e-journal

Linkage mapping with paralogs exposes regions of residual tetrasomic inheritance in chum salmon (Oncorhynchus keta)

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Gene sequence similarity due to shared ancestry after a duplication event, that is paralogy, complicates the assessment
of genetic variation, as sequences originating from paralogs can be difficult to distinguish. These confounded
sequences are often removed prior to further analyses, leaving the underlying loci uncharacterized. Salmonids have
only partially rediploidized subsequent to a whole-genome duplication; residual tetrasomic inheritance has been
observed in males. We present a maximum-likelihood-based method to resolve confounded paralogous loci by
observing the segregation of alleles in gynogenetic haploid offspring and demonstrate its effectiveness by constructing
two linkage maps for chum salmon (Oncorhynchus keta), with and without these newly resolved loci. We find
that the resolved paralogous loci are not randomly distributed across the genome. A majority are clustered in
expanded subtelomeric regions of 14 linkage groups, suggesting a significant fraction of the chum salmon genome
may be missed by the exclusion of paralogous loci. Transposable elements have been proposed as drivers of genome
evolution and, in salmonids, may have an important role in the rediploidization process by driving differentiation
between homeologous chromosomes. Consistent with that hypothesis, we find a reduced fraction of transposable element
annotations among paralogous loci, and these loci predominately occur in the genomic regions that lag in the
rediploidization process.

Keywords: chum salmon, haploid, homeolog, linkage mapping, tetrasomic inheritance, whole-genome duplication

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Informasi Detail

Judul Seri

Molecular Ecology Resources

No. Panggil

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Penerbit

: John Wiley & Sons, Ltd.., 2016

Deskripsi Fisik

Molecular Ecology Resources (2016) 16, 17–28

Bahasa

English

ISBN/ISSN

doi: 10.1111/1755-09

Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

Lampiran Berkas

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