Bulked segregant analysis of the pirarucu (Arapaima gigas) genome for identification of sex-specific molecular markers

Almeida, Inaê Guion de; Ianella, P.; Faria, M. T.; Paiva, Samuel Rezende; Caetano, Alexandre Rodrigues

doi:10.4238/2013.december.4.17

Cited by 17 publications

(14 citation statements)

References 41 publications

(39 reference statements)

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“…However, no technology exists today to manipulate the reproduction of pirarucu, and this situation means a huge hindrance and delay for the commercial production of the species. Because the main bottleneck is the reproduction in captivity, most of these studies on the species aimed at understanding patterns and mechanisms of sex determination, molecular differentiation, and gonadal activity of A. gigas (Almeida, Ianella, Faria, Paiva, & Caetano, ; Du et al, ; Prado‐Lima & Val, ; Torati et al, ; Torati, Lima, Kirschnik, & Migaud, ; Watanabe et al, ). However, sex determination and regulation of the sexual maturation remain largely unknown in the species (Almeida et al, ).…”

Section: Introductionmentioning

confidence: 99%

Morphological characterization of pirarucu Arapaima gigas (Schinz, 1822) gonadal differentiation

Amaral

Lima

Ganeco-Kirschnik

et al. 2020

Journal of Morphology

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Arapaima gigas is a giant air-breathing and bony tongue fish from the Amazon basin and a promising species for aquaculture. A. gigas farming industry is still not established because of the lack of information on its reproductive physiology. Reproduction in captivity cannot be manipulated or stimulated, and the identification of males and females in a broodstock is not easy. We aimed to reveal the morphological sex differentiation of pirarucu as studies involving gonad development are essential to understanding the reproductive physiology of any species. We performed histological analysis on the whole body and extracted the gonads of 150 juveniles. The first sign of ovary differentiation is the sex-specific rearrangement of the germ cells.In 9 cm total length females, the germ cells group into nests and are restricted to the lateral face of the gonad, in close contact with the abdomen wall. With further development, this region invaginates and that later develops into ovigerous lamellae. Meiosis starts soon after ovary differentiation. In males, the germ cells are scattered along the elongated differentiating testis at first, and later become more restricted to the central region where the spermatogonial cysts start to develop. Somatic and germ cells are jointly involved in the cellular reorganization during gonadal differentiation, specifically when the germ cells begin to establish new associations during the development of both the germinal epithelium and stroma. Research highlightsIn Arapaima gigas, the ovary differentiation occurs in 9 cm TL females and it is marked by the rearrangement of germ and somatic cells; and the germ cells entering meiosis with no formation of ovarian cavity; testis differentiation occurs later and meiosis does not start in males smaller than 80 cm TL. K E Y W O R D S early development, fish reproduction, germ cells, ovary, testis

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Section: Introductionmentioning

confidence: 99%

Morphological characterization of pirarucu Arapaima gigas (Schinz, 1822) gonadal differentiation

Amaral

Lima

Ganeco-Kirschnik

et al. 2020

Journal of Morphology

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“…Its main supply is provided by wild-caught fish and fish farming conducted by riverbank population of the Amazonas ( Froese and Pauly 2018 ). Aquaculture production is attractive due to high carcass yields and rapid juvenile growth, with yearlings reaching up to 10 kg (22 lb) ( Almeida et al. 2013 ).…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades

Vialle

Souza

Lopes

et al. 2018

Genome Biology and Evolution

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The Pirarucu (Arapaima gigas) is one of the world’s largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103-Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was ∼661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of nine exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons, and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of ∼30 Myr in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.

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“…DNA concentrations were determined using a Q5000 UV-V is spectrophotometer (Quawell Technology, USA). DNA was divided into a male DNA pool, which contained equal quantities from the five individual male plants, and a female DNA pool, which contained equal quantities from the five individual female plants, in accordance with the bulk segregant analysis procedure (Michelmore et al, 1991;Almeida et al, 2013). The DNA pools were diluted to a concentration of 50 ng/μL for use in agarose gel electrophoresisand were stored at -20°C until required.…”

Section: Dna Isolationmentioning

confidence: 99%

Sex differential marker FD for rapid sex identification of Litsea cubeba

Wang

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Litsea cubeba is an important economic tree in China.Sex identification of the species is required to reduce breeding costs. Molecular biology is an ideal method to achieve this aim because of the lack of morphological differences between male and female plants, especially at the seedling stage. Sequence-related amplified polymorphism was used to amplify sex-related bands. Following sequencing, the amplified fragment Dwas used to create a sequencecharacterized amplified region (SCAR) marker, FD. The SCAR marker is approximately 750 bp, is female-specific, and is expected to be useful for L. cubeba breeding programs. Furthermore, the amplified fragment L had homology to sex-determining-related genes of other species. Quantitative real-time polymerase chain reaction analysis of this fragment during flower bud development identified expression differences between male and female plants.

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Bulked segregant analysis of the pirarucu (Arapaima gigas) genome for identification of sex-specific molecular markers

Cited by 17 publications

References 41 publications

Morphological characterization of pirarucu Arapaima gigas (Schinz, 1822) gonadal differentiation

Morphological characterization of pirarucu Arapaima gigas (Schinz, 1822) gonadal differentiation

Whole Genome Sequencing of the Pirarucu (Arapaima gigas) Supports Independent Emergence of Major Teleost Clades

Sex differential marker FD for rapid sex identification of Litsea cubeba

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