Open Access Research article

Rapid evolution and copy number variation of primate RHOXF2, an X-linked homeobox gene involved in male reproduction and possibly brain function

Ao-lei Niu12, Yin-qiu Wang13, Hui Zhang1, Cheng-hong Liao1, Jin-kai Wang1, Rui Zhang1, Jun Che1 and Bing Su1*

Author Affiliations

1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology and Kunming Primate Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China

2 Graduate School of the Chinese Academy of Sciences, Beijing 100039, China

3 Department of Internal Medicine, Renal Division, Washington University School of Medicine, St. Louis, MO 63110, USA

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BMC Evolutionary Biology 2011, 11:298  doi:10.1186/1471-2148-11-298

Published: 12 October 2011

Additional files

Additional file 1:

Table S1 The relative RHOXF2 gene copies determined by qPCR in human population. Using TKTL1, an X-linked single copy gene as control, the copy numbers were calculated by setting one male individual with heterozygous sites (PG1302) as "2". There are no RHOXF2 genomic DNA quantity difference between the group without heterozygous sites and the group with heterozygous sites (P = 0.12, T test).

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Additional file 2:

Figure S1 The coding DNA sequence alignment of primate RHOXF2. The coding DNA sequences of chimpanzee are denoted by schematic figures. Rhesus macaque (RM) CDS was inferred from cDNA; Pig-tailed macaque (PTM), black leaf monkey (BLM) and grey leaf monkey (GLM) CDSs were inferred from clone sequencing of genomic DNA. '.' indicates identical to the first sequence in each alignment.

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Additional file 3:

Table S2 The cDNA clone counting of RHOXF2. The brain and testicle samples of human, chimpanzee and rhesus macaque were included. The lung sample of rhesus macaque was also counted. Brain 1(40 yrs), brain 2 (28 yrs) and brain 3 (newborn, 1 month) are all male individuals. Brain 4 was from a 36 weeks female embryo.

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Additional file 4:

Figure S2 FISH (Fluorescence In Situ Hybridization) analysis in human, chimpanzee and gorilla using the RHOXF2 probe. The red arrows indicate the positive signals.

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Figure S3 The ERV sequence alignment in human (hum), chimpanzee (CHP), gorilla (GOR), orangutan (ORA) and rhesus macaque (RM). '.' indicates identical to the first sequence in each alignment. '-' indicates an alignment gap.

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Additional file 6:

Figure S4. The phylogenetic tree showing sequence substitution pattern of each primate lineage. The numbers of non-synonymous and synonymous substitutions (N/S) and the amino-acid insertions-deletions are labeled for each lineage. The sequences of of human and chimpanzee were reconstructed by excluding the within-species non-synonymous changes. Using marmoset sequence as outgroup, all internal node sequences were inferred by PAML. The lineages showing Ka/Ks ratios significantly larger than one are denoted by '*' (p < 0.05) or '**' (p < 0.01). For the abbreviations of the primate species, refer to table 1.

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Additional file 7:

Figure S5 Protein sequence alignment of primate RHOXF2. '.' indicates identical to the first sequence in each alignment. '-' indicates an alignment gap and '*' indicates a stop codon. The homeodomain region and proline-rich domain region are underlined. HUM-1/HUM-2 and CHP-1/CHP-2 represent the polymorphic sites in populations and the sequence difference among the within-species copies. The ancestral amino acid 151R is still in human population besides 151H and 151C. For the abbreviations of the primate species names, refer to table 1.

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Additional file 8:

Table S3 The pairwise Ka/Ks ratios of RHOXF2 in the primate species tested. The Ka/Ks ratios were estimated following Pamilo-Bianchi-Li's method.

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Additional file 9:

Figure S6 The expression pattern of RHOXF2 determined by qPCR in two extra rhesus macaque individuals. (a) a 2 yr male; (b) a 2 yr female. The relative expression levels were calculated by setting the value in the testicle as "1". The result is consistent with the data presented in Figure 5.

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Additional file 10:

Table S4 The primer sequences of PCR and sequencing in this study.

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