Journal articles: 'Avian W chromosome'

1

Rutkowska, Joanna, Malgorzata Lagisz, and Shinichi Nakagawa. "The long and the short of avian W chromosomes: no evidence for gradual W shortening." Biology Letters 8, no. 4 (March 14, 2012): 636–38. http://dx.doi.org/10.1098/rsbl.2012.0083.

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The well-established view of the evolution of sex chromosome dimorphism is of a gradual genetic and morphological degeneration of the hemizygous chromosome. Yet, no large-scale comparative analysis exists to support this view. Here, we analysed karyotypes of 200 bird species to test whether the supposed directional changes occur in bird sex chromosomes. We found no support for the view that W chromosomes gradually become smaller over evolutionary time. On the contrary, the length of the W chromosome can fluctuate over short time scales, probably involving both shortening and elongation of non-coding regions. Recent discoveries of near-identical palindromes and neo-sex chromosomes in birds may also contribute to the observed variation. Further studies are now needed to investigate how chromosome morphology relates to its gene content, and whether the changes in size were driven by selection.

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Ellegren, Hans, and Ariane Carmichael. "Multiple and Independent Cessation of Recombination Between Avian Sex Chromosomes." Genetics 158, no. 1 (May 1, 2001): 325–31. http://dx.doi.org/10.1093/genetics/158.1.325.

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Abstract Birds are characterized by female heterogamety; females carry the Z and W sex chromosomes, while males have two copies of the Z chromosome. We suggest here that full differentiation of the Z and W sex chromosomes of birds did not take place until after the split of major contemporary lineages, in the late Cretaceous. The ATP synthase α-subunit gene is now present in one copy each on the nonrecombining part of the W chromosome (ATP5A1W) and on the Z chromosome (ATP5A1Z). This gene seems to have evolved on several independent occasions, in different lineages, from a state of free recombination into two sex-specific and nonrecombining variants. ATP5A1W and ATP5A1Z are thus more similar within orders, relative to what W (or Z) are between orders. Moreover, this cessation of recombination apparently took place at different times in different lineages (estimated at 13, 40, and 65 million years ago in Ciconiiformes, Galliformes, and Anseriformes, respectively). We argue that these observations are the result of recent and traceable steps in the process where sex chromosomes gradually cease to recombine and become differentiated. Our data demonstrate that this process, once initiated, may occur independently in parallel in sister lineages.

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Rogers, Thea F., Tommaso Pizzari, and Alison E. Wright. "Multi-Copy Gene Family Evolution on the Avian W Chromosome." Journal of Heredity 112, no. 3 (March 24, 2021): 250–59. http://dx.doi.org/10.1093/jhered/esab016.

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Abstract The sex chromosomes often follow unusual evolutionary trajectories. In particular, the sex-limited chromosomes frequently exhibit a small but unusual gene content in numerous species, where many genes have undergone massive gene amplification. The reasons for this remain elusive with a number of recent studies implicating meiotic drive, sperm competition, genetic drift, and gene conversion in the expansion of gene families. However, our understanding is primarily based on Y chromosome studies as few studies have systematically tested for copy number variation on W chromosomes. Here, we conduct a comprehensive investigation into the abundance, variability, and evolution of ampliconic genes on the avian W. First, we quantified gene copy number and variability across the duck W chromosome. We find a limited number of gene families as well as conservation in W-linked gene copy number across duck breeds, indicating that gene amplification may not be such a general feature of sex chromosome evolution as Y studies would initially suggest. Next, we investigated the evolution of HINTW, a prominent ampliconic gene family hypothesized to play a role in female reproduction and oogenesis. In particular, we investigated the factors driving the expansion of HINTW using contrasts between modern chicken and duck breeds selected for different female-specific selection regimes and their wild ancestors. Although we find the potential for selection related to fecundity in explaining small-scale gene amplification of HINTW in the chicken, purifying selection seems to be the dominant mode of evolution in the duck. Together, this challenges the assumption that HINTW is key for female fecundity across the avian phylogeny.

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Rabenold, Patricia P., Walter H. Piper, Mark D. Decker, and Dennis J. Minchella. "Polymorphic minisatellite amplified on avian W chromosome." Genome 34, no. 3 (June 1, 1991): 489–93. http://dx.doi.org/10.1139/g91-074.

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Jeffrey's minisatellite probe 33.15, which screens dozens of hypervariable loci throughout the genome, detects female-specific fragments in stripe-backed wrens (Campylorhynchus nuchalis). HaeIII subdivides the single large female-specific fragment observed with other enzymes into a polymorphic suite of fragments of similar total molecular weight among patterns. Sex-linked HaeIII haplotypes are perfectly transmitted from mother to daughter but not to sons. These results suggest that the female-specific HaeIII fragments represent variable subunits of a single long tandem repetitive array composed of approximately 20-bp repetitive units located outside the pairing region of the W chromosome. That sex-linked fragments do not occur in the congener Campylorhynchus griseus suggests that their entrapment and amplification on the W chromosome in C. nuchalis occurred since the divergence of the two species.Key words: minisatellites, sex chromosome, W chromosome, amplification.

