Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

Conte, Matthew A.; Joshi, Rajesh; Moore, Emily C.; Nandamuri, Sri Pratima; Gammerdinger, William J; Roberts, Reade B.; Carleton, Karen L.; Lien, Sigbjørn; Köcher, Thomas

doi:10.1101/383992

Cited by 37 publications

(69 citation statements)

References 105 publications

(176 reference statements)

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“…The genomic population structure and linkage disequilibrium (LD) have also been reported using dense SNP panels in different tilapia populations (Xia et al, 2014;Joshi et al, 2018;Conte et al, 2019;Yoshida et al, 2019c). For farmed Nile tilapia, strong admixture among three different farmed populations from Latin America and a rapid decrease in LD with increasing inter-marker distance were observed (Yoshida et al, 2019c), in accordance with Xia et al (2014), who found similar LD patterns for GIFT populations from South Africa, Singapore and China.…”

Section: Population Genetic Studiessupporting

confidence: 56%

Genomics to accelerate genetic improvement in tilapia

2020

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Summary Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth‐, quality‐ and robustness‐related traits. Novel phenotyping technologies (i.e. phenomics), lower‐cost whole‐genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.

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Section: Population Genetic Studiessupporting

confidence: 56%

Genomics to accelerate genetic improvement in tilapia

2020

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“…PacBio sequencing was carried out on the PacBio RS II platform with P6-C4 chemistry using 9 SMRT cells and on the PacBio Sequel platform using 9 additional SMRT cells. Illumina and PacBio sequencing reads were aligned to the reference assembly of a M. zebra 'Mazinzi Reef' NoB male individual sequenced with PacBio [41], (publicly available on NCBI, Accession: GCA_000238955.4, [42]) with BWA [43] and NGM-LR [44], respectively. BWA alignments were then run through Picard version 2.1.0 'MarkDuplicates' to identify PCR duplicates.…”

Section: Methodsmentioning

confidence: 99%

Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

Clark

Conte

Kocher

2018

Preprint

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B chromosomes (Bs) were discovered a century ago, and since then most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many questions regarding the origin, structure, function and evolution of B chromosomes remain unanswered. Here we identify B chromosome sequences from several species of cichlid fish from Lake Malawi by examining the ratios of DNA sequence coverage in individuals with and without B chromosomes. We examine the efficiency of this method, and compare results using both Illumina and PacBio sequence data. The B chromosome sequences detected in 13 individuals from 7 species were compared to assess the rates of sequence replacement. B-specific sequence common to at least 12 of the 13 datasets are identified as the “Core” B chromosome. The location of B sequence homologs throughout the genome provides further support for theories of B chromosome evolution. Finally, we identified candidate genes located on the B chromosome which may regulate the segregation and maintenance of the B chromosome.

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“…Morgans (Conte et al, 2018). Thus the 11,000 to 21,000 markers are required for Nile 346 tilapia populations.…”

Section: Philippines 300mentioning

confidence: 99%

Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

Yoshida

Barría

Cáceres³

et al. 2019

Preprint

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24 Nile tilapia (Oreochromis niloticus) is one of the most produced farmed fish in the 25 world and represents an important source of protein for human consumption. Farmed 26 Nile tilapia populations are increasingly based on genetically improved stocks, which 27 have been established from admixed populations. To date, there is scarce information 28 about the population genomics of farmed Nile tilapia, assessed by dense single 29 nucleotide polymorphism (SNP) panels. The patterns of linkage disequilibrium (LD) 30 may affect the success of genome-wide association studies (GWAS) and genomic 31 selection and can also provide key information about demographic history of farmed 32 Nile tilapia populations. The objectives of this study were to provide further knowledge 33 about the population structure and LD patterns, as well as, estimate the effective 34 population size (Ne) for three farmed Nile tilapia populations, one from Brazil (POP A) 35 and two from Costa Rica (POP B and POP C). A total of 55, 56 and 57 individuals from 36 POP A, POP B and POP C, respectively, were genotyped using a 50K SNP panel 37 selected from a whole-genome sequencing (WGS) experiment. Two principal 38 components explained about 20% of the total variation and clearly discriminated 39 between the three populations. Population genetic structure analysis showed evidence of 40 admixture, especially for POP C. The contemporary Ne values calculated based to LD 41 values, ranged from 71 to 141. No differences were observed in the LD decay among 42 populations, with a rapid decrease of r 2 when increasing inter-marker distance. Average 43 r 2 between adjacent SNP pairs ranged from 0.03 to 0.18, 0.03 to 0.17 and 0.03 to 0.16 44 for POP A, POP B and POP C, respectively. Based on the number of independent 45 chromosome segments in the Nile tilapia genome, at least 4.2 K SNP are required for 46 the implementation of GWAS and genomic selection in farmed Nile tilapia populations. niloticus, population structure

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Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes

Abstract: Background

Cited by 37 publications

References 105 publications

Genomics to accelerate genetic improvement in tilapia

Genomics to accelerate genetic improvement in tilapia

Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

Genome-wide patterns of population structure and linkage disequilibrium in farmed Nile tilapia (Oreochromis niloticus)

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