The evolution of vertebrate tetraspanins: gene loss, retention, and massive positive selection after whole genome duplications

<p>Abstract</p> <p>Background</p> <p>The vertebrate tetraspanin family has many features which make it suitable for preserving the imprint of ancient sequence evolution and amenable for phylogenomic analysis. So we believe that an in-depth analysis of the tetraspanin evolution not only provides more complete understanding of tetraspanin biology, but offers new insights into the influence of the two rounds of whole genome duplication (2R-WGD) at the origin of vertebrates.</p> <p>Results</p> <p>A detailed phylogeny of vertebrate tetraspanins was constructed by using multiple lines of information, including sequence-based phylogenetics, key structural features, intron configuration and genomic synteny. In particular, a total of 38 modern tetraspanin ortholog lineages in bony vertebrates have been identified and subsequently classified into 17 ancestral lineages existing before 2R-WGD. Based on this phylogeny, we found that the ohnolog retention rate of tetraspanins after 2R-WGD was three times as the average (a rate similar to those of transcription factors and protein kinases). This high rate didn't increase the tetrapanin family size, but changed the family composition, possibly by displacing vertebrate-specific gene lineages with the lineages conserved across deuterostomes. We also found that the period from 2R-WGD to recent time is controlled by gene losses. Meanwhile, positive selection has been detected on 80% of the branches right after 2R-WGDs, which declines significantly on both magnitude and extensity on the following speciation branches. Notably, the loss of mammalian RDS2 is accompanied by strong positive selection on mammalian ROM1, possibly due to gene loss-induced compensatory evolution.</p> <p>Conclusions</p> <p>First, different from transcription factors and kinases, high duplicate retention rate after 2R-WGD didn't increase the tetraspanin family size but just reshaped the family composition. Second, the evolution of tetraspanins right after 2R-WGD had been impacted by a massive wave of gene loss and positive selection on coding sequences. Third, the lingering effect of 2R-WGD on tetraspanin gene loss and positive selection might last for 300-400 million years.</p

Genome-wide identification and expression analysis of NF-Y gene family in tobacco (Nicotiana tabacum L.)

Abstract Nuclear factor Y (NF-Y) gene family is an important transcription factor composed of three subfamilies of NF-YA, NF-YB and NF-YC, which is involved in plant growth, development and stress response. In this study, 63 tobacco NF-Y genes (NtNF-Ys) were identified in Nicotiana tabacum L., including 17 NtNF-YAs, 30 NtNF-YBs and 16 NtNF-YCs. Phylogenetic analysis revealed ten pairs of orthologues from tomato and tobacco and 25 pairs of paralogues from tobacco. The gene structure of NtNF-YAs exhibited similarities, whereas the gene structure of NtNF-YBs and NtNF-YCs displayed significant differences. The NtNF-Ys of the same subfamily exhibited a consistent distribution of motifs and protein 3D structure. The protein interaction network revealed that NtNF-YC12 and NtNF-YC5 exhibited the highest connectivity. Many cis-acting elements related to light, stress and hormone response were found in the promoter of NtNF-Ys. Transcriptome analysis showed that more than half of the NtNF-Y genes were expressed in all tissues, and NtNF-YB9/B14/B15/B16/B17/B29 were specifically expressed in roots. A total of 15, 12, 5, and 6 NtNF-Y genes were found to respond to cold, drought, salt, and alkali stresses, respectively. The results of this study will lay a foundation for further study of NF-Y genes in tobacco and other Solanaceae plants

Overcoming Nanoscale Inhomogeneities in Thin-Film Perovskites via Exceptional Post-annealing Grain Growth for Enhanced Photodetection.

Antisolvent-assisted spin coating has been widely used for fabricating metal halide perovskite films with smooth and compact morphology. However, localized nanoscale inhomogeneities exist in these films owing to rapid crystallization, undermining their overall optoelectronic performance. Here, we show that by relaxing the requirement for film smoothness, outstanding film quality can be obtained simply through a post-annealing grain growth process without passivation agents. The morphological changes, driven by a vaporized methylammonium chloride (MACl)-dimethylformamide (DMF) solution, lead to comprehensive defect elimination. Our nanoscale characterization visualizes the local defective clusters in the as-deposited film and their elimination following treatment, which couples with the observation of emissive grain boundaries and excellent inter- and intragrain optoelectronic uniformity in the polycrystalline film. Overcoming these performance-limiting inhomogeneities results in the enhancement of the photoresponse to low-light (<0.1 mW cm-2) illumination by up to 40-fold, yielding high-performance photodiodes with superior low-light detection.The authors thank the EPSRC Plastic Electronics CDT (EP/ L016702/1) for financial support and provision of equipment resources. J.B. and T.D. acknowledge the QMUL-EPSRC Impact Accelerator Account for financial support. T.D. gratefully acknowledges the Stephen and Anna Hui Scholar- ship (Imperial College London) for financially supporting his doctoral studies. F.R., F.A.C., and S.W. acknowledge funding from the European Union’s Horizon 2020 research and Innovation programme under the Marie Skłodowska-Curie grant agreement number 721874 (SPM2.0) and from the UK National Measurement System via the Department for Business, Energy and Industrial Strategy. K.F. acknowledges a George and Lilian Schiff Studentship, Winton Studentship, the Engineering and Physical Sciences Research Council (EPSRC) studentship, Cambridge Trust Scholarship, and Robert Gardiner Scholarship. S.D.S. acknowledges the Royal Society and Tata Group (UF150033). The work has received funding from the European Research Council under the European Union’s Horizon 2020 research and Innovation programme (HYPERION, grant agreement no. 756962). S.D.S. acknowledges EPSRC (EP/R023980/1) for funding