosmopolitan taxa, as well as some characteristic of fossilCentral American assemblages (e.g. Selaginellaceae), and others previously identified from thePaleogene northern Gulf of Mexico coastal plain. The assemblage generally indicates the presence ofnearby moist to seasonally dry lowland tropical forest, with some taxa suggestive of higher elevationforests. Ephedroid pollen grains may be indicative of the presence of more arid conditions

Palynology from ground zero of the Chicxulub impact, southern Gulf of Mexico

Palynological analysis of Site M0077A in the Chicxulub impact crater has yielded a record of the immediate Cretaceous/Paleogene (K/Pg) recovery from ground zero of the end-Cretaceous mass extinction, followed by a record of the Paleocene–Eocene Thermal Maximum (PETM) and later Ypresian (Eocene), including the Early Eocene Climatic Optimum (EECO). Eight specimens of the dinoflagellate cyst Trithyrodinium evittii have been observed near the base of the K/Pg transitional unit; these likely representa post-impact dinoflagellate disaster recovery assemblage deposited within several days following the impact, although the possibility that some or all of the T. evittii specimens are reworked Maastrichtian cysts cannot be fully excluded. Despite high-resolution sampling of the lowermost Paleocene successions, the oldest identifiable terrestrial palynomorphs observed in the Site M0077A core, two specimens of Deltoidospora fern spores, occur at least c. 200,000 years after the impact. Other than these occurrences, the Paleocene section is nearly barren in terms of palynomorphs, likely a result of poor preservation of organic material combined with a long recovery time for vegetation in the vicinity of the crater. Pollen and fungal spore concentrations spike in an anoxic dark shale deposited during the PETM around 56 Ma, with a diverse pollen assemblage indicating the presence of a coastal shrubby tropical forest in the geographic vicinity, likely in the Yucatan Peninsula to the south. In the marine realm, this interval is characterized by thermophilic assemblages of dinoflagellate cysts. Stratigraphically constrained cluster analysis identified four statistically robust sample clusters in the lower Eocene successions, with Malvacipollis spp. and Milfordia spp. abundances driving the highest average dissimilarity between clusters. A second notable spike in palynological concentrations above the PETM section may represent another early Eocene hyperthermal event. Pollen and plant spore concentrations generally increased during the EECO, associated with increases in terrestrial input during basin infilling.Also funded by the Research Foundation Flanders (FWO grant 12Z6618N)</p

Coprolites as evidence for plant–animal interaction in Siluro–Devonian terrestrial ecosystems

A FEW remarkable finds document the colonization of land by animals and plants in the mid-Palaeozoic1–3, but much rarer is unequivocal evidence for plant–animal interaction4,5. Here we announce the discovery of coprolites (fossil faeces) in Upper Silurian (412 Myr) and Lower Devonian (390 Myr) rocks from the Welsh Borderland that pre-date examples of similar composition in the Carboniferous by about 90 million years6,7. The majority consist predominantly of undigested land-plant spores with varying proportions of cuticles, tubes and less readily identifiable (presumably plant) material. Because coeval animal fossils of suitable size are carnivores8, direct evidence for the coprolite producers is lacking, but we speculate that they could have been spore eaters (and hence the earliest example of herbivory of higher plants) or detritivores similar to modern millipedes. In either case, they demonstrate the cycling of primary productivity in early terrestrial ecosystems

Paleocene–Eocene palynomorphs from the Chicxulub impact crater, Mexico.Part 2: angiosperm pollen

At the end of the Cretaceous Period, an asteroid collided with the Earth and formed the Chicxulub impact structure on the Yucatan Platform. International Ocean Discovery Program (IODP) Expedition 364 drilled into the peak ring of the Chicxulub impact crater. The post-impact section of the core was sampled for terrestrial palynological analysis, yielding a high-resolution record ranging from the early Paleocene to the earliest Eocene (Ypresian), including a black shale deposited during the Paleocene–Eocene Thermal Maximum (PETM). The IODP 364 core provides the first record of floral recovery following the K–Pg mass extinction from inside the Chicxulub impact crater. The systematic taxonomy of the angiosperm pollen provided here follows a separate publication describing the systematic paleontology of the plant spores and gymnosperm pollen from the IODP 364 core (Smith et al. 2019). The Paleocene section of the core is nearly barren, but with unusually high relative abundances of the angiosperm pollen Chenopodipollis sp. A (comparable to the Amaranthaceae), possibly indicating an estuarine pollen source. Pollen recovery is higher in the PETM section, and variable but generally increasing in the later Ypresian section, with excellent preservation in several samples. Estimated absolute ages of several potentially useful regional biostratigraphic events are provided. One new genus (Scabrastephanoporites) and five new species (Brosipollis reticulatus, Echimonocolpites chicxulubensis, Psilastephanocolporites hammenii, Scabrastephanoporites variabilis, and Striatopollisgrahamii) are formally described