scholarly journals A chromosome‐level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination

2021 ◽  
Author(s):  
Jianjian Lv ◽  
Ronghua Li ◽  
Zhencheng Su ◽  
Baoquan Gao ◽  
Xingbin Ti ◽  
...  
Keyword(s):  
Sex Determination ◽  
Portunus Trituberculatus ◽  
Salinity Adaptation ◽  
Chromosome Level

scholarly journals Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (Reinhardtius hippoglossoides)

2021 ◽  
Author(s):  
Anne-Laure Ferchaud ◽  
Claire Mérot ◽  
Eric Normandeau ◽  
Jiannis Ragoussis ◽  
Charles Babin ◽  
...  
Keyword(s):  
Sex Determination ◽  
Single Molecule ◽  
Sex Chromosome ◽  
Whole Genome Sequence ◽  
Greenland Halibut ◽  
Syntenic Relationship ◽  
Greenland Halibut Reinhardtius Hippoglossoides ◽  
Reinhardtius Hippoglossoides ◽  
Sex Determination System ◽  
Chromosome Level

Abstract Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1 594 scaffolds (scaffold N50 = 25 Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that, similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex-determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.

scholarly journals Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Boping Tang ◽  
Daizhen Zhang ◽  
Haorong Li ◽  
Senhao Jiang ◽  
Huabin Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Repetitive Sequences ◽  
Asia Pacific ◽  
Portunus Trituberculatus ◽  
Swimming Crab ◽  
Protein Coding ◽  
Eukaryotic Genes ◽  
Long Reads ◽  
Commercial Species ◽  
Chromosome Level

Abstract Background The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking. Findings Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology. Conclusions We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.

scholarly journals Discovery of Sex-Determining Genes in Portunus trituberculatus: A Comparison of Male and Female Transcriptomes During Early Developmental Stages

2022 ◽  
Vol 8 ◽  
Author(s):  
Wen Zhang ◽  
Jianjian Lv ◽  
Weikang Lan ◽  
Baoquan Gao ◽  
Ping Liu
Keyword(s):  
Sex Determination ◽  
Developmental Stages ◽  
Economic Value ◽  
Portunus Trituberculatus ◽  
Transcriptome Data ◽  
Early Developmental Stages ◽  
Folate Biosynthesis ◽  
Retinol Metabolism ◽  
Sex Determination Mechanisms ◽  
Early Developmental

Portunus trituberculatus is one of the main mariculture crabs of high economic value. To identify genes involved in sex determination, we first performed sex-specific transcriptome sequencing at six larval development stages using a DNA/RNA co-extraction method. A total of 907,952,938 and 828,774,880 reads were obtained from female and male crabs, respectively. 2,379 differentially expressed genes (DEGs) were found between females and males, and were mainly enriched in DNA replication, folate biosynthesis, and retinol metabolism pathways. Furthermore, transcription patterns of genes in the sex-determining region (SD) were analyzed based on the transcriptome data, and one Dmrt gene (PtDMY) was found to be exclusively expressed in males during early developmental stages. Notably, some known sex-related genes, including IAG, Dmrt11E, DmrtB1, and DmrtC2 were significantly down-regulated after knocking down PtDMY. Our results suggested that PtDMY is involved in sex determination and may be one of the key upstream regulators of the sex determination pathway. In addition, the massive volume of transcriptome data obtained in this study provided an important basis for the systematic study of sex determination mechanisms in P. trituberculatus.

scholarly journals The Aphid X Chromosome Is a Dangerous Place for Functionally Important Genes: Diverse Evolution of Hemipteran Genomes Based on Chromosome-Level Assemblies

2020 ◽  
Vol 37 (8) ◽  
pp. 2357-2368 ◽  
Author(s):  
Yiyuan Li ◽  
Bo Zhang ◽  
Nancy A Moran
Keyword(s):  
Sex Determination ◽  
Sex Chromosome ◽  
Purifying Selection ◽  
Life Cycles ◽  
Gene Content ◽  
Sequence Evolution ◽  
Opposite Pattern ◽  
Evolutionary Forces ◽  
Sex Determination System ◽  
Chromosome Level

