Extreme axial equalization and wide distribution of recombination nodules in the primitive ZW pair of Rhea americana (Aves, Ratitae)

Germline-restricted chromosomes of the songbirds

Germline-restricted chromosomes (GRCs) are present in the genomes of germline cells and absent from somatic cells. A GRC is found in all species of the songbirds (Passeri) and in none of the other bird orders studied to date. This indicates that GRC originated in the common ancestor of the songbirds. The germline-restricted chromosome is permanently absent from somatic cells of the songbird, while female germline cells usually contain two copies of GRC and male ones have one copy. In females, GRCs undergo synapsis and restricted recombination in their terminal regions during meiotic prophase. In males, it is almost always eliminated from spermatocytes. Thus, GRC is inherited almost exclusively through the maternal lineage. The germline-restricted chromosome is a necessary genomic element in the germline cells of songbirds. To date, the GRC genetic composition has been studied in four species only. Some GRC genes are actively expressed in female and male gonads, controlling the development of germline cells and synthesis of the proteins involved in the organization of meiotic chromosomes. Songbird species vary in GRC size and genetic composition. The GRC of each bird species consists of amplified and modified copies of genes from the basic genome of that species. The level of homology between GRCs of different species is relatively low, indicating a high rate of genetic evolution of this chromosome. Transmission through the maternal lineage and suppression of the recombination contribute significantly to the accelerated evolution of GRCs. One may suggest that the rapid coordinated evolution between the GRC genes and the genes of the basic genome in the songbirds might be responsible for the explosive speciation and adaptive radiation of this most species-rich and diverse infraorder of birds.

Highly Conservative Pattern of Sex Chromosome Synapsis and Recombination in Neognathae Birds

We analyzed the synapsis and recombination between Z and W chromosomes in the oocytes of nine neognath species: domestic chicken Gallus gallus domesticus, grey goose Anser anser, black tern Chlidonias niger, common tern Sterna hirundo, pale martin Riparia diluta, barn swallow Hirundo rustica, European pied flycatcher Ficedula hypoleuca, great tit Parus major and white wagtail Motacilla alba using immunolocalization of SYCP3, the main protein of the lateral elements of the synaptonemal complex, and MLH1, the mismatch repair protein marking mature recombination nodules. In all species examined, homologous synapsis occurs in a short region of variable size at the ends of Z and W chromosomes, where a single recombination nodule is located. The remaining parts of the sex chromosomes undergo synaptic adjustment and synapse non-homologously. In 25% of ZW bivalents of white wagtail, synapsis and recombination also occur at the secondary pairing region, which probably resulted from autosome-sex chromosome translocation. Using FISH with a paint probe specific to the germline-restricted chromosome (GRC) of the pale martin on the oocytes of the pale martin, barn swallow and great tit, we showed that both maternally inherited songbird chromosomes (GRC and W) share common sequences.

Evolution and meiotic organization of heteromorphic sex chromosomes

The evolution of heteromorphic sex chromosomes has occurred independently many times in different lineages. The differentiation of sex chromosomes leads to dramatic changes in sequence composition and function and guides the evolutionary trajectory and utilization of genes in pivotal sex determination and reproduction roles. In addition, meiotic recombination and pairing mechanisms are key in orchestrating the resultant impact, retention and maintenance of heteromorphic sex chromosomes, as the resulting exposure of unpaired DNA at meiosis triggers ancient repair and checkpoint pathways. In this review, we summarize the different ways in which sex chromosome systems are organized at meiosis, how pairing is affected, and differences in unpaired DNA responses. We hypothesize that lineage specific differences in meiotic organization is not only a consequence of sex chromosome evolution, but that the establishment of epigenetic changes on sex chromosomes contributes toward their evolutionary conservation.

Broad-scale recombination pattern in the primitive bird Rhea americana (Ratites, Palaeognathae)

Birds have genomic and chromosomal features that make them an attractive group to analyze the evolution of recombination rate and the distribution of crossing over. Yet, analyses are biased towards certain species, especially domestic poultry and passerines. Here we analyze for the first time the recombination rate and crossover distribution in the primitive ratite bird, Rhea americana (Rheiformes, Palaeognathae). Using a cytogenetic approach for in situ mapping of crossovers we found that the total genetic map is 3050 cM with a global recombination rate of 2.1 cM/Mb for female rheas. In the five largest macrobivalents there were 3 or more crossovers in most bivalents. Recombination rates for macrobivalents ranges between 1.8-2.1 cM/Mb and the physical length of their synaptonemal complexes is highly predictive of their genetic lengths. The crossover rate at the pseudoautosomal region is 2.1 cM/Mb, similar to those of autosomal pairs 5 and 6 and only slightly higher compared to other macroautosomes. It is suggested that the presence of multiple crossovers on the largest macrobivalents is a feature common to many avian groups, irrespective of their position throughout phylogeny. These data provide new insights to analyze the heterogeneous recombination landscape of birds.