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Fridolfsson, Anna-Karin, and Hans Ellegren. "Molecular Evolution of the Avian CHD1 Genes on the Z and W Sex Chromosomes." Genetics 155, no. 4 (August 1, 2000): 1903–12. http://dx.doi.org/10.1093/genetics/155.4.1903.

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Abstract Genes shared between the nonrecombining parts of the two types of sex chromosomes offer a potential means to study the molecular evolution of the same gene exposed to different genomic environments. We have analyzed the molecular evolution of the coding sequence of the first pair of genes found to be shared by the avian Z (present in both sexes) and W (female-specific) sex chromosomes, CHD1Z and CHD1W. We show here that these two genes evolve independently but are highly conserved at nucleotide as well as amino acid levels, thus not indicating a female-specific role of the CHD1W gene. From comparisons of sequence data from three avian lineages, the frequency of nonsynonymous substitutions (Ka) was found to be higher for CHD1W (1.55 per 100 sites) than for CHD1Z (0.81), while the opposite was found for synonymous substitutions (Ks, 13.5 vs. 22.7). We argue that the lower effective population size and the absence of recombination on the W chromosome will generally imply that nonsynonymous substitutions accumulate faster on this chromosome than on the Z chromosome. The same should be true for the Y chromosome relative to the X chromosome in XY systems. Our data are compatible with a male-biased mutation rate, manifested by the faster rate of neutral evolution (synonymous substitutions) on the Z chromosome than on the female-specific W chromosome.

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6

Kretschmer, Rafael, Ricardo José Gunski, Analía del Valle Garnero, Thales Renato Ochotorena de Freitas, Gustavo Akira Toma, Marcelo de Bello Cioffi, Edivaldo Herculano Corrêa de Oliveira, Rebecca E. O’Connor, and Darren K. Griffin. "Chromosomal Analysis in Crotophaga ani (Aves, Cuculiformes) Reveals Extensive Genomic Reorganization and an Unusual Z-Autosome Robertsonian Translocation." Cells 10, no. 1 (December 22, 2020): 4. http://dx.doi.org/10.3390/cells10010004.

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Although cytogenetics studies in cuckoos (Aves, Cuculiformes) have demonstrated an interesting karyotype variation, such as variations in the chromosome morphology and diploid number, their chromosome organization and evolution, and relation with other birds are poorly understood. Hence, we combined conventional and molecular cytogenetic approaches to investigate chromosome homologies between chicken and the smooth-billed ani (Crotophaga ani). Our results demonstrate extensive chromosome reorganization in C. ani, with interchromosomal rearrangements involving macro and microchromosomes. Intrachromosomal rearrangements were observed in some macrochromosomes, including the Z chromosome. The most evolutionary notable finding was a Robertsonian translocation between the microchromosome 17 and the Z chromosome, a rare event in birds. Additionally, the simple short repeats (SSRs) tested here were preferentially accumulated in the microchromosomes and in the Z and W chromosomes, showing no relationship with the constitutive heterochromatin regions, except in the W chromosome. Taken together, our results suggest that the avian sex chromosome is more complex than previously postulated and revealed the role of microchromosomes in the avian sex chromosome evolution, especially cuckoos.

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Sundström, Hannah, Matthew T. Webster, and Hans Ellegren. "Is the Rate of Insertion and Deletion Mutation Male Biased?: Molecular Evolutionary Analysis of Avian and Primate Sex Chromosome Sequences." Genetics 164, no. 1 (May 1, 2003): 259–68. http://dx.doi.org/10.1093/genetics/164.1.259.

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Abstract The rate of mutation for nucleotide substitution is generally higher among males than among females, likely owing to the larger number of DNA replications in spermatogenesis than in oogenesis. For insertion and deletion (indel) mutations, data from a few human genetic disease loci indicate that the two sexes may mutate at similar rates, possibly because such mutations arise in connection with meiotic crossing over. To address origin- and sex-specific rates of indel mutation we have conducted the first large-scale molecular evolutionary analysis of indels in noncoding DNA sequences from sex chromosomes. The rates are similar on the X and Y chromosomes of primates but about twice as high on the avian Z chromosome as on the W chromosome. The fact that indels are not uncommon on the nonrecombining Y and W chromosomes excludes meiotic crossing over as the main cause of indel mutation. On the other hand, the similar rates on X and Y indicate that the number of DNA replications (higher for Y than for X) is also not the main factor. Our observations are therefore consistent with a role of both DNA replication and recombination in the generation of short insertion and deletion mutations. A significant excess of deletion compared to insertion events is observed on the avian W chromosome, consistent with gradual DNA loss on a nonrecombining chromosome.

