High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis

Abstract Background Ants with complex societies have fascinated scientists for centuries. Comparative genomic and transcriptomic analyses across ant species and castes have revealed important insights into the molecular mechanisms underlying ant caste differentiation. However, most current ant genomes and transcriptomes are highly fragmented and incomplete, which hinders our understanding of the molecular basis for complex ant societies. Findings By hybridizing Illumina, Pacific Biosciences, and Hi-C sequencing technologies, we de novo assembled a chromosome-level genome for Monomorium pharaonis, with a scaffold N50 of 27.2 Mb. Our new assembly provides better resolution for the discovery of genome rearrangement events at the chromosome level. Analysis of full-length isoform sequencing (ISO-seq) suggested that ∼15 Gb of ISO-seq data were sufficient to cover most expressed genes, but the number of transcript isoforms steadily increased with sequencing data coverage. Our high-depth ISO-seq data greatly improved the quality of gene annotation and enabled the accurate detection of alternative splicing isoforms in different castes of M. pharaonis. Comparative transcriptome analysis across castes based on the ISO-seq data revealed an unprecedented number of transcript isoforms, including many caste-specific isoforms. We also identified a number of conserved long non-coding RNAs that evolved specifically in ant lineages and several that were conserved across insect lineages. Conclusions We produced a high-quality chromosome-level genome for M. pharaonis, which significantly improved previous short-read assemblies. Together with full-length transcriptomes for all castes, we generated a highly accurate annotation for this ant species. These long-read sequencing results provide a useful resource for future functional studies on the genetic mechanisms underlying the evolution of social behaviors and organization in ants.

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Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)

GigaScience ◽

10.1093/gigascience/giaa092 ◽

2020 ◽

Vol 9 (8) ◽

Cited By ~ 1

Author(s):

Feng Shao ◽

Arne Ludwig ◽

Yang Mao ◽

Ni Liu ◽

Zuogang Peng

Keyword(s):

Dna Sequences ◽

Genome Assembly ◽

Gambusia Affinis ◽

Comparative Genomic ◽

Suitable Model ◽

High Quality ◽

Western Mosquitofish ◽

Poeciliid Fish ◽

Oxford Nanopore ◽

Chromosome Level

Abstract Background The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it. Results The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated. Conclusions The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.

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Chromosome-level genome assembly of Scapharca kagoshimensis reveals the expanded molecular basis of heme biosynthesis in ark shell

10.22541/au.162155566.67560449/v1 ◽

2021 ◽

Author(s):

Teng Weiming ◽

Xie Xi ◽

Hongtao Nie ◽

Yamin Sun ◽

Liu Xiangfeng ◽

...

Keyword(s):

Genome Assembly ◽

Molecular Basis ◽

Molecular Mechanisms ◽

Heme Biosynthesis ◽

High Quality ◽

Protein Coding ◽

Conserved Genes ◽

Long Time ◽

Muddy Sediments ◽

Chromosome Level

Ark shells are commercially important clam species that inhabit in muddy sediments of shallow coasts in East Asia. For a long time, the lack of genome resources has hindered scientific research of ark shells. Here, we reported a high-quality chromosome-level genome assembly of Scapharca kagoshimensis, with an aim to unravel the molecular basis of heme biosynthesis, and develop genomic resources for genetic breeding and population genetics in ark shells. Nineteen scaffolds corresponding to 19 chromosomes were constructed from 938 contigs (contig N50=2.01 Mb) to produce a final high-quality assembly with a total length of 1.11 Gb and scaffold N50 around 60.64 Mb. The genome assembly represents 93.4% completeness via matching 303 eukaryota core conserved genes. A total of 24,908 protein-coding genes were predicted and 24,551 genes (98.56%) of which were functionally annotated. The enrichment analyses suggested that genes in heme biosynthesis pathways were expanded and positive selection of the hemoglobin genes was also found in the genome of S. kagoshimensis, which gives important insights into the molecular mechanisms and evolution of the heme biosynthesis in mollusca. The valuable genome assembly of S. kagoshimensis would provide a solid foundation for investigating the molecular mechanisms that underlie the diverse biological functions and evolutionary adaptations of S. kagoshimensis.

