Gene Expression Modification by an Autosomal Inversion Associated With Three Male Mating Morphs

Chromosomal inversions are structural rearrangements that frequently provide genomic substrate for phenotypic diversity. In the ruff Philomachus pugnax, three distinct male reproductive morphs (Independents, Satellites and Faeders) are genetically determined by a 4.5 Mb autosomal inversion. Here we test how this stable inversion polymorphism affects gene expression in males during the lekking season. Gene expression may be altered through disruptions at the breakpoints and the accumulation of mutations due to suppressed recombination. We used quantitative PCR to measure expression of 11 candidate inversion genes across three different tissues (liver, adrenal glands and gonads) and tested for allelic imbalance in four inversion genes across 12 males of all three morphs (8 Independents, 2 Satellites, 2 Faeders). We quantified transcripts of CENPN, an essential gene disrupted by the inversion at the proximal breakpoint, at different exons distributed near and across the breakpoint region. Consistent with dosage dependent gene expression for the breakpoint gene CENPN, we found that expression in Independents was broadly similar for transcripts segments from inside and outside the inversion regions, whereas for Satellites and Faeders, transcript segments outside of the inversion showed at least twofold higher expression than those spanning over the breakpoint. Within the inversion, observed expression differences for inversion males across all four genes with allele-specific primers were consistent with allelic imbalance. We further analyzed gonadal expression of two inversion genes, HSD17B2 and SDR42E1, along with 12 non-inversion genes related to steroid metabolism and signaling in 25 males (13 Independents, 7 Satellites, 5 Faeders). Although we did not find clear morph differentiation for many individual genes, all three morphs could be separated based on gene expression differences when using linear discriminant analysis (LDA), regardless of genomic location (i.e., inside or outside of the inversion). This was robust to the removal of genes with the highest loadings. Pairwise correlations in the expression of genes showed significant correlations for 9–18 pairs of genes within morphs. However, between morphs, we only found a single association between genes SDR42E1 and AROM for Independents and Satellites. Our results suggest complex and wide-ranging changes in gene expression caused by structural variants.

Genome-Wide Analyses of the Relict Gull (Larus Relictus) Insights Into Evolutionary Implications

BackgroundThe relict gull (Larus relictus), one of the least known Aves, was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. relictus are lacking, which limits the study of its evolution and its conservation.ResultsIn this study, based on the Illumina and PacBio sequencing platforms, we successfully assembled the genome of L. relictus, the first reference genome of the genus Larus. The size of the final assembled genome was 1.21 Gb, with a contig N50 of 8.11 Mb. A total of 18,454 protein-coding genes were predicted from the assembly results, with 16,967 (91.94%) of these genes annotated. The genome contained 92.52 Mb of repeat sequence, accounting for 7.63% of the assembly. The phylogenetic tree was constructed using 7,339 single-copy orthologous genes, which showed Charadriiformes located at the basal position and Philomachus pugnax as the closest relative of L. relictus. The divergence time between L. relictus and P. pugnax was ~68.44 Mya. The population dynamics of the Ordos breeding subpopulation in Hongjian Nur is a good confirmation that these birds are suffering from habitat loss and fragmentation.ConclusionsThis assembled genome will be a valuable genomic resource for a range of genomic and conservation studies of L. relictus and helps to establish a foundation for further studies investigating whether the other three breeding subpopulations have combined with the Ordos breeding subpopulation. As the species is threatened by habitat loss and fragmentation, actions to protect L. relictus are suggested to improve the fragmentation of breeding populations.

Gli uccelli della provincia di Novara (Piemonte, Italia): distribuzione, abbondanza e stato di conservazione

<p>In questo lavoro viene riportato un elenco commentato degli uccelli noti per la provincia di Novara (1.340 km2) aggiornato al 31/12/2016 e vengono forniti dati di sintesi relativi alle attività di monitoraggio condotte in anni recenti (2009-2016). I dati sono stati raccolti sia attraverso revisione bibliografica sia attraverso attività di ricerca diretta sul campo. L’avifauna della provincia di Novara annovera o ha annoverato (dal 1860 al 2016) 304 specie delle quali 135 nidificanti certe o probabili in tempi recenti (dopo il 2000), 85 di interesse comunitario (Allegato I della Direttiva “Uccelli”), 116 SPEC - <em>Species of European Conservation Concern</em> secondo BirdLife International e 53 inserite nella <em>European Red List of Birds.</em> L’area è di importanza europea e/o nazionale per la nidificazione di specie di interesse conservazionistico quali <em>Egretta</em> <em>garzetta</em> (650-1.100 nidi), <em>Nycticorax</em> <em>nycticorax</em> (200-300 nidi), <em>Botaurus</em> <em>stellaris</em> (5-7 maschi cantori), <em>Ciconia nigra</em> (1-2 coppie), <em>Ciconia</em> <em>ciconia</em> (4-6 coppie), <em>Himantopus</em> <em>himantopus</em> (300-500 coppie), <em>Vanellus vanellu</em>s (500-600 coppie), <em>Columba oenas</em> (20-30 coppie), nonché per la migrazione di <em>Philomachus pugnax</em> (5.000-7.000 ind.) e <em>Tringa glareola</em> (500-1.500 ind.). Negli ultimi anni (2009-2016) si segnalano in particolare: la nidificazione accertata per la prima volta nel Novarese di<em> Ardea alba,</em> <em>Galerida cristata</em> e <em>Lullula arborea</em>; il ritorno di <em>Burhinus oedicnemus</em> e <em>Chlidonias niger</em> in periodo riproduttivo dopo decenni di assenza; la colonizzazione da parte di <em>Dryocopus</em> <em>martius</em> degli ambienti forestali di collina e di pianura.</p>