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8

Sigeman, Hanna, Suvi Ponnikas, Pallavi Chauhan, Elisa Dierickx, M. de L. Brooke, and Bengt Hansson. "Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes." Proceedings of the Royal Society B: Biological Sciences 286, no. 1916 (November 27, 2019): 20192051. http://dx.doi.org/10.1098/rspb.2019.2051.

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Sex chromosomes have evolved from the same autosomes multiple times across vertebrates, suggesting that selection for recombination suppression has acted repeatedly and independently on certain genetic backgrounds. Here, we perform comparative genomics of a bird clade (larks and their sister lineage; Alaudidae and Panuridae) where multiple autosome–sex chromosome fusions appear to have formed expanded sex chromosomes. We detected the largest known avian sex chromosome (195.3 Mbp) and show that it originates from fusions between parts of four avian chromosomes: Z, 3, 4A and 5. Within these four chromosomes, we found evidence of five evolutionary strata where recombination had been suppressed at different time points, and show that stratum age explained the divergence rate of Z–W gametologs. Next, we analysed chromosome content and found that chromosome 3 was significantly enriched for genes with predicted sex-related functions. Finally, we demonstrate extensive homology to sex chromosomes in other vertebrate lineages: chromosomes Z, 3, 4A and 5 have independently evolved into sex chromosomes in fish (Z), turtles (Z, 5), lizards (Z, 4A), mammals (Z, 4A) and frogs (Z, 3, 4A, 5). Our results provide insights into and support for repeated evolution of sex chromosomes in vertebrates.

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9

Küpper, Clemens, Jakob Augustin, Scott Edwards, Tamás Székely, András Kosztolányi, Terry Burke, and Daniel E. Janes. "Triploid plover female provides support for a role of the W chromosome in avian sex determination." Biology Letters 8, no. 5 (May 30, 2012): 787–89. http://dx.doi.org/10.1098/rsbl.2012.0329.

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Two models, Z Dosage and Dominant W , have been proposed to explain sex determination in birds, in which males are characterized by the presence of two Z chromosomes, and females are hemizygous with a Z and a W chromosome. According to the Z Dosage model, high dosage of a Z-linked gene triggers male development, whereas the Dominant W model postulates that a still unknown W-linked gene triggers female development. Using 33 polymorphic microsatellite markers, we describe a female triploid Kentish plover Charadrius alexandrinus identified by characteristic triallelic genotypes at 14 autosomal markers that produced viable diploid offspring. Chromatogram analysis showed that the sex chromosome composition of this female was ZZW. Together with two previously described ZZW female birds, our results suggest a prominent role for a female determining gene on the W chromosome. These results imply that avian sex determination is more dynamic and complex than currently envisioned.

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10

Itoh, Yuichiro, Kathy Kampf, and Arthur P. Arnold. "Molecular cloning of zebra finch W chromosome repetitive sequences: evolution of the avian W chromosome." Chromosoma 117, no. 2 (October 31, 2007): 111–21. http://dx.doi.org/10.1007/s00412-007-0130-8.

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11

Sigeman, Hanna, Suvi Ponnikas, Elin Videvall, Hongkai Zhang, Pallavi Chauhan, Sara Naurin, and Bengt Hansson. "Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat." Genes 9, no. 8 (July 26, 2018): 373. http://dx.doi.org/10.3390/genes9080373.

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Non-recombining sex chromosomes (Y and W) accumulate deleterious mutations and degenerate. This poses a problem for the heterogametic sex (XY males; ZW females) because a single functional gene copy often implies less gene expression and a potential imbalance of crucial expression networks. Mammals counteract this by dosage compensation, resulting in equal sex chromosome expression in males and females, whereas birds show incomplete dosage compensation with significantly lower expression in females (ZW). Here, we study the evolution of Z and W sequence divergence and sex-specific gene expression in the common whitethroat (Sylvia communis), a species within the Sylvioidea clade where a neo-sex chromosome has been formed by a fusion between an autosome and the ancestral sex chromosome. In line with data from other birds, females had lower expression than males at the majority of sex-linked genes. Results from the neo-sex chromosome region showed that W gametologs have diverged functionally to a higher extent than their Z counterparts, and that the female-to-male expression ratio correlated negatively with the degree of functional divergence of these gametologs. We find it most likely that sex-linked genes are being suppressed in females as a response to W chromosome degradation, rather than that these genes experience relaxed selection, and thus diverge more, by having low female expression. Overall, our data of this unique avian neo-sex chromosome system suggest that incomplete dosage compensation evolves, at least partly, through gradual accumulation of deleterious mutations at the W chromosome and declining female gene expression.

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12

Peona, Valentina, Octavio M. Palacios-Gimenez, Julie Blommaert, Jing Liu, Tri Haryoko, Knud A. Jønsson, Martin Irestedt, Qi Zhou, Patric Jern, and Alexander Suh. "The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1833 (July 26, 2021): 20200186. http://dx.doi.org/10.1098/rstb.2020.0186.