Sex-specific recombination maps for individual macrochromosomes in the Japanese quail (Coturnix japonica)

Meiotic recombination in the Japanese quail was directly studied by immunolocalization of mutL homolog 1 (MLH1), a mismatch repair protein of mature recombination nodules. In total, 15,862 crossovers were scored along the autosomal synaptonemal complexes in 308 meiotic nuclei from males and females. Crossover frequencies calculated from MLH1 foci show wide similitude between males and females with slightly higher number of foci in females. From this analysis, we predict that the sex-averaged map length of the Japanese quail is 2580 cM, with a genome-wide recombination rate of 1.9 cM/Mb. MLH1 focus mapping along the six largest bivalents showed few intersex differences in the distribution of crossovers along with variant patterns in metacentric and acrocentric macrobivalents. These results provide valuable information to complement linkage map analysis in the species while providing insight into our understanding of the mechanisms of crossover distribution along chromosome arms.

Tracing the evolution of amniote chromosomes

A great deal of diversity in chromosome number and arrangement is observed across the amniote phylogeny. Understanding how this diversity is generated is important for determining the role of chromosomal rearrangements in generating phenotypic variation and speciation. Gaining this understanding is achieved by reconstructing the ancestral genome arrangement based on comparisons of genome organization of extant species. Ancestral karyotypes for several amniote lineages have been reconstructed, mainly from cross-species chromosome painting data. The availability of anchored whole genome sequences for amniote species has increased the evolutionary depth and confidence of ancestral reconstructions from those made solely from chromosome painting data. Nonetheless, there are still several key lineages where the appropriate data required for ancestral reconstructions is lacking. This review highlights the progress that has been made towards understanding the chromosomal changes that have occurred during amniote evolution and the reconstruction of ancestral karyotypes.

Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches

Sex chromosome evolution is usually seen as a process that, once initiated, will inevitably progress toward an advanced stage of degeneration of the nonrecombining chromosome. However, despite evidence that avian sex chromosome evolution was initiated >100 Ma, ratite birds have been trapped in an arrested stage of sex chromosome divergence. We performed RNA sequencing of several tissues from male and female ostriches and assembled the transcriptome de novo. A total of 315 Z-linked genes fell into two categories: those that have equal expression level in the two sexes (for which Z–W recombination still occurs) and those that have a 2-fold excess of male expression (for which Z–W recombination has ceased). We suggest that failure to evolve dosage compensation has constrained sex chromosome divergence in this basal avian lineage. Our results indicate that dosage compensation is a prerequisite for, not only a consequence of, sex chromosome evolution.

Diverse stages of sex-chromosome differentiation in tinamid birds: evidence from crossover analysis in Eudromia elegans and Crypturellus tataupa

All extant birds share the same sex-chromosome system: ZZ males and ZW females with striking differences in the stages of sex-chromosome differentiation between the primitive palaeognathus ratites and the large majority of avian species grouped within neognaths. Evolutionarily close to ratites is the neotropical order Tinamiformes that has been scarcely explored regarding their ZW pair morphology and constitution. Tinamous, when compared to ratites, constitute a large group among Palaeognathae, therefore, exploring the extent of homology between the Z and W chromosomes in this group might reveal key features on the evolution of the avian sex chromosomes. We mapped MLH1 foci that are crossover markers on pachytene bivalents to determine the size and localization of the homologous region shared by the Z and W chromosomes in two tinamous: Eudromia elegans and Crypturellus tataupa. We found that the homologous (pseudoautosomal) region differ significantly in size between these two species. They both have a single recombination event on the long arm of the acrocentric Z and W chromosomes. However, in E. elegans the pseudoautosomal region occupies one-fourth of the W chromosome, while in C. tataupa it is restricted to the tip of the long arm of the W. The W chromosomes in these two species differ in their heterochromatin content: in E. elegans it shows a terminal euchromatic segment and in C. tataupa is completely heterochromatic. These results show that tinamous have ZW pairs with more diversified stages of differentiation compared to ratites. Finally, the idea that the avian proto-sex chromosomes started to diverge from the end of the long arm towards the centromere of an acrocentric pair is discussed.

