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Species and population level molecular profiling reveals cryptic recombination and emergent asymmetry in the dimorphic mating locus of C. reinhardtii.

De Hoff PL, Ferris P, Olson BJ, Miyagi A, Geng S, Umen JG - PLoS Genet. (2013)

Bottom Line: We used new sequence information to redefine the genetic contents of MT and found repeated translocations from autosomes as well as sexually controlled expression patterns for several newly identified genes.Our population data revealed two previously unreported types of genetic exchange in Chlamydomonas MT--gene conversion in the rearranged domains, and crossover exchanges in flanking domains--both of which contribute to maintenance of genetic homogeneity between haplotypes.Together our findings reveal new evolutionary dynamics for mating loci and have implications for the evolution of heteromorphic sex chromosomes and other non-recombining genomic regions.

View Article: PubMed Central - PubMed

Affiliation: The Salk Institute for Biological Studies, La Jolla, California, United States of America.

ABSTRACT
Heteromorphic sex-determining regions or mating-type loci can contain large regions of non-recombining sequence where selection operates under different constraints than in freely recombining autosomal regions. Detailed studies of these non-recombining regions can provide insights into how genes are gained and lost, and how genetic isolation is maintained between mating haplotypes or sex chromosomes. The Chlamydomonas reinhardtii mating-type locus (MT) is a complex polygenic region characterized by sequence rearrangements and suppressed recombination between its two haplotypes, MT+ and MT-. We used new sequence information to redefine the genetic contents of MT and found repeated translocations from autosomes as well as sexually controlled expression patterns for several newly identified genes. We examined sequence diversity of MT genes from wild isolates of C. reinhardtii to investigate the impacts of recombination suppression. Our population data revealed two previously unreported types of genetic exchange in Chlamydomonas MT--gene conversion in the rearranged domains, and crossover exchanges in flanking domains--both of which contribute to maintenance of genetic homogeneity between haplotypes. To investigate the cause of blocked recombination in MT we assessed recombination rates in crosses where the parents were homozygous at MT. While normal recombination was restored in MT+ ×MT+ crosses, it was still suppressed in MT- ×MT- crosses. These data revealed an underlying asymmetry in the two MT haplotypes and suggest that sequence rearrangements are insufficient to fully account for recombination suppression. Together our findings reveal new evolutionary dynamics for mating loci and have implications for the evolution of heteromorphic sex chromosomes and other non-recombining genomic regions.

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Expression patterns of mating locus genes.Panels A–F show expression values from quantitative RT-PCR (qRT-PCR) experiments for indicated genes calculated as described in Materials and Methods. Each panel groups genes by their overall expression pattern as follows: A, MT+ gametic; B, MT− gametic; C, MT− only; D, early zygotic; E, zygotic; F, reduced in zygotes. RNA samples were derived from MT+ vegetative cells (PV) and gametes (PG), MT− vegetative cells (MV) and gametes (MG), and from zygotes at 10 minutes, 30 minutes, 1 hour, 2 hours and 3 hours after mating (Z10, Z30, Z1h, Z2h and Z3h respectively). Panels G, H show gels from semi-quantitative RT-PCR experiments in which G. MTA4 cDNA or H. internal control 18S ribosomal cDNA were amplified. * No expression detected.
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pgen-1003724-g004: Expression patterns of mating locus genes.Panels A–F show expression values from quantitative RT-PCR (qRT-PCR) experiments for indicated genes calculated as described in Materials and Methods. Each panel groups genes by their overall expression pattern as follows: A, MT+ gametic; B, MT− gametic; C, MT− only; D, early zygotic; E, zygotic; F, reduced in zygotes. RNA samples were derived from MT+ vegetative cells (PV) and gametes (PG), MT− vegetative cells (MV) and gametes (MG), and from zygotes at 10 minutes, 30 minutes, 1 hour, 2 hours and 3 hours after mating (Z10, Z30, Z1h, Z2h and Z3h respectively). Panels G, H show gels from semi-quantitative RT-PCR experiments in which G. MTA4 cDNA or H. internal control 18S ribosomal cDNA were amplified. * No expression detected.

Mentions: A ∼160 kb region of MT+ Chromosome 6 consists of around nine or ten copies of a ∼17 kb (17,217 bp) tandem repeat termed the “16 kb repeats” in [19]. At least three genes are found within the 16 kb repeats: EZY2 encodes a predicted chloroplast protein with no recognizable domains or similarity, and its mRNA is zygote specific [19] (Figure 4D). There are at least six copies of EZY2 in the 16 kb repeat region (Figure 1, Table S4) designated EZY2a-EZY2f and a single EZY2 pseudogene in the MT− locus (Figure 1). Based on its presence in MT+, its zygotic expression pattern, and predicted chloroplast localization EZY2 was proposed to be involved in uniparental chloroplast DNA inheritance [18], [19]. OTU2 encodes a putative otubain-related protease [18]. The three copies of OTU2 that could be distinguished based on polymorphisms are designated OTU2a-OTU2c. A single copy of OTU2a that resides in the MT− R-domain (Figure 1) was not previously described. INT1 encodes a putative retroviral-related integrase that is present in some of the 16 kb repeats but nowhere else in the Chlamydomonas genome (Figure 1 and Table S4). The open reading frame of the INT1 gene contains a frame-shift mutation that would prevent production of a full-length polypeptide in the absence translational frame shifting; however, we were unable to detect any mRNA corresponding to INT1 (Figure 1 and data not shown).