Abstract Different evolutionary forces shape gene content and sequence evolution on autosomes versus sex chromosomes. Location on a sex chromosome can favor male-beneficial or female-beneficial mutations depending on the sex determination system and selective pressure on different sexual morphs. An X0 sex determination can lead to autosomal enrichment of male-biased genes, as observed in some hemipteran insect species. Aphids share X0 sex determination; however, models predict the opposite pattern, due to their unusual life cycles, which alternate between all-female asexual generations and a single sexual generation. Predictions include enrichment of female-biased genes on autosomes and of male-biased genes on the X, in contrast to expectations for obligately sexual species. Robust tests of these models require chromosome-level genome assemblies for aphids and related hemipterans with X0 sex determination and obligate sexual reproduction. In this study, we built the first chromosome-level assembly of a psyllid, an aphid relative with X0 sex determination and obligate sexuality, and compared it with recently resolved chromosome-level assemblies of aphid genomes. Aphid and psyllid X chromosomes differ strikingly. In aphids, female-biased genes are strongly enriched on autosomes and male-biased genes are enriched on the X. In psyllids, male-biased genes are enriched on autosomes. Furthermore, functionally important gene categories of aphids are enriched on autosomes. Aphid X-linked genes and male-biased genes are under relaxed purifying selection, but gene content and order on the X is highly conserved, possibly reflecting constraints imposed by unique chromosomal mechanisms associated with the unusual aphid life cycle.

scholarly journals A Chromosome-Level Genome Assembly of Mozambique Tilapia (Oreochromis mossambicus) Reveals the Structure of Sex Determining Regions

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenjing Tao ◽  
Jianmeng Cao ◽  
Hesheng Xiao ◽  
Xi Zhu ◽  
Junjian Dong ◽  
...  
Keyword(s):  
Sex Determination ◽  
Genome Assembly ◽  
Oreochromis Mossambicus ◽  
Missense Mutations ◽  
Sequencing Data ◽  
High Coverage ◽  
Mozambique Tilapia ◽  
High Quality Genome ◽  
Chromosome Level

The Mozambique tilapia (Oreochromis mossambicus) is a fascinating taxon for evolutionary and ecological research. It is an important food fish and one of the most widely distributed tilapias. Because males grow faster than females, genetically male tilapia are preferred in aquaculture. However, studies of sex determination and sex control in O. mossambicus have been hindered by the limited characterization of the genome. To address this gap, we assembled a high-quality genome of O. mossambicus, using a combination of high coverage of Illumina and Nanopore reads, coupled with Hi-C and RNA-Seq data. Our genome assembly spans 1,007 Mb with a scaffold N50 of 11.38 Mb. We successfully anchored and oriented 98.6% of the genome on 22 linkage groups (LGs). Based on re-sequencing data for male and female fishes from three families, O. mossambicus segregates both an XY system on LG14 and a ZW system on LG3. The sex-patterned SNPs shared by two XY families narrowed the sex determining regions to ∼3 Mb on LG14. The shared sex-patterned SNPs included two deleterious missense mutations in ahnak and rhbdd1, indicating the possible roles of these two genes in sex determination. This annotated chromosome-level genome assembly and identification of sex determining regions represents a valuable resource to help understand the evolution of genetic sex determination in tilapias.

scholarly journals Chromosome-level Genome Assembly of the Blue Crab, Callinectes sapidus

2021 ◽  
Author(s):  
Tsvetan R Bachvaroff ◽  
Ryan C McDonald ◽  
Louis V Plough ◽  
J Sook Chung
Keyword(s):  
Blue Crab ◽  
Developmental Stages ◽  
Callinectes Sapidus ◽  
Atlantic Coast ◽  
Portunus Trituberculatus ◽  
Protein Coding ◽  
Important Species ◽  
Protein Coding Genes ◽  
Repeat Content ◽  
Chromosome Level