Synapsis and recombination in inversion heterozygotes

Inversion heterozygotes are expected to suffer from reduced fertility and a high incidence of chromosomally unbalanced gametes due to recombination within the inverted region. Non-homologous synapsis of the inverted regions can prevent recombination there and diminish the deleterious effects of inversion heterozygosity. The choice between non-homologous and homologous synapsis depends on the size of inversion, its genetic content, its location in relation to the centromere and telomere, and genetic background. In addition, there is a class of inversions in which homologous synapsis is gradually replaced by non-homologous synapsis during meiotic progression. This process is called synaptic adjustment. The degree of synaptic adjustment depends critically on the presence and location of the COs (crossovers) within the inversion loop. Only bivalents without COs within the loop and those with COs in the middle of the inversion can be completely adjusted and became linear.

Different origins of bird and reptile sex chromosomes inferred from comparative mapping of chicken Z-linked genes

Recent progress of chicken genome projects has revealed that bird ZW and mammalian XY sex chromosomes were derived from different autosomal pairs of the common ancestor; however, the evolutionary relationship between bird and reptilian sex chromosomes is still unclear. The Chinese soft-shelled turtle (Pelodiscus sinensis) exhibits genetic sex determination, but no distinguishable (heteromorphic) sex chromosomes have been identified. In order to investigate this further, we performed molecular cytogenetic analyses of this species, and thereby identified ZZ/ZW-type micro-sex chromosomes. In addition, we cloned reptile homologues of chicken Z-linked genes from three reptilian species, the Chinese soft-shelled turtle and the Japanese four-striped rat snake (Elaphe quadrivirgata), which have heteromorphic sex chromosomes, and the Siam crocodile (Crocodylus siamensis), which exhibits temperature-dependent sex determination and lacks sex chromosomes. We then mapped them to chromosomes of each species using FISH. The linkage of the genes has been highly conserved in all species: the chicken Z chromosome corresponded to the turtle chromosome 6q, snake chromosome 2p and crocodile chromosome 3. The order of the genes was identical among the three species. The absence of homology between the bird Z chromosome and the snake and turtle Z sex chromosomes suggests that the origin of the sex chromosomes and the causative genes of sex determination are different between birds and reptiles.

The molecular basis of chromosome orthologies and sex chromosomal differentiation in palaeognathous birds

Palaeognathous birds (Struthioniformes and Tinamiformes) have morphologically conserved karyotypes and less differentiated ZW sex chromosomes. To delineate interspecific chromosome orthologies in palaeognathous birds we conducted comparative chromosome painting with chicken (Gallus gallus, GGA) chromosome 1-9 and Z chromosome paints (GGA1-9 and GGAZ) for emu, double-wattled cassowary, ostrich, greater rhea, lesser rhea and elegant crested tinamou. All six species showed the same painting patterns: each probe was hybridized to a single pair of chromosomes with the exception that the GGA4 was hybridized to the fourth largest chromosome and a single pair of microchromosomes. The GGAZ was also hybridized to the entire region of the W chromosome, indicating that extensive homology remains between the Z and W chromosomes on the molecular level. Comparative FISH mapping of four Z- and/or W-linked markers, the ACO1/IREBP, ZOV3 and CHD1 genes and the EE0.6 sequence, revealed the presence of a small deletion in the proximal region of the long arm of the W chromosome in greater rhea and lesser rhea. These results suggest that the karyotypes and sex chromosomes of palaeognathous birds are highly conserved not only morphologically, but also at the molecular level; moreover, palaeognathous birds appear to retain the ancestral lineage of avian karyotypes.

Comparison of the Z and W sex chromosomal architectures in elegant crested tinamou (Eudromia elegans) and ostrich (Struthio camelus) and the process of sex chromosome differentiation in palaeognathous birds

To clarify the process of avian sex chromosome differentiation in palaeognathous birds, we performed molecular and cytogenetic characterization of W chromosome-specific repetitive DNA sequences for elegant crested tinamou (Eudromia elegans, Tinamiformes) and constructed comparative cytogenetic maps of the Z and W chromosomes with nine chicken Z-linked gene homologues for E. elegans and ostrich (Struthio camelus, Struthioniformes). A novel family of W-specific repetitive sequences isolated from E. elegans was found to be composed of guanine- and cytosine-rich 293-bp elements that were tandemly arrayed in the genome as satellite DNA. No nucleotide sequence homologies were found for the Struthioniformes and neognathous birds. The comparative cytogenetic maps of the Z and W chromosomes of E. elegans and S. camelus revealed that there are partial deletions in the proximal regions of the W chromosomes in the two species, and the W chromosome is more differentiated in E. elegans than in S. camelus. These results suggest that a deletion firstly occurred in the proximal region close to the centromere of the acrocentric proto-W chromosome and advanced toward the distal region. In E. elegans, the W-specific repeated sequence elements were amplified site-specifically after deletion of a large part of the W chromosome occurred.

