Chromosome Evolution and Genome Miniaturization in Minifish

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.

A RAD-based linkage map and comparative genomics in the gudgeons (genus Gnathopogon, Cyprinidae)

“…Cyprinid fishes show great cytogenetic variation. Their chromosome numbers range from 2 n = 42 ( Acheilognathus gracilis [52], or 2 n = 30 if the taxonomically controversial Paedocypris carbunculus is placed within Cyprinidae [53]) to 2 n = 417–470 ( Ptychobarbus dipogon [54,55]), with a mode at 2 n = 50, followed by 2 n = 48 [56]. Thus, it has been suggested that the ancestral karyotype of cyprinid fishes was 2 n = 48–50, and that polyploidisation occurred in several groups within the Cyprinidae [57-63].…”

Miniatures, morphology and molecules:Paedocyprisand its phylogenetic position (Teleostei, Cypriniformes)

“…Recently, Liu et al . () studied the chromosome structure in two species of the genus Paedocypris ( Paedocypris carbunculus Kottelat & Britz, 2008 and Paedocypris sp. Singkep).…”

“…The very low DNA content per cell of 0.36 pg, indicating a genome size of approximately 350 Mb in Paedocypris [compared with 0.34 pg in Sphoeroides spengleri (Bloch, 1785), the fish with the smallest genome reported to date] was interpreted by Liu et al . () as a case of genome miniaturization. Surprisingly, Liu et al .…”

“…Surprisingly, Liu et al . (: 5) concluded that ‘Cytogenetically, Paedocypris cannot be placed in any cypriniform taxa at subfamily, family and superfamily levels’. As the reason why this was impossible, they argued that: ‘Extensive cytogenetic studies in Cypriniformes have revealed chromosome numbers in more than 200 species belonging to all the six families, most of them have ≥ 48 chromosomes.…”

A rapid chromosome preparation technique without metaphase arrest for ploidy determination in Nile tilapia,Oreochromis niloticus

“…In most fish chromosome preparation techniques, tissues are collected from different parts of the fish body, such as kidney (Blanco et al 2010;Poletto et al 2010;Martinez et al 2011;Liu et al 2012), liver (Affonso and Galetti 2005), spleen (Affonso and Galetti 2005), intestine (Kligerman and Bloom 1977), gill epithelium (Hashimoto et al 2009;Liu et al 2012), whole body (Shao et al 2010;Pradeep et al 2011), blood (Gold et al 1990;Eugenio et al 1993;Jacobina et al 2011), skin fibroblasts (Tantithakura et al 1993), bone marrow (Manosroi et al 2003), gonads (Liu et al 2012) and fin epithelium (Fontana et al 2008). The above preparation techniques involved the use of metaphase arresting agents, such as colchicine or colcemid.…”