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Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (Physeter macrocephalus)

Genes ◽

10.3390/genes12020233 ◽

2021 ◽

Vol 12 (2) ◽

pp. 233

Author(s):

Daling Wang ◽

Ying Li ◽

Reyilamu Aierken ◽

Qi Kang ◽

Xianyan Wang ◽

...

Keyword(s):

Immune System ◽

Molecular Mechanisms ◽

Gene Annotation ◽

Average Length ◽

Enrichment Analysis ◽

Sperm Whale ◽

Living Environment ◽

Full Length ◽

Physeter Macrocephalus ◽

Rna Seq

Cetaceans are a group of secondary aquatic mammals whose ancestors returned to the ocean from land, and during evolution, their immune systems adapted to the aquatic environment. Their skin, as the primary barrier to environmental pathogens, supposedly evolved to adapt to a new living environment. However, the immune system in the skin of cetaceans and the associated molecular mechanisms are still largely unknown. To better understand the immune system, we extracted RNA from the sperm whale’s (Physeter macrocephalus) skin and performed PacBio full-length sequencing and RNA-seq sequencing. We obtained a total of 96,350 full-length transcripts with an average length of 1705 bp and detected 5150 genes that were associated with 21 immune-related pathways by gene annotation enrichment analysis. Moreover, we found 89 encoding genes corresponding to 33 proteins were annotated in the NOD-like receptor (NLR)-signaling pathway, including NOD1, NOD2, RIP2, and NF-κB genes, which were discussed in detail and predicted to play essential roles in the immune system of the sperm whale. Furthermore, NOD1 was highly conservative during evolution by the sequence comparison and phylogenetic tree. These results provide new information about the immune system in the skin of cetaceans, as well as the evolution of immune-related genes.

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Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation

GigaScience ◽

10.1093/gigascience/giz157 ◽

2020 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Gangchun Xu ◽

Chao Bian ◽

Zhijuan Nie ◽

Jia Li ◽

Yuyu Wang ◽

...

Keyword(s):

Molecular Mechanisms ◽

Genetic Resource ◽

Economic Importance ◽

Seasonal Migration ◽

Migratory Fish ◽

High Quality ◽

Coilia Nasus ◽

High Quality Genome ◽

Important Fish ◽

Chromosome Level

Abstract Background Seasonal migration is one of the most spectacular events in nature; however, the molecular mechanisms related to this phenomenon have not been investigated in detail. The Chinese tapertail, or Japanese grenadier anchovy, Coilia nasus, is a valuable migratory fish of high economic importance and special migratory dimorphism (with certain individuals as non-migratory residents). Results In this study, an 870.0-Mb high-quality genome was assembled by the combination of Illumina and Pacific Biosciences sequencing. Approximately 812.1 Mb of scaffolds were linked to 24 chromosomes using a high-density genetic map from a family of 104 full siblings and their parents. In addition, population sequencing of 96 representative individuals from diverse areas along the putative migration path identified 150 candidate genes, which are mainly enriched in 3 Ca2+-related pathways. Based on integrative genomic and transcriptomic analyses, we determined that the 3 Ca2+-related pathways are critical for promotion of migratory adaption. A large number of molecular markers were also identified, which distinguished migratory individuals and non-migratory freshwater residents. Conclusions We assembled a chromosome-level genome for the Chinese tapertail anchovy. The genome provided a valuable genetic resource for understanding of migratory adaption and population genetics and will benefit the aquaculture and management of this economically important fish.

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Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis

Scientific Reports ◽

10.1038/s41598-021-92494-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xue Gao ◽

Fengxia Guo ◽

Yuan Chen ◽

Gang Bai ◽

Yuxiao Liu ◽

...

Keyword(s):