A novel family of repetitive DNA sequences amplified site-specifically on the W chromosomes in Neognathous birds

A novel family of repetitive DNA sequences was molecularly cloned from ApaI-digested genomic DNA of two Galliformes species, Japanese quail (Coturnix japonica) and guinea fowl (Numida meleagris), and characterized by chromosome in-situ hybridization and filter hybridization. Both the repeated sequence elements produced intensely painted signals on the W chromosomes, whereas they weakly hybridized to whole chromosomal regions as interspersed-type repetitive sequences. The repeated elements of the two species had high similarity of nucleotide sequences, and cross-hybridized to chromosomes of two other Galliformes species, chicken (Gallus gallus) and blue-breasted quail (Coturnix chinensis). The nucleotide sequences were conserved in three other orders of Neognathous birds, the Strigiformes, Gruiformes and Falconiformes, but not in Palaeognathous birds, the Struthioniformes and Tinamiformes, indicating that the repeated sequence elements were amplified on the W chromosomes in the lineage of Neognathous birds after the common ancestor diverged into the Palaeognathae and Neognathae. They are components of the W heterochromatin in Neognathous birds, and a good molecular cytogenetic marker for estimating the phylogenetic relationships and for clarifying the origin of the sex chromosome heterochromatin and the process of sex chromosome differentiation in birds.

How did the platypus get its sex chromosome chain? A comparison of meiotic multiples and sex chromosomes in plants and animals

The duck-billed platypus is an extraordinary mammal. Its chromosome complement is no less extraordinary, for it includes a system in which ten sex chromosomes form an extensive meiotic chain in males. Such meiotic multiples are unprecedented in vertebrates but occur sporadically in plant and invertebrate species. In this paper, we review the evolution and formation of meiotic multiples in plants and invertebrates to try to gain insights into the origin of the platypus meiotic multiple. We describe the meiotic hurdles that translocated mammalian chromosomes face, which make longer chains disadvantageous in mammals, and we discuss how sex chromosomes and dosage compensation might have affected the evolution of sex-linked meiotic multiples. We conclude that the evolutionary conservation of the chain in monotremes, the structural properties of the translocated chromosomes and the highly accurate segregation at meiosis make the platypus system remarkably different from meiotic multiples in other species. We discuss alternative evolutionary models, which fall broadly into two categories: either the chain is the result of a sequence of translocation events from an ancestral pair of sex chromosomes (Model I) or the entire chain came into being at once by hybridization of two populations with different chromosomal rearrangements sharing monobrachial homology (Model II).

Meiotic recombination in the ZW pair of a tinamid bird shows a differential pattern compared with neognaths

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.

DMRT1 in a ratite bird: evidence for a role in sex determination and discovery of a putative regulatory element

Unlike mammals, birds have a ZZ male/ZW female sex-determining system. In most birds, the Z is large and gene rich, whereas the W is small and heterochromatic, but the ancient group of ratite birds are characterized by sex chromosomes that are virtually homomorphic. Any gene differentially present on the ratite Z and W is therefore a strong candidate for a sex-determining role. We have cloned part of the candidate bird sex-determining gene DMRT1 from the emu, a ratite bird, and have shown that it is expressed during the stages of development corresponding to gonadal differentiation in the chicken. The gene maps to the distal region of the Z short arm and is absent from the large W chromosome. Because most sequences on the emu W chromosome are shared with the Z, the Z-specific location constitutes strong evidence that differential dosage of DMRT1 is involved in sex determination in all birds. The sequence of emu DMRT1 has 88% homology with chicken DMRT1 and 65% with human DMRT1. Unexpectedly, an unexpressed 270-bp region in intron 3 of emu DMRT1 showed 90% homology with a sequence in the corresponding intron of human DMRT1. This extraordinarily high conservation across 300 million years of evolution suggests an important function, perhaps involved in control of DMRT1 expression and vertebrate sex determination.

Multiple and independent cessation of recombination between avian sex chromosomes

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 alpha-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.