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It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the ‘toxic-Y’ effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

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Pigozzi, M. I., and A. J. Solari. "Meiotic recombination in the ZW pair of a tinamid bird shows a differential pattern compared with neognaths." Genome 48, no. 2 (April 1, 2005): 286–90. http://dx.doi.org/10.1139/g04-117.

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The tinamid bird Nothura maculosa, along with other species of the order Tinamiformes and all of the existent ratites, form the infraclass Paleognathae, the most primitive living birds. Previous work has shown that in all studied Neognathae, the ZW pair shows strictly localized recombination in a very short pseudoautosomal region, while in paleognath birds, the ZW pairs have mostly free recombination. The present observations show that the ZW pair of N. maculosa has a recombination pattern departing from both neognaths and other Paleognath birds, as there is a single crossover but occurring at random points along a significant part of the long arm of the W chromosome. This recombination pattern agrees with the presence of intercalary and terminal heterochromatin in the W chromosome, suggesting an exceptional, additional step of recombination suppression.Key words: recombination, ZW pair, avian sex chromosomes, sex chromosome heteromorphism.

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14

Mank, Judith E., and Hans Ellegren. "Parallel divergence and degradation of the avian W sex chromosome." Trends in Ecology & Evolution 22, no. 8 (August 2007): 389–91. http://dx.doi.org/10.1016/j.tree.2007.05.003.

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15

Mayr, B., and H. Auer. "A method to induce Giemsa staining resistance of avian W chromosomes: detection of an additional W chromosome in a turkey." Genome 30, no. 3 (June 1, 1988): 395–98. http://dx.doi.org/10.1139/g88-068.

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A hypotonic treatment using a low osmolal solution (0.038 Os/kg) led to a poor staining of the W chromosome in all our investigated bird species (chicken, turkey, pheasant, goose, pigeon, bearded vulture, and barn owl). A turkey establishing a ZWW karyotype was detected.Key words: birds, W chromosome, differential Giemsa staining, ZWW karyotype.

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Purwaningrum, Medania, Herjuno Ari Nugroho, Machmud Asvan, Karyanti Karyanti, Bertha Alviyanto, Randy Kusuma, and Aris Haryanto. "Molecular techniques for sex identification of captive birds." Veterinary World 12, no. 9 (September 2019): 1506–13. http://dx.doi.org/10.14202/vetworld.2019.1506-1513.

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Background and Aim: Many avian species are considered sexually monomorphic. In monomorphic bird species, especially in young birds, sex is difficult to identify based on an analysis of their external morphology. Accurate sex identification is essential for avian captive breeding and evolutionary studies. Methods with varying degrees of invasiveness such as vent sexing, laparoscopic surgery, steroid sexing, and chromosome inspection (karyotyping) are used for sex identification in monomorphic birds. This study aimed to assess the utility of a non-invasive molecular marker for gender identification in a variety of captive monomorphic birds, as a strategy for conservation. Materials and Methods: DNA was isolated from feather samples from 52 individuals representing 16 species of 11 families indigenous to both Indonesia and elsewhere. We amplified the chromodomain helicase DNA-binding (CHD) gene using polymerase chain reaction with MP, NP, and PF primers to amplify introns with lengths that differ between the CHD-W and the CHD-Z genes, allowing sex discrimination because the W chromosome is exclusively present in females. Results: Molecular bird sexing confirmed 33 females and 19 males with 100% accuracy. We used sequencing followed by alignment on one protected bird species (Probosciger aterrimus). Conclusion: Sex identification may be accomplished noninvasively in birds, because males only have Z sex chromosomes, whereas females have both Z and W chromosomes. Consequently, the presence of a W-unique DNA sequence identifies an individual as female. Sexing of birds is vital for scientific research, and to increase the success rate of conservation breeding programs.

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Degrandi, Tiago M., Analía del Valle Garnero, Patricia C. M. O'Brien, Malcolm A. Ferguson-Smith, Rafael Kretschmer, Edivaldo H. C. de Oliveira, and Ricardo J. Gunski. "Chromosome Painting in Trogon s. surrucura (Aves, Trogoniformes) Reveals a Karyotype Derived by Chromosomal Fissions, Fusions, and Inversions." Cytogenetic and Genome Research 151, no. 4 (2017): 208–15. http://dx.doi.org/10.1159/000471782.

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Trogons are forest birds with a wide distribution, being found in Africa, Asia, and America, and are included in the order Trogoniformes, family Trogonidae. Phylogenetic studies using molecular data have not been able to determine the phylogenetic relationship among the different genera of trogons. So far, no cytogenetic data for these birds exist. Hence, the aim of this study was to characterize the karyotype of Trogon surrucura surrucura by means of classical and molecular cytogenetics. We found a diploid chromosome number of 2n = 82, similar to most birds, with several derived features compared to chicken and the putative ancestral avian karyotype. T. s. surrucura showed 3 pairs of microchromosomes bearing 18S rDNA clusters. The Z and W sex chromosomes were of similar size but could readily be identified by morphological differences. Using chromosome painting with whole chromosome probes from Gallus gallus and Leucopternis albicollis, we found that the chromosomes homologous to chicken chromosomes 2 and 5 correspond to 2 different pairs in T. s. surrucura and L. albicollis, due to the occurrence of centric fissions. Paracentric inversions were detected in the segment homologous to chicken chromosome 1q, and we confirmed the recurrence of breakpoints when our results were compared to other species of birds already analyzed by FISH or by in silico genome assembly.

