A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection

Pettersson, Mats E.; Rochus, Christina Marie; Fan, Han; Chen, Junfeng; Hill, Jason; Wallerman, Ola; Fan, Guangyi; Hong, Xiaoning; Xu, Qiwu; He, Zhonghu; Liu, Shanshan; Liu, Xin; Haggerty, Leanne; Hunt, Toby; Martin, Fergal J.; Flicek, Paul; Bunikis, Ignas; Folkvord, Arild; Andersson, Leif

doi:10.1101/gr.253435.119

Cited by 89 publications

(146 citation statements)

References 45 publications

(70 reference statements)

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“…Little to no spatial genetic structuring is a relatively common observation in pelagic fish species with continuous habitats (e.g. However, many studies show that pelagic fish species harbour genetic structure that does not correspond with geographic distance, but instead correlates with ecological adaptation (Berg et al, 2017;Kirubakaran et al, 2016;Martinez Barrio et al, 2016;Pettersson et al, 2019) or with cryptic species structure (Doenz, Bittner, Vonlanthen, Wagner, & Seehausen, 2018). We present here the largest genomic data sets analysed for the two freshwater sardines of Lake Tanganyika to date.…”

Section: Discussionmentioning

confidence: 99%

“…Because the L. miodon reference genome is not chromosome-level and many of the sex-linked SNPs were located on short scaffolds, we used LASTZ (v1.04, Harris, 2007) to align scaffolds containing sex-linked SNPs from the L. miodon reference genome to the most closely related species with a chromosome-level reference genome, Clupea harengus (Pettersson et al, 2019). We then identified the chromosome with the best alignment score for each scaffold and visualized alignments using GMAJ (Blanchette et al, 2004).…”

Section: Population Structure and Outlier Detectionmentioning

confidence: 99%

“…Pelagic habitats allow for high dispersal rates due to the lack of predominant physical barriers. Well-known examples of species from pelagic habitats that carry chromosomal inversions or sexlinked genomic differentiation include Atlantic cod (Gadus moruha; Berg et al, 2017;Kirubakaran et al, 2019;Kirubakaran et al, 2016) and Atlantic herring (Clupea harengus; Lamichhaney et al, 2017;Martinez Barrio, Lamichhaney, & Fan, 2016;Pettersson et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…In Atlantic cod and herring populations, low genome-wide divergence is interspersed with highly divergent inverted regions. These inversions in cod distinguish between resident and migrating ecotypes (Berg et al, 2017;Kirubakaran et al, 2016) and males and females (Kirubakaran et al, 2019), and in herring, they separate spring and fall spawners (Lamichhaney et al, 2017;Martinez Barrio et al, 2016;Pettersson et al, 2019). Additionally, inverted genomic regions in sticklebacks are involved in the divergence between lake and stream ecotypes (Marques et al, 2016;Roesti, Kueng, Moser, & Berner, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

et al. 2020

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Identifying patterns in genetic structure and the genetic basis of ecological adaptation is a core goal of evolutionary biology and can inform the management and conservation of species that are vulnerable to population declines exacerbated by climate change. We used reduced‐representation genomic sequencing methods to gain a better understanding of genetic structure among and within populations of Lake Tanganyika's two sardine species, Limnothrissa miodon and Stolothrissa tanganicae. Samples of these ecologically and economically important species were collected across the length of Lake Tanganyika, as well as from nearby Lake Kivu, where L. miodon was introduced in 1959. Our results reveal differentiation within both S. tanganicae and L. miodon that is not explained by geography. Instead, this genetic differentiation is due to the presence of large sex‐specific regions in the genomes of both species, but involving different polymorphic sites in each species. Our results therefore indicate rapidly evolving XY sex determination in the two species. Additionally, we found evidence of a large chromosomal rearrangement in L. miodon, creating two homokaryotypes and one heterokaryotype. We found all karyotypes throughout Lake Tanganyika, but the frequencies vary along a north–south gradient and differ substantially in the introduced Lake Kivu population. We do not find evidence for significant isolation by distance, even over the hundreds of kilometres covered by our sampling, but we do find shallow population structure.

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Section: Discussionmentioning

confidence: 99%

Section: Population Structure and Outlier Detectionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

et al. 2020

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“…Here, we report a chromosome‐scale genome of A. pernyi that was assembled with the combination of the Illumina Hiseq and PacBio Sequel II platforms along with Hi‐C technology. This strategy of long‐read sequencing and Hi‐C‐assisted assembly has previously produced high‐quality genome assembly in plants (Schmidt et al., 2017; Teh et al., 2017; Wu et al., 2019; Zhang et al., 2018) and animals (Li et al., 2019; Pettersson et al., 2019; Wan et al., 2019). Our high‐quality genome assembly for A. pernyi demonstrated that this combined method with an improved algorithm (Zhang et al., 2019) could also be effectively used to assemble a complex diploid genome.…”

Section: Discussionmentioning

confidence: 99%

A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae, Lepidoptera)

Duan

Liu

et al. 2020

Molecular Ecology Resources

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Antheraea pernyi is a semi‐domesticated lepidopteran insect species valuable to the silk industry, human health, and ecological tourism. Owing to its economic influence and developmental properties, it serves as an ideal model for investigating divergence of the Bombycoidea super family. However, studies on the karyotype evolution and functional genomics of A. pernyi are limited by scarce genomic resource. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first high‐quality A. pernyi genome from a single male individual. The genome is 720.67 Mb long with 49 chromosomes and a 13.77‐Mb scaffold N50. Approximately 441.75 Mb, accounting for 60.74% of the genome, was identified as repeats. The genome comprises 21,431 protein‐coding genes, 85.22% of which were functionally annotated. Comparative genomics analysis suggested that A. pernyi diverged from its common ancestor with A. yamamai ~30.3 million years ago, and that chromosome fission contributed to the increased chromosome number. The genome assembled in this work will not only facilitate future research on A. pernyi and related species but also help to progress comparative genomics analyses in Lepidoptera.

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A chromosome‐level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae)

Chen

Zhu

Wang

et al. 2022

Arch Insect Biochem Physiol

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Paracymoriza distinctalis is a semiaquatic lepidopteran insect, which is of great value for studying the differentiation of the Pyraloidea superfamily. However, the understanding of heredity, evolution, and functional genomics of P. distinctalis are limited by few genomewide resources. Here, we applied PacBio sequencing and the chromosome capture technique to assemble the first P. distinctalis genome from a single female individual. The genome size is 1.2 Gb with 32 chromosomes and the N50 is 38.91 Mb. Approximately 576.37 Mb, accounting for 48.93% of the genome, was identified as repeats. The genome comprises 39,003 protein-coding genes, 66.56% of which were functionally annotated. Comparative genomics analysis suggested that the common ancestor of P. distinctalis and Chilo suppressalis lived ~83.5 million years ago. This chromosome-level genome assembly work is not only conducive to the understanding of P. distinctalis, but also may promote the study of the genomes of other lepidopteran species.

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A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection

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Cited by 89 publications

References 45 publications

Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

Structural genomic variation leads to genetic differentiation in Lake Tanganyika's sardines

A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae, Lepidoptera)

A chromosome‐level genome assembly of Paracymoriza distinctalis (Lepidoptera: Crambidae: Acentropinae)

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