International Journal of Molecular Evolution and Biodiversity, 2025, Vol.15, No.1, 10-28 http://ecoevopublisher.com/index.php/ijmeb 12 turkey genome is slightly larger (~1.1 Gb), and a draft was published in 2010 by multi-platform sequencing and upgraded to the chromosome level in recent years (Barros et al., 2022). The Japanese quail genome is about 1.0 Gb, and a chromosome-level sequence has also been assembled. The genome sizes of Galliformes birds are relatively similar, ranging from 0.95 Gb to 1.3 Gb, which are significantly smaller than mammalian genomes. These high-quality genomic datasets provide a basis for cross-species comparisons, allowing us to examine the evolutionary differences of Galliformes species from a whole-genome scale. 2.2 Comparative analysis of genome size and chromosomal structure Galliformes birds have highly conserved karyotype characteristics: relatively few large chromosomes and a large number of microchromosomes coexist, which is one of the important characteristics of bird genomes. For example, the domestic chicken has 2n=78 (i.e., 39 pairs of chromosomes), including 8 pairs of macrochromosomes, 30 pairs of microchromosomes, and sex chromosomes ZW/ZZ. The chromosome composition of other Phasianidae species is roughly similar to that of the domestic chicken, although the specific chromosome number may differ slightly (such as turkey 2n=80). Comparison of the chromosome colinearity of different species revealed that most autosomes remain highly colinear within the Galliformes, and only a few chromosomes have undergone fusion or splitting. For example, a comparison of the chromosomes of the ring-necked pheasant and the domestic chicken showed that most of the chromosome structure of the pheasant is consistent with that of the domestic chicken, with rearrangements only in a few segments (He et al., 2020). A significant difference is the microchromosome region where the major histocompatibility complex (MHC) genes are located: compared with the red junglefowl, the ancestor of the domestic chicken, the pheasant has undergone three large inversion rearrangements in this region, forming a unique gene arrangement pattern. This structural variation suggests that the pheasant immune genome has undergone special evolutionary events that may affect its immune function. In general, the genome of Galliformes is quite conservative in terms of chromosomal macrostructure, and the genome size of each species is not much different, mostly about 1.0 Gb. However, local structural variation is still widespread, especially in certain trait-related regions and sex chromosomes. It is worth noting that sex chromosomes are highly heteromorphic in Galliformes birds, especially the W chromosome of females, which is severely degraded, carries very few genes, but is rich in repetitive sequences and transposons. Studies have shown that the transposable element density of chicken W chromosomes exceeds 55%, which is much higher than the average level of less than 10% in the genome, and contains more than half of the complete endogenous retroviral copies of the whole genome. This "repetitive sequence shelter" phenomenon makes the W chromosome an accumulation of harmful mutations, which may cause female individuals to carry a higher mutation load (Peona et al., 2021). At the same time, the length and composition of W chromosomes in different species also vary. For example, the W chromosome of domestic chicken carries about 40 Mb of sequence, while the W chromosome of turkey is smaller. These differences indicate that during the evolution of Galliformes, sex chromosomes have undergone rapid transposon expansion and sequence loss. In terms of minichromosomes, all species generally have about 30 pairs of minichromosomes, which are rich in genes, high in GC content, and low in repetitive sequences, and are gene-dense regions. However, it was not until recently that many minichromosomes were completely spliced out through long-read sequencing and graphical assembly. These new data help to discover the core genes hidden on minichromosomes. 2.3 Variation in repetitive elements and regulatory sequences Repetitive sequences, especially transposable elements (TEs), play an important role in genome evolution. A typical feature of bird genomes is that the transposon content is relatively low, generally accounting for only 7%~15%. The genomic repetitive sequences of Galliformes species generally follow this rule, but there are certain variations between different groups. For example, about 9%~10% of the domestic chicken genome is transposon sequences, among which LINE-1 (CR1) type transposons are the most abundant. In contrast, the proportion of transposons in passerine birds such as sparrows can be as high as 30%, reflecting that different evolutionary lineages have different degrees of inhibition of transposon expansion. Recent studies have found that the dynamic balance of transposons in bird genomes mainly depends on the balance of amplification and deletion rates, rather than just limited amplification. In Galliformes, there is also evidence that different species have experienced
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