Chromosome Evolution and Genome Miniaturization in Minifish

Stephanie Ann White,Tan Heok Hui,Yunhan Hong,Shaojun Liu,Sze Ley Tan

doi:10.1371/journal.pone.0037305

Stephanie Ann White, Tan Heok Hui + Show 3 more

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https://doi.org/10.1371/journal.pone.0037305

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Abstract

Background Paedocypris is a newly established genus of fish in Southeast Asia. Paedocypris is characterized by several unique features, including a tiny adult size (thus named miniature fish or minifish), fragmentary habitats of acidic peat blackwater swamps, an unusual reproduction mode and truncated development. These peculiarities lend themselves excellent for studying chromosome evolution and rapid speciation in vertebrates but also make them highly controversial for the phylogenetic position.Methodology and Principal FindingsWe have established an organ procedure to prepare chromosome spreads from tiny organs of minifish and performed a cytogenetic study on two species of the genus Paedocypris, namely P. carbunculus (Pc) and P. sp. “Singkep” (Ps). We found 30 and 34 chromosomes in diploid cells of Pc and Ps, respectively, which are unusual in teleost fishes. The diploid metaphase has 5 pairs of metacentrics and 7 pairs of subtelocentrics in Pc compared to 3 pairs of metacentrics and 11 pairs of subtelocentrics in Ps, whereas the haploid metaphase contains 5 metacentrics and 7 subtelocentrics in Pc compared to 3 metacentrics and 11 subtelocentrics Ps. Chromosome behavior in first meiosis revealed the presence of a chromosomal ring consisting of 2 metacentrics in Pc, suggesting that centric fusion rather than fission was responsible for the karyotypic evolution from Ps to Pc. Flow cytometry revealed that Pc had a 45% nuclear staining intensity relative to medaka whose genome is 700 Mb in size and contains 0.81 pg DNA. The Pc genome should have 315 Mb in length and 0.36 pg of DNA, which represent one of the smallest values in vertebrates, suggesting genome miniaturization in this organism.ConclusionsOur data demonstrate that gross chromosome rearrangements and genome miniaturization have accompanied the evolution of Paedocypris fishes. Our data also place Paedocypris outside currently described taxa of the Cypriniformes.

Highlights

The genus Paedocypris is a newly established group of miniature fishes with the discovery of two species, namely Paedocypris sp. ‘‘Singkep’’ (Ps). micromegethes and P. progenetica [1]
Our data demonstrate that gross chromosome rearrangements and genome miniaturization have accompanied the evolution of Paedocypris fishes
Chromosome preparation procedure The two species we studied were P. carbunculus (Pc) collected from the Central Kalimantan in Indonesia and Paedocypris sp. ‘‘Singkep’’ (Ps) island, the latter being a species to be described

Summary

Introduction

The genus Paedocypris is a newly established group of miniature fishes with the discovery of two species, namely P. micromegethes and P. progenetica [1]. There are additional miniature populations/species of this genus, which remain to be described, from other areas of Southeast Asia, such as Pulau Singkep, Pontianak, Pulau Banka and Kalimantan Tengah [1,2] Paedocypris is characterized by several unique features, including a tiny adult size ( named miniature fish or minifish), fragmentary habitats of acidic peat blackwater swamps, an unusual reproduction mode and truncated development. These peculiarities lend themselves excellent for studying chromosome evolution and rapid speciation in vertebrates and make them highly controversial for the phylogenetic position

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