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Wright, Alison E., Peter W. Harrison, Stephen H. Montgomery, Marie A. Pointer, and Judith E. Mank. "INDEPENDENT STRATUM FORMATION ON THE AVIAN SEX CHROMOSOMES REVEALS INTER-CHROMOSOMAL GENE CONVERSION AND PREDOMINANCE OF PURIFYING SELECTION ON THE W CHROMOSOME." Evolution 68, no. 11 (August 29, 2014): 3281–95. http://dx.doi.org/10.1111/evo.12493.

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Parks, Kristen P., Heather Seidle, Nathan Wright, Jeffrey B. Sperry, Pawel Bieganowski, Konrad Howitz, Dennis L. Wright, and Charles Brenner. "Altered specificity of Hint-W123Q supports a role for Hint inhibition by ASW in avian sex determination." Physiological Genomics 20, no. 1 (December 15, 2004): 12–14. http://dx.doi.org/10.1152/physiolgenomics.00204.2004.

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Hint is a universally conserved, dimeric AMP-lysine hydrolase encoded on the avian Z chromosome. Tandemly repeated on the female-specific W chromosome, Asw encodes a potentially sex-determining, dominant-negative Hint dimerization partner whose substrate-interacting residues were specifically altered in evolution. To test the hypothesis that Gln127 of Asw is responsible for depression and/or alteration of Hint enzyme activity, a corresponding mutant was created in the chicken Hint homodimer, and a novel substrate was developed that links reversal of AMP-lysine modification to aminomethylcoumarin release. Strikingly, the Hint-W123Q substitution reduced kcat/ Km for AMP-lysine hydrolysis 17-fold, while it increased specificity for AMP- para-nitroaniline hydrolysis by 160-fold. The resulting 2,700-fold switch in enzyme specificity suggests that Gln127 could be the dominant component of Asw dominant negativity in avian feminization.

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Liang, Shao-jie, Ming-xia Chen, Chun-qi Gao, Hui-chao Yan, Guo-long Zhang, and Xiu-qi Wang. "Sex identification of pigeons using polymerase chain reaction analysis with simple DNA extraction." Avian Biology Research 12, no. 2 (March 4, 2019): 45–48. http://dx.doi.org/10.1177/1758155919832141.

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Sex identification plays an important role in avian production. Hitherto, it is difficult to distinguish the sexes of monomorphic birds based on their external features. The chromo-helicase-DNA-binding genes contain CHD-W gene and CHD-Z gene, which are located on the W chromosome and Z chromosome, respectively. Since CHD-W gene is unique to females, the polymerase chain reaction can be used for sex identification. However, extracting DNA procedures for verifying the sex is tedious and expensive. To address these disadvantages, the objective of this study was to develop a simple DNA extraction assay to efficiently process blood, liver, and feather samples. The results showed that 2% dimethylsulfoxide was suitable for processing blood, and phosphate-buffered saline was suitable for processing liver and feather samples. The specific primers were designed, and the length of the targets is 474 bp on Z chromosome and 319 bp on W chromosome. The pigeons were identified as females based on the presence of two bands on the gel, and as males based on the presence of one band. Taken together, our results suggested that feather samples were more appropriate than blood or liver for sex identification of pigeons. Compared to the traditional DNA extraction, this method shortened the assay time and reduced the cost.

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Lemos Costa, Alice, Cassiane Furlan Lopes, Marcelo Santos de Souza, Suziane Alves Barcellos, Pâmela Giordani Vielmo, Ricardo José Gunski, and Analía Del Valle Garnero. "Comparative cytogenetics in three species of Wood-Warblers (Aves: Passeriformes: Parulidae) reveal divergent banding patterns and chromatic heterogeneity for the W chromosome." Caryologia 74, no. 1 (July 20, 2021): 43–51. http://dx.doi.org/10.36253/caryologia-839.

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Chromosomal rearrangements are an important process in the evolution of species. It is assumed that these rearrangements occur near repetitive sequences and heterochromatic regions. Avian karyotypes have diverse chromosomal band patterns and have been used as the parameters for phylogenetic studies. Although the group has a high diversity of species, no more than 12% has been analyzed cytogenetically, and the Parulidae family are extremely underrepresented in these studies. The aim of this study was to detect independent or simultaneous chromosomal rearrangements, and also to analyze chromosomal banding convergences and divergences of three Wood-Warblers species (Myiothlypis leucoblephara, Basileuterus culicivorus, and Setophaga pitiayumi). Our CBG-band results reveal an unusual W sex chromosome in the three studied species, containing a telomeric euchromatic region. The GTG and RBG bands identify specific regions in the macrochromosomes involved in the rearrangements. Cytogenetic data confirm the identification of speciation processes at the karyotypic of this group.