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Raw Materials ◽

Gene Annotation ◽

Blood Stasis ◽

Angelica Sinensis ◽

Plant Hormone Signaling ◽

Pollen Formation ◽

Functional Analyses ◽

Generation Sequencing

AbstractAngelica sinensis (Oliv.) Diels root part is an integral component of traditional Chinese medicine, widely prescribed to improve blood circulation and blood stasis. However, early bolting of A. sinensis compromises the quality of the roots and hence is a major limitation for yield of medicinal materials. To date, little information about the molecular mechanisms underlying bolting is available for this important medicinal plant. To identify genes putatively involved in early bolting, we have conducted the transcriptome analysis of the shoot tips of the early-bolting plants and non-bolting (normal) plants of A. sinensis, respectively, using a combination of third-generation sequencing and next-generation sequencing. A total of 43,438 non-redundant transcripts were collected and 475 unique differentially expressed genes (DEGs) were identified. Gene annotation and functional analyses revealed that DEGs were highly involved in plant hormone signaling and biosynthesis pathways, three main flowering pathways, pollen formation, and very-long-chain fatty acids biosynthesis pathways. The levels of endogenous hormones were also changed significantly in the early bolting stage of A. sinensis. This study provided new insights into the transcriptomic control of early bolting in A. sinensis, which could be further applied to enhance the yield of medicinally important raw materials.

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Chromosome-level genome assembly of the sweet potato weevil, Cylas formicarius (Fabricius) (Coleoptera: Brentidae) and functional characteristics of CforOBP4-6

10.22541/au.162460541.11570297/v1 ◽

2021 ◽

Author(s):

Jinfeng Hua ◽

Lei Zhang ◽

Xiaofeng Dong ◽

Yonghua Han ◽

Xiaowan Gou ◽

...

Keyword(s):

Sweet Potato ◽

Genome Assembly ◽

New Technologies ◽

Gene Families ◽

Sequence Length ◽

Economic Damage ◽

Comparative Genomic ◽

High Quality ◽

Cylas Formicarius ◽

Chromosome Level

Cylas formicarius is one of the most important pests of sweet potato worldwide, causing considerable ecological and economic damage. To improve the effect of comprehensive management and understanding of genetic mechanisms, the genetic functions of C. formicarius have been the subject of intensive study. Using Illumina and PacBio sequencing, we obtained a chromosome-level genome assembly of adult weevils from lines inbred for 15 generations. The high-quality assembly obtained had a size of 338.84 Mb, with contig and scaffold N50 values of 14.97 Mb and 34.23 Mb, respectively. In total, 157.51 Mb of repeat sequences and 11,907 protein-coding genes were predicted. A total of 337.06 Mb of genomic sequences was located on the 11 chromosomes, and the sequence length that could be used to determine the sequence and direction accounted for 99.03% of the total length of the associated chromosome. Comparative genomic analysis showed that C. formicarius was sister to Dendroctonus ponderosae, and C. formicarius diverged from D. ponderosae approximately 138.89 million years ago (Mya). Many important gene families that were expanded in the C. formicarius genome were involved in the chemosensory system. In an in-depth study, the binding assay results indicated that CforOBP4-6 had strong binding affinities for sex pheromones and other ligands. Overall, the high-quality C. formicarius genome provides a valuable resource to reveal the molecular ecological basis, genetic mechanism and evolutionary process of major agricultural pests, deepen the understanding of environmental adaptability and apparent plasticity, and provide new ideas and new technologies for ecologically sustainable pest control.

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Antennal transcriptome analysis and candidate olfactory genes in Crematogaster rogenhoferi

Bulletin of Entomological Research ◽

10.1017/s0007485321000134 ◽

2021 ◽

pp. 1-12

Author(s):

Xiang Zhou ◽

Jixing Guo ◽

Mingxia Zhang ◽

Chunxiu Bai ◽

Zheng Wang ◽

...

Keyword(s):

Biological Control ◽

Transcriptome Analysis ◽

Molecular Basis ◽

Molecular Mechanisms ◽

Biological Control Agent ◽

Control Agent ◽

Vital Role ◽

Neuron Membrane ◽

Ionotropic Receptors ◽

Soft Scale

Abstract Crematogaster rogenhoferi (Hymenoptera: Formicidae), an omnivorous ant, is one of the dominant predatory natural enemies of a soft scale pest, Parasaissetia nigra Nietner (Homoptera: Coccidae), and can effectively control P. nigra populations in rubber forests. Olfaction plays a vital role in the process of predation. However, the information about the molecular mechanism of olfaction-evoked behaviour in C. rogenhoferi is limited. In this study, we conducted antennal transcriptome analysis to identify candidate olfactory genes. We obtained 53,892 unigenes, 16,185 of which were annotated. Based on annotations, we identified 49 unigenes related to chemoreception, including four odourant-binding proteins, three chemosensory proteins, 37 odourant receptors, two odourant ionotropic receptors and three sensory neuron membrane proteins. This is the first report on the molecular basis of the chemosensory system of C. rogenhoferi. The findings provide a basis for elucidating the molecular mechanisms of the olfactory-related behaviours of C. rogenhoferi, which would facilitate a better application of C. rogenhoferi as a biological control agent.