Abstract The blue crab, Callinectes sapidus (Rathbun, 1896) is an economically, culturally, and ecologically important species found across the temperate and tropical North and South American Atlantic coast. A reference genome will enable research for this high-value species. Initial assembly combined 200x coverage Illumina paired-end reads, a 60x 8 kb mate-paired library, and 50x PacBio data using the MaSuRCA assembler resulting in a 985 Mb assembly with a scaffold N50 of 153 kb. Dovetail Chicago and HiC sequencing with the 3d DNA assembler and Juicebox assembly tools were then used for chromosome scaffolding. The fifty largest scaffolds span 810 Mb are 1.5 to 37 Mb long and have a repeat content of 36%. The 190 Mb unplaced sequence is in 3921 sequences over 10kb with a repeat content of 68%. The final assembly N50 is 18.9 Mb for scaffolds and 9317 bases for contigs. Of arthropod BUSCO, ∼88% (888/1,013) were complete and single copies. Using 309 million RNAseq read pairs from 12 different tissues and developmental stages, 25,249 protein-coding genes were predicted. Between C. sapidus and Portunus trituberculatus genomes, 41 of 50 large scaffolds had high nucleotide identity and protein-coding synteny, but nine scaffolds in both assemblies were not clear matches. The protein-coding genes included 9423 one-to-one putative orthologs, of which 7165 were syntenic between the two crab species. Overall, the two crab genome assemblies show strong similarities at the nucleotide, protein, and chromosome level and verify the blue crab genome as an excellent reference for this important seafood species.

scholarly journals Chromosome-level genome assembly reveals female-biased genes for sex determination and differentiation in the human blood fluke Schistosoma japonicum

2021 ◽  
Author(s):  
Xindong Xu ◽  
Yifeng Wang ◽  
Qingtian Guan ◽  
Gangqiang Guo ◽  
Xinyu Yu ◽  
...  
Keyword(s):  
Sex Determination ◽  
Schistosoma Japonicum ◽  
Human Blood ◽  
Sex Chromosomes ◽  
Regulatory Control ◽  
Z Chromosome ◽  
W Chromosome ◽  
Blood Fluke ◽  
Stage Of Development ◽  
Chromosome Level

Schistosomiasis is a neglected tropical disease of humans caused by blood flukes of the genus Schistosoma – the only dioecious parasitic flatworms. Although aspects of sex determination, differentiation and reproduction have been studied in some Schistosoma species, almost nothing is understood for Schistosoma japonicum - the causative agent of schistosomiasis japonica. This relates mainly to a lack of high-quality genomic and transcriptomic resources for this species. As current draft genomes for S. japonicum are highly fragmented, we assembled here a chromosome-level reference genome (seven autosomes, the Z-chromosome and partial W-chromosome), achieving a substantially enhanced gene annotation. Utilising this genome, we discovered that the sex chromosomes of S. japonicum and its congener S. mansoni independently suppressed recombination during evolution, forming four and two ‘strata’, respectively. By exploring the W-chromosome and sex-specific transcriptomes, we identified 35 W-linked genes and 257 female-preferentially transcribed genes (FTGs) and identified a signature for sex determination and differentiation in S. japonicum. These FTGs cluster within autosomes or the Z-chromosome and exhibit a highly dynamic transcription profile during the pairing of female and male schistosomules (advanced juveniles), representing a critical phase for the maturation of the female worms, suggesting distinct layers of regulatory control of gene transcription at this stage of development. Collectively, these data provide a valuable resource for further functional genomic characterisation of S. japonicum, shed light on the evolution of sex chromosomes in this highly virulent human blood fluke and provide a pathway to identify novel targets for development of intervention tools against schistosomiasis.

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