Meiotic chromosomes: integrating structure and function

Meiotic chromosomes have been studied for many years, in part because of the fundamental life processes they represent, but also because meiosis involves the formation of homolog pairs, a feature which greatly facilitates the study of chromosome behavior. The complex events involved in homolog juxtaposition necessitate prolongation of prophase, thus permitting resolution of events that are temporally compressed in the mitotic cycle. Furthermore, once homologs are paired, the chromosomes are connected by a specific structure: the synaptonemal complex. Finally, interaction of homologs includes recombination at the DNA level, which is intimately linked to structural features of the chromosomes. In consequence, recombination-related events report on diverse aspects of chromosome morphogenesis, notably relationships between sisters, development of axial structure, and variations in chromatin status. The current article reviews recent information on these topics in an historical context. This juxtaposition has suggested new relationships between structure and function. Additional issues were addressed in a previous chapter (551).

Differentiation of Z and W chromosomes revealed by replication banding and FISH mapping of sex-chromosome-linked DNA markers in the cassowary (Aves, Ratitae)

We identified sex chromosomes of the double-wattled cassowary (Casuarius casuarius) by a replication banding method. The acrocentric Z chromosome, the fifth largest pair in males and slightly smaller W chromosome show no sign of heterochromatinization and share a nearly identical banding pattern in the distal half of the long arm. These chromosomes were further characterized by FISH with three probes linked either to Z or W chromosome in most avian species examined thus far. Contrary to the situation in the chicken, we obtained positive signals with Z-specific ZOV3 and W-specific EEO.6 in the distal region of both Z and W chromosomes. However, IREBP signals localized to the proximal half of the Z chromosome were not detected on the W chromosome. Thus, structural rearrangements such as deletions and inversions might have been the initial step of W chromosome differentiation from an ancestral homomorphic pair in this species.

The ZW pairs of two paleognath birds from two orders show transitional stages of sex chromosome differentiation

Pachytene oocytes from the two presumably most primitive orders (Paleognathae) among living birds were used to study the pairing behaviour and location of recombination nodules (RNs) in the sex pair. In the ratite Pterocnemia pennata (Rheiformes), the 42 analyzed ZW pairs show an average of 2.2 RNs distributed along 80% of the synaptonemal complex (SC) that covers the long arm of the acrocentric Z and W chromosomes in this homomorphic sex pair. In the tinamid Rynchotus rufescens (Tinamiformes), the 60 analyzed ZW pairs show an average of 1.35 RNs distributed along 66% of the SC covering most of the long arms of this visibly heteromorphic ZW pair. RNs are non-randomly distributed and show interference in both species, but in the tinamou they are restricted to a significantly smaller stretch. The discovery of an intermediate degree in the restriction of RN location, between the extremes of free recombination along most of the W in ratites and strict localization of a single RN in Neognath birds, suggests its relationship with the mechanism of sex chromosome differentiation among Aves.

Comparative painting reveals strong chromosome homology over 80 million years of bird evolution

Chickens and the great flightless emu belong to two distantly related orders of birds in the carinate and ratite subclasses that diverged at least 80 million years ago. In the first ZOO-FISH study between bird species, we hybridized single chromosome paints from the chicken (Gallus domesticus) onto the emu chromosomes. We found that the nine macrochromosomes show remarkable homology between the two species, indicating strong conservation of karyotype through evolution. One chicken macrochromosome (4) was represented by a macro- and a microchromosome in the emu, suggesting that microchromosomes and macrochromosomes are interconvertible. The chicken Z chromosome paint hybridized to the emu Z and most of the W, confirming that ratite sex chromosomes are largely homologous; the centromeric region of the W which hybridized weakly may represent the location of the sex determining gene(s).

Distribution of crossing over on mouse synaptonemal complexes using immunofluorescent localization of MLH1 protein

We have used immunofluorescent localization to examine the distribution of MLH1 (MutL homolog) foci on synaptonemal complexes (SCs) from juvenile male mice. MLH1 is a mismatch repair protein necessary for meiotic recombination in mice, and MLH1 foci have been proposed to mark crossover sites. We present evidence that the number and distribution of MLH1 foci on SCs closely correspond to the number and distribution of chiasmata on diplotene-metaphase I chromosomes. MLH1 foci were typically excluded from SC in centromeric heterochromatin. For SCs with one MLH1 focus, most foci were located near the middle of long SCs, but near the distal end of short SCs. For SCs with two MLH1 foci, the distribution of foci was bimodal regardless of SC length, with most foci located near the proximal and distal ends. The distribution of MLH1 foci indicated interference between foci. We observed a consistent relative distance (percent of SC length in euchromatin) between two foci on SCs of different lengths, suggesting that positive interference between MLH1 foci is a function of relative SC length. The extended length of pachytene SCs, as compared to more condensed diplotene-metaphase I bivalents, makes mapping crossover events and interference distances using MLH1 foci more accurate than using chiasmata.