Species and population level molecular profiling reveals cryptic recombination and emergent asymmetry in the dimorphic mating locus of C. reinhardtii.

De Hoff PL, Ferris P, Olson BJ, Miyagi A, Geng S, Umen JG - PLoS Genet. (2013)

Expression patterns of mating locus genes.Panels A–F show expression values from quantitative RT-PCR (qRT-PCR) experiments for indicated genes calculated as described in Materials and Methods. Each panel groups genes by their overall expression pattern as follows: A, MT+ gametic; B, MT− gametic; C, MT− only; D, early zygotic; E, zygotic; F, reduced in zygotes. RNA samples were derived from MT+ vegetative cells (PV) and gametes (PG), MT− vegetative cells (MV) and gametes (MG), and from zygotes at 10 minutes, 30 minutes, 1 hour, 2 hours and 3 hours after mating (Z10, Z30, Z1h, Z2h and Z3h respectively). Panels G, H show gels from semi-quantitative RT-PCR experiments in which G. MTA4 cDNA or H. internal control 18S ribosomal cDNA were amplified. * No expression detected.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3757049&req=5

pgen-1003724-g004: Expression patterns of mating locus genes.Panels A–F show expression values from quantitative RT-PCR (qRT-PCR) experiments for indicated genes calculated as described in Materials and Methods. Each panel groups genes by their overall expression pattern as follows: A, MT+ gametic; B, MT− gametic; C, MT− only; D, early zygotic; E, zygotic; F, reduced in zygotes. RNA samples were derived from MT+ vegetative cells (PV) and gametes (PG), MT− vegetative cells (MV) and gametes (MG), and from zygotes at 10 minutes, 30 minutes, 1 hour, 2 hours and 3 hours after mating (Z10, Z30, Z1h, Z2h and Z3h respectively). Panels G, H show gels from semi-quantitative RT-PCR experiments in which G. MTA4 cDNA or H. internal control 18S ribosomal cDNA were amplified. * No expression detected.
Mentions: A ∼160 kb region of MT+ Chromosome 6 consists of around nine or ten copies of a ∼17 kb (17,217 bp) tandem repeat termed the “16 kb repeats” in [19]. At least three genes are found within the 16 kb repeats: EZY2 encodes a predicted chloroplast protein with no recognizable domains or similarity, and its mRNA is zygote specific [19] (Figure 4D). There are at least six copies of EZY2 in the 16 kb repeat region (Figure 1, Table S4) designated EZY2a-EZY2f and a single EZY2 pseudogene in the MT− locus (Figure 1). Based on its presence in MT+, its zygotic expression pattern, and predicted chloroplast localization EZY2 was proposed to be involved in uniparental chloroplast DNA inheritance [18], [19]. OTU2 encodes a putative otubain-related protease [18]. The three copies of OTU2 that could be distinguished based on polymorphisms are designated OTU2a-OTU2c. A single copy of OTU2a that resides in the MT− R-domain (Figure 1) was not previously described. INT1 encodes a putative retroviral-related integrase that is present in some of the 16 kb repeats but nowhere else in the Chlamydomonas genome (Figure 1 and Table S4). The open reading frame of the INT1 gene contains a frame-shift mutation that would prevent production of a full-length polypeptide in the absence translational frame shifting; however, we were unable to detect any mRNA corresponding to INT1 (Figure 1 and data not shown).

Bottom Line: We used new sequence information to redefine the genetic contents of MT and found repeated translocations from autosomes as well as sexually controlled expression patterns for several newly identified genes.Our population data revealed two previously unreported types of genetic exchange in Chlamydomonas MT--gene conversion in the rearranged domains, and crossover exchanges in flanking domains--both of which contribute to maintenance of genetic homogeneity between haplotypes.Together our findings reveal new evolutionary dynamics for mating loci and have implications for the evolution of heteromorphic sex chromosomes and other non-recombining genomic regions.

View Article: PubMed Central - PubMed

Affiliation: The Salk Institute for Biological Studies, La Jolla, California, United States of America.

ABSTRACT
Heteromorphic sex-determining regions or mating-type loci can contain large regions of non-recombining sequence where selection operates under different constraints than in freely recombining autosomal regions. Detailed studies of these non-recombining regions can provide insights into how genes are gained and lost, and how genetic isolation is maintained between mating haplotypes or sex chromosomes. The Chlamydomonas reinhardtii mating-type locus (MT) is a complex polygenic region characterized by sequence rearrangements and suppressed recombination between its two haplotypes, MT+ and MT-. We used new sequence information to redefine the genetic contents of MT and found repeated translocations from autosomes as well as sexually controlled expression patterns for several newly identified genes. We examined sequence diversity of MT genes from wild isolates of C. reinhardtii to investigate the impacts of recombination suppression. Our population data revealed two previously unreported types of genetic exchange in Chlamydomonas MT--gene conversion in the rearranged domains, and crossover exchanges in flanking domains--both of which contribute to maintenance of genetic homogeneity between haplotypes. To investigate the cause of blocked recombination in MT we assessed recombination rates in crosses where the parents were homozygous at MT. While normal recombination was restored in MT+ ×MT+ crosses, it was still suppressed in MT- ×MT- crosses. These data revealed an underlying asymmetry in the two MT haplotypes and suggest that sequence rearrangements are insufficient to fully account for recombination suppression. Together our findings reveal new evolutionary dynamics for mating loci and have implications for the evolution of heteromorphic sex chromosomes and other non-recombining genomic regions.

Show MeSH
Related in: MedlinePlus