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Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant

Genes ◽

10.3390/genes12030341 ◽

2021 ◽

Vol 12 (3) ◽

pp. 341

Author(s):

Lei Zhang ◽

Haoyun Sun ◽

Tao Xu ◽

Tianye Shi ◽

Zongyun Li ◽

...

Keyword(s):

Transcriptome Analysis ◽

Morphological Analysis ◽

Molecular Mechanisms ◽

Flavonoid Biosynthesis ◽

Phenotypic Characterization ◽

Comparative Transcriptome ◽

Hub Genes ◽

Breeding Programs ◽

Comparative Transcriptome Analysis ◽

Key Pathways

Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.

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Transcriptome Analysis of Pre-Storage 1-MCP and High CO2-Treated ‘Madoka’ Peach Fruit Explains the Reduction in Chilling Injury and Improvement of Storage Period by Delaying Ripening

International Journal of Molecular Sciences ◽

10.3390/ijms22094437 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4437

Author(s):

Han Ryul Choi ◽

Min Jae Jeong ◽

Min Woo Baek ◽

Jong Hang Choi ◽

Hee Cheol Lee ◽

...

Keyword(s):

Cold Storage ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Chilling Injury ◽

Chemical Properties ◽

Storage Period ◽

Differentially Expressed ◽

Peach Fruit ◽

High Co2 ◽

Physico Chemical

Cold storage of peach fruit at low temperatures may induce chilling injury (CI). Pre-storage 1-MCP and high CO2 treatments were reported among the methods to ameliorate CI and reduce softening of peach fruit. However, molecular data indicating the changes associated with pre-storage 1-MCP and high CO2 treatments during cold storage of peach fruit are insufficient. In this study, a comparative analysis of the difference in gene expression and physico-chemical properties of fruit at commercial harvest vs. stored fruit for 12 days at 0 °C (cold-stored (CS), pre-storage 1-MCP+CS, and pre-storage high CO2+CS) were used to evaluate the variation among treatments. Several genes were differentially expressed in 1-MCP+CS- and CO2+CS-treated fruits as compared to CS. Moreover, the physico-chemical and sensory data indicated that 1-MCP+CS and CO2+CS suppressed CI and delayed ripening than the CS, which could lead to a longer storage period. We also identified the list of genes that were expressed commonly and exclusively in the fruit treated by 1-MCP+CS and CO2+CS and compared them to the fruit quality parameters. An attempt was also made to identify and categorize genes related to softening, physiological changes, and other ripening-related changes. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR). These results add information on the molecular mechanisms of the pre-storage treatments during cold storage of peach fruit. Understanding the genetic response of susceptible cultivars such as ‘Madoka’ to CI-reducing pre-storage treatments would help breeders release CI-resistant cultivars and could help postharvest technologists to develop more CI-reducing technologies.

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Transmembrane-truncated αvβ3 integrin retains high affinity for ligand binding: evidence for an ‘inside-out’ suppressor?

Biochemical Journal ◽

10.1042/bj3300861 ◽

1998 ◽

Vol 330 (2) ◽

pp. 861-869 ◽

Cited By ~ 59

Author(s):

J. Raj MEHTA ◽

Beate DIEFENBACH ◽

Alex BROWN ◽

Eilish CULLEN ◽

Alfred JONCZYK ◽

...

Keyword(s):

Ligand Binding ◽

Wound Repair ◽

Molecular Mechanisms ◽

Full Length ◽

Αvβ3 Integrin ◽

Cytoplasmic Domains ◽

Bivalent Cation ◽

High Affinity ◽

Cellular Environment

The molecular mechanisms of αvβ3 integrin affinity regulation have important biological implications in tumour development, wound repair and angiogenesis. We expressed, purified and characterized recombinant forms of human αvβ3 (r-αvβ3) and compared the activation state of these with αvβ3 in its cellular environment. The ligand specificity and selectivity of recombinant full-length and double transmembrane truncations of r-αