Draft genome of the protandrous Chinese black porgy, <i>Acanthopagrus schlegelii</i>

Zhang, Zhiyong; Zhang, Kai; Chen, Shuyin; Zhang, Zhiwei; Zhang, Jinyong; You, Xinxin; Bian, Chao; Xu, Jin; Jia, Chaofeng; Qiang, Jun; Zhu, Fei; Li, Hongxia; Liu, Hailin; Shen, D. Rong; Ren, Zhonghong; Chen, Jieming; Li, Jia; Gao, Tianheng; Gu, Ruobo; Xu, Junmin; Shi, Qiong; Xu, Pao

doi:10.1093/gigascience/giy012

Cited by 83 publications

(57 citation statements)

References 63 publications

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“…Sparidae genetic data have been recently greatly enriched by transcriptomic studies (Tsakogiannis et al, 2018; Manousaki et al, 2014) and two whole-genome sequencing datasets, those of gilthead seabream (Pauletto et al, 2018) and Chinese black porgy (Zhang et al, 2018). In the phylogenomic analysis of Pauletto et al using 2,032 genes from 14 species, the large yellow croaker ( Larimichthys crocea , family: Sciaenidae) and the European seabass ( Dicentrarchus labrax , family: Moronidae) were placed as sister groups to gilthead seabream with high confidence.…”

Section: Introductionmentioning

confidence: 99%

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Natsidis

Tsakogiannis

Pavlidis

et al. 2019

Preprint

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19Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 20 species with high popularity and commercial value, such as porgies and seabreams. Although 21 the phylogeny of this family has been investigated multiple times, its position among other 22 teleost groups remains ambiguous. Most studies have used a single or few genes to decipher 23 the phylogenetic relationships of sparids. Here, we conducted a phylogenomic attempt to 24 resolve the position of the family using five recently available Sparidae gene-sets and 26 25 available fish proteomes from species with a sequenced genome, to ensure higher quality of 26 the predicted genes. A thorough phylogenomic analysis suggested that Tetraodontiformes 27 (puffer fish, sunfish) are the closest relatives to sparids than all other groups used, a finding 28 that contradicts our previous phylogenomic analysis that proposed the yellow croaker and the 29 european seabass as closest taxa of sparids. By analytically comparing the methodologies 30 applied in both cases, we show that this discordance is not due to different orthology 31 assignment algorithms; on the contrary, we prove that it is caused by the increased taxon 32 sampling of the present study, outlining the great importance of this aspect in phylogenomic 33 analyses in general. 34 35 Keywords: Sparidae; fish phylogenomics; orthology assignment; jackknife phylogeny test; 36 taxon sampling; 37Teleostei represent the dominant group within ray-finned fish (Actinopterygii), with 39 more than 26,000 extant species. Their evolution has been extensively studied through past 40 decades, using a variety of data including fossil records, morphological characters and 41 molecular data, leading to a gradual resolution of teleost phylogeny (Betancur-R. et al., 2013(Betancur-R. et al., 42 & 2017. 43 With the continuous emergence of new whole-genome sequences, phylogenomic 44 techniques are applied to characterise the evolutionary relationships among species. Whole-45 genome information can help in resolving uncertain nodes, as well as provide stronger evidence 46 on already established relationships. Regarding fish phylogeny, several genome-wide 47 approaches have been implemented so far. One of the first efforts to study ray-finned fish 48 phylogenomics was conducted by (Li et al., 2007). Since then, several studies have been 49 published using not only gene markers, but also noncoding elements such as the work of 50 (Faircloth et al., 2013) who used UCE (ultra-conserved elements) to investigate the 51 diversification of basal clades in ray-finned fish. Most genome papers include a phylogenomic 52 analysis albeit with limited taxon sampling (e.g. Vij et al., 2016 and Xu et al., 2017), while the 53 use of whole-transcriptome data is being employed to uncover phylogenetic relationships of 54 specific taxonomic groups as well (Dai et al., 2018; Rodgers et al., 2018). With the emergence 55 of new genomes and the possibilities of modern sequencing technologies, bigger datasets are ...