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Griffiths, Richard, and Peter W. H. Holland. "A novel avian W chromosome DNA repeat sequence in the lesser black-backed gull (Larus fuscus)." Chromosoma 99, no. 4 (August 1990): 243–50. http://dx.doi.org/10.1007/bf01731699.

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Backström, Niclas, Helene Ceplitis, Sofia Berlin, and Hans Ellegren. "Gene Conversion Drives the Evolution of HINTW, an Ampliconic Gene on the Female-Specific Avian W Chromosome." Molecular Biology and Evolution 22, no. 10 (June 22, 2005): 1992–99. http://dx.doi.org/10.1093/molbev/msi198.

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Hori, Tetsuya, Shuichi Asakawa, Yuichiro Itoh, Nobuyoshi Shimizu, and Shigeki Mizuno. "Wpkci, Encoding an Altered Form of PKCI, Is Conserved Widely on the Avian W Chromosome and Expressed in Early Female Embryos: Implication of Its Role in Female Sex Determination." Molecular Biology of the Cell 11, no. 10 (October 2000): 3645–60. http://dx.doi.org/10.1091/mbc.11.10.3645.

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Two W chromosome–linked cDNA clones, p5fm2 and p5fm3, were obtained from a subtracted (female minus male) cDNA library prepared from a mixture of undifferentiated gonads and mesonephroi of male or female 5-d (stages 26–28) chicken embryos. These two clones were demonstrated to be derived from the mRNA encoding an altered form of PKC inhibitor/interacting protein (PKCI), and its gene was namedWpkci. The Wpkci gene reiterated ∼40 times tandemly and located at the nonheterochromatic end of the chicken W chromosome. The W linkage and the moderate reiteration ofWpkci were conserved widely in Carinatae birds. The chicken PKCI gene, chPKCI, was shown to be a single-copy gene located near the centromere on the long arm of the Z chromosome. Deduced amino acid sequences of Wpkci and chPKCI showed ∼65% identity. In the deduced sequence of Wpkci, the HIT motif, which is essential for PKCI function, was absent, but the α-helix region, which was conserved among the PKCI family, and a unique Leu- and Arg-rich region, were present. Transcripts from bothWpkci and chPKCI genes were present at significantly higher levels in 3- to 6-d (stages 20–29) embryos. These transcripts were detected in several embryonic tissues, including undifferentiated left and right gonads. When the green fluorescent protein–fused form of Wpkci was expressed in male chicken embryonic fibroblast, it was located almost exclusively in the nucleus. A model is presented suggesting that Wpkci may be involved in triggering the differentiation of ovary by interfering with PKCI function or by exhibiting its unique function in the nuclei of early female embryos.

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Yang, Shang-Fang, Chia-Wei Lu, Cheng-Te Yao, and Chih-Ming Hung. "To Trim or Not to Trim: Effects of Read Trimming on the De Novo Genome Assembly of a Widespread East Asian Passerine, the Rufous-Capped Babbler (Cyanoderma ruficeps Blyth)." Genes 10, no. 10 (September 23, 2019): 737. http://dx.doi.org/10.3390/genes10100737.

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Trimming low quality bases from sequencing reads is considered as routine procedure for genome assembly; however, we know little about its pros and cons. Here, we used empirical data to examine how read trimming affects assembled genome quality and computational time for a widespread East Asian passerine, the rufous-capped babbler (Cyanoderma ruficeps Blyth). We found that scaffolds assembled from raw reads were always longer than those from trimmed ones, whereas computational times for the former were sometimes much longer than the latter. Nevertheless, assembly completeness showed little difference among the trimming strategies. One should determine the optimal trimming strategy based on what the assembled genome will be used for. For example, to identify single nucleotide polymorphisms (SNPs) associated with phenotypic evolution, applying PLATANUS to gently trim reads would yield a reference genome with a slightly shorter scaffold length (N50 = 15.64 vs. 16.89 Mb) than the raw reads, but would save 75% of computational time. We also found that chromosomes Z, W, and 4A of the rufous-capped babbler were poorly assembled, likely due to a recently fused, neo-sex chromosome. The rufous-capped babbler genome with long scaffolds and quality gene annotation can provide a good system to study avian ecological adaptation in East Asia.

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Xu, Luohao, and Qi Zhou. "The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized." Genes 11, no. 10 (September 25, 2020): 1126. http://dx.doi.org/10.3390/genes11101126.

