Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution

Abstract

We report here the isolation and sequencing of 10 Y-specific tammar wallaby (Macropus eugenii) BAC clones, revealing five hitherto undescribed tammar wallaby Y genes (in addition to the five genes already described) and several pseudogenes. Some genes on the wallaby Y display testis-specific expression, but most have low widespread expression. All have partners on the tammar X, along with homologs on the human X. Nonsynonymous and synonymous substitution ratios for nine of the tammar XY gene pairs indicate that they are each under purifying selection. All 10 were also identified as being on the Y in Tasmanian devil (Sarcophilus harrisii; a distantly related Australian marsupial); however, seven have been lost from the human Y. Maximum likelihood phylogenetic analyses of the wallaby YX genes, with respective homologs from other vertebrate representatives, revealed that three marsupial Y genes (HCFC1X/Y, MECP2X/Y, and HUWE1X/Y) were members of the ancestral therian pseudoautosomal region (PAR) at the time of the marsupial/eutherian split; three XY pairs (SOX3/SRY, RBMX/Y, and ATRX/Y) were isolated from each other before the marsupial/eutherian split, and the remaining three (RPL10X/Y, PHF6X/Y, and UBA1/UBE1Y) have a more complex evolutionary history. Thus, the small marsupial Y chromosome is surprisingly rich in ancient genes that are retained in at least Australian marsupials and evolved from testis-brain expressed genes on the X.

Figure 1.

DNA FISH of sequenced Y chromosome BACs. (A) ME_VIA-112D12, containing SRY and HUWE1Y; (B) ME_VIA-80O22, containing RBMY and PHF6Y; (C) ME_VIA- 53A23, containing ATRY; and (D) MEB1-052D08, containing HUWE1Y, SRY, HCFC1Y, RPL10Y, and MECP2Y. Bars, 5 μm.

Figure 2.

Maximum likelihood trees of marsupial XY gene pairs. Bootstrap values >50% are shown. These analyses indicate that (A) HCFC1X/Y, (B) MECP2X/Y, and (C) HUWE1X/Y were members of the ancestral therian PAR at the time of the marsupial/eutherian split; the (D) SOX3/SRY, (E) RBMX/Y, and (F) ATRX/Y gene pairs were isolated from each other before the marsupial/eutherian split; and (G) RPL10X/Y, (H) PHF6X/Y, and (I) UBA1/UBE1Y have a more complex evolutionary history (see text). Species code: (HSA) Human; (MMU) mouse; (OCU) rabbit; (CFA) dog; (FCA) cat; (BTA) cow; (ECA) horse; (AME) panda; (DNO) armadillo; (LAF) elephant; (PCA) hyrax; (ETE) tenrec; (MDO) Monodelphis domestica; (MEU) tammar wallaby; (MRU) Macropus rufus; (OAN) platypus; (GGA) chicken; (ACA) anolis; (XTR) Xenopus tropicalis. Trees reflect outgroup rooting.

Figure 3.

Expression pattern of tammar Y genes and their X homologs, assessed by (A) qPCR and (B) endpoint PCR in different tissues (NTC: no template control). All qPCR results were normalized to the autosomal gene GAPDH.

Figure 4.

Two marsupial X chromosomes compared with the human X. Green is recently added to the eutherian sex chromosomes. No marsupial sequence was available for RPS4Y or KDM5D, so we could not predict when the X–Y gametologues diverged from each other. The three shades of blue represent X genes that diverged from their respective gametologues either pre-therian radiation, post-therian radiation, or unknown. Genes retained from the proto-Y on the tammar wallaby and human Y chromosomes are shown. These results highlight the poor resolution of human X chromosome Stratum 1.