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Section: Introductionmentioning

confidence: 99%

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Natsidis

Tsakogiannis

Pavlidis

et al. 2019

Preprint

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“…Raw reads were filtered first to remove low-quality reads and adaptor sequences by SOAPnuke 20 . Clean reads were mapped to the reference genome of B. terrestris (GenBank: GCF_000214255.1) using Bowtie2 21 .…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq

Zhao

et al. 2020

Sci Data

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Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. Although protein-coding genes in bumblebees have been extensively annotated, regulatory sequences of the genome, such as promoters and enhancers, have been poorly annotated. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we performed ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) on Bombus terrestris samples derived from four developmental stages: egg, larva, pupa, and adult, respectively. The ATAC-seq reads were mapped to the B. terrestris reference genome, and its accessible chromatin regions were identified and characterized using bioinformatic methods. We identified 36,390 chromatin accessible regions in total, including both shared and stage-specific chromatin accessible signals. Our study will provide an important resource, not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology throughout development.

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“…The osmosensory signalling networks, controlling above effector genes, are most obvious and effective in euryhaline species involving in osmoregulatory mechanism (Kültz 2012). Moreover, several genomic datasets of Sparidae fish have been published in recent years, such as those for A. schlegelii (Zhang et al, 2018), S. aurata (Pauletto et al, 2018), and red seabream (Pagrus major) (Shin et al, 2018). However, no genomic research has been conducted thus far to identify the candidate genes and pathways for survival over a large range of salinities, which severely hinders studies examining their osmoregulatory mechanisms.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, in gilthead sea bream (Sparus aurata), fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode (Pauletto et al, 2018). By performing a comparative genomic analysis, Zhang et al (2018) found three types of genes that are potentially associated with sex reversal and are useful for studying the genetic basis of protandrous hermaphroditism in black seabream (Acanthopagrus schlegelii). Moreover, comparative transcriptomic analyse has been conducted to identify the male-and female-specific genes and pathways that are most likely involved in sex maintenance in Sparidae (Tsakogiannis et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus) (Hottuyn, 1782) provides insights into its osmoregulation and sex reversal

Zhu

Zhang

Liu

et al. 2020

Preprint

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The yellowfin seabream Acanthopagrus latus is the economically most important Sparidae fish species in the northern South China Sea. As euryhaline fish, they are perfect model for investigating osmoregulatory mechanisms in teleosts. Moreover, the reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. To elucidate genetic mechanisms of osmoregulation and sex reversal in this fish, a high-quality reference genome of the yellowfin seabream was generated by a combination of Illumina and PacBio technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23% universal single-copy orthologues based on benchmarking universal single-copy orthologs (BUSCO) analysis. Moreover, among the 19,631 protein-coding genes, we found that the ARRDC3 and GSTA gene families related to osmoregulation underwent an extensive expansion in two euryhaline Sparidae fish genomes compared to other teleost genomes. Moreover, integrating sex-specific transcriptome analyses, several genes related to the transforming growth factor beta (TGF-β) signalling pathway involved in sex differentiation and development. This genomic resource will not only be valuable for studying the osmoregulatory mechanisms in estuarine fish and sex determination in hermaphrodite vertebrate species, but also provide useful genomic tools for facilitating breeding of the yellowfin seabream. Abstract 1 The yellowfin seabream Acanthopagrus latus is the economically most important 2 Sparidae fish species in the northern South China Sea. As euryhaline fish, they are perfect 3 model for investigating osmoregulatory mechanisms in teleosts. Moreover, the 4 reproductive biology of hermaphrodites has long been intriguing; however, very little is 5 known about the molecular pathways underlying their sex change. To elucidate genetic 6 mechanisms of osmoregulation and sex reversal in this fish, a high-quality reference 7 genome of the yellowfin seabream was generated by a combination of Illumina and 8 PacBio technologies. The draft genome of yellowfin seabream was 806 Mb, with 732 Mb 9 scaffolds anchored on 24 chromosomes. The contig N50 and scaffold N50 were 2.6 Mb 1 0and 30.17 Mb, respectively. The assembly is of high integrity and includes 92.23%

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Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii

Cited by 83 publications

References 63 publications

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq

A chromosome-level genome assembly of the yellowfin seabream (Acanthopagrus latus) (Hottuyn, 1782) provides insights into its osmoregulation and sex reversal

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