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Sex chromosomes are unique genomic regions with sex-specific or sex-biased inherent patterns and are expected to be more frequently subject to sex-specific selection. Substantial knowledge on the evolutionary patterns of sex-linked genes have been gained from the studies on the male heterogametic systems (XY male, XX female), but the understanding of the role of sex-specific selection in the evolution of female-heterogametic sex chromosomes (ZW female, ZZ male) is limited. Here we collect the W-linked genes of 27 birds, covering the three major avian clades: Neoaves (songbirds), Galloanserae (chicken), and Palaeognathae (ratites and tinamous). We find that the avian W chromosomes exhibit very conserved gene content despite their independent evolution of recombination suppression. The retained W-linked genes have higher dosage-sensitive and higher expression level than the lost genes, suggesting the role of purifying selection in their retention. Moreover, they are not enriched in ancestrally female-biased genes, and have not acquired new ovary-biased expression patterns after becoming W-linked. They are broadly expressed across female tissues, and the expression profile of the W-linked genes in females is not deviated from that of the homologous Z-linked genes. Together, our new analyses suggest that female-specific positive selection on the avian W chromosomes is limited, and the gene content of the W chromosomes is mainly shaped by purifying selection.

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Bellott, Daniel W., Helen Skaletsky, Ting-Jan Cho, Laura Brown, Devin Locke, Nancy Chen, Svetlana Galkina, et al. "Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators." Nature Genetics 49, no. 3 (January 30, 2017): 387–94. http://dx.doi.org/10.1038/ng.3778.

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Montell, Hannah, Anna-Karin Fridolfsson, and Hans Ellegren. "Contrasting Levels of Nucleotide Diversity on the Avian Z and W Sex Chromosomes." Molecular Biology and Evolution 18, no. 11 (November 1, 2001): 2010–16. http://dx.doi.org/10.1093/oxfordjournals.molbev.a003742.

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Blagoveschensky, I. Yu, A. L. Sazanova, V. A. Stekol’nikova, K. A. Fomichev, O. Yu Barkova, M. N. Romanov, and A. A. Sazanov. "Investigation of pseudoautosomal and bordering regions in avian Z and W chromosomes with the use of large insert genomic BAC clones." Russian Journal of Genetics 47, no. 3 (March 2011): 272–78. http://dx.doi.org/10.1134/s1022795411020050.

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Valentin, C., R. West, and C. Herr. "269 THE ENHANCEMENT OF THE SENSITIVITY OF A PCR-BASED AVIAN SEX DETERMINATION ASSAY." Reproduction, Fertility and Development 20, no. 1 (2008): 214. http://dx.doi.org/10.1071/rdv20n1ab269.

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For over a decade it has been possible to externally sex monomorphic birds using PCR. A major drawback of the protocol developed by Richard Griffiths is that DNA from at least 20 000 cells is needed (Griffiths et al. 1996 Proc. Royal Soc. London B 263, 1249–1254). Our study attempted to decrease the number of cells required. A sequence within the chromobox-helicase-DNA-binding (CHD) gene, located on the sex chromosomes of all avian species, was amplified. The sequence lengths were 362 and 354 base pairs for the CHD-W and CHD-Z, respectively. The polyacrylamide gel electrophoresis (PAGE) purified primers used were 5´-TCTGCATCGCTAAATCCTTT-3´ and 5´-CTCCCAAGGATGAGRAAYTG-3´ (2.5 µm) (IDT, Inc., San Jose, CA, USA). All assays used Taq DNA polymerase (2.7 U) (M0273L, New England BioLabs, Ipswich, MA, USA) and deoxyribonucleotides (5 µm) (C01581, GenScript Corp, Piscataway, NJ, USA). Lymphocytes from chickens (Gallus domesticus) (10 cells/2 µL) were used as the DNA source for all experiments. Assays were run with positive and negative DNA controls. The DNA was replicated in a Corbett Rapid Thermocycler (Model FTS-IS, Corbett Research, Sydney, Australia) in 20 µL volumes with an annealing temperature of 48�C. All of the PCR products were separated using PAGE. An 8% gel (17:1, con- to bis-acrylamide) with 10 mm TRIS (pH 8) was formed in an agarose gel chamber (M12 Electrophoresis Unit, Edvotek, Bethesda, MD, USA) under Ar. The gel was placed in 10 mm TRIS (pH 8) in the electrophoresis apparatus and the PCR products were added to wells. The applied voltage was 200 and the duration was 2 h (PS500ST, Hoefer Scientific Instruments, San Francisco, CA, USA). The gel was stained for 30 min in 1.25 µm ethidium bromide in 100 mL of 10 mm TRIS (pH 8). Destaining was carried out over 45 min in 100 mL of H2O. The gel was viewed using a transilluminator (3–300, Fotodyne, Hartland, WI, USA) and photographed with an Olympus digital camera. An initial experiment established Griffiths' assay in our lab. Results were consistent with published data, albeit with the same troubling signal-to-noise problems. No signals were observed in assays with less than 20 000 cells. The next experiment compared the use of Griffiths' amplification buffer to a buffer we developed, Bart: 50 mm barbital, 1% dextran T-500, 50 mm KCl, 2.5 mm MgCl2, and 0.035% 2-mercaptoethanol. Signals were produced and a working assay was established with only 10 cells needed, significantly fewer cells than the 20 000 cells necessary for Griffiths' protocol. It was possible to increase the number of productive replication cycles from 35 to 45 without generation of noise. In fact, use of Bart eliminated primer-generated noise, leaving only sexing bands in the gel. Interestingly, when Bart was used with 20 000 cells, no signals were observed. Assays incorporating Bart were run in triplicate and signals were consistently observed. Reduction in the number of cells required for avian sex determination provides potential applications for the sexing of embryos or sexing from a single down feather. Our assay makes sex determination prior to hormonal treatment simple. We are currently replacing the use of the CHD gene with a conserved W-specific sequence.

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Smeds, Linnéa, Vera Warmuth, Paulina Bolivar, Severin Uebbing, Reto Burri, Alexander Suh, Alexander Nater, et al. "Evolutionary analysis of the female-specific avian W chromosome." Nature Communications 6, no. 1 (June 4, 2015). http://dx.doi.org/10.1038/ncomms8330.

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Li, Jing, Jilin Zhang, Jing Liu, Yang Zhou, Cheng Cai, Luohao Xu, Xuelei Dai, et al. "A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals." GigaScience 10, no. 1 (January 2021). http://dx.doi.org/10.1093/gigascience/giaa142.

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Abstract Background Ducks have a typical avian karyotype that consists of macro- and microchromosomes, but a pair of much less differentiated ZW sex chromosomes compared to chickens. To elucidate the evolution of chromosome architectures between ducks and chickens, and between birds and mammals, we produced a nearly complete chromosomal assembly of a female Pekin duck by combining long-read sequencing and multiplatform scaffolding techniques. Results A major improvement of genome assembly and annotation quality resulted from the successful resolution of lineage-specific propagated repeats that fragmented the previous Illumina-based assembly. We found that the duck topologically associated domains (TAD) are demarcated by putative binding sites of the insulator protein CTCF, housekeeping genes, or transitions of active/inactive chromatin compartments, indicating conserved mechanisms of spatial chromosome folding with mammals. There are extensive overlaps of TAD boundaries between duck and chicken, and also between the TAD boundaries and chromosome inversion breakpoints. This suggests strong natural selection pressure on maintaining regulatory domain integrity, or vulnerability of TAD boundaries to DNA double-strand breaks. The duck W chromosome retains 2.5-fold more genes relative to chicken. Similar to the independently evolved human Y chromosome, the duck W evolved massive dispersed palindromic structures, and a pattern of sequence divergence with the Z chromosome that reflects stepwise suppression of homologous recombination. Conclusions Our results provide novel insights into the conserved and convergently evolved chromosome features of birds and mammals, and also importantly add to the genomic resources for poultry studies.

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Bravo, Gustavo A., C. Jonathan Schmitt, and Scott V. Edwards. "What Have We Learned from the First 500 Avian Genomes?" Annual Review of Ecology, Evolution, and Systematics 52, no. 1 (September 8, 2021). http://dx.doi.org/10.1146/annurev-ecolsys-012121-085928.

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The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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"Proposed role of W chromosome inactivadon and the absence of dosage compensation in avian sex determination." Proceedings of the Royal Society of London. Series B: Biological Sciences 258, no. 1351 (October 22, 1994): 79–82. http://dx.doi.org/10.1098/rspb.1994.0145.

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"First gene on the avian W chromosome (CHD) provides a tag for universal sexing of non-ratite birds." Proceedings of the Royal Society of London. Series B: Biological Sciences 263, no. 1377 (December 22, 1996): 1635–41. http://dx.doi.org/10.1098/rspb.1996.0239.

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Gruszczyñska, J., A. Alama, M. Mi¹sko, P. Florczuk - Ko³omyja, and B. Grzegrzó³ka. "Molecular identification of sex in the monomorphic breed of pigeons." Indian Journal of Animal Research, of (March 26, 2019). http://dx.doi.org/10.18805/ijar.b-951.

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In many avian species, especially in monomorphic species and breeds, sex identification creates a serious problem, as they do not show any phenotypic differences. One of such breeds is the Wroclaw Meat Pigeon. In this study, molecular identification of sex with P2 and P8 primers used for the CHD1 (chromo-helicase-DNA-binding-protein) gene amplification was performed. Peripheral blood samples were analyzed from 46 birds, and their DNA was isolated with the phenol-chloroform method. The fragments (370 bp CHD1-Z; 350 bp CHD1-W) obtained from the PCR were cut with the BsuRI. Only the sequence in the Z chromosome was cut into fragments of 305 and 65 bp by the restriction enzyme. The difference between CHD1-Z and CHD1-W was visualized in 3% agarose gel. A single band was identified as male, whereas two bands (plus 1 invisible) were identified as female. Consequently, 23 specimens in each sex were identified.

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Journal articles on the topic 'Avian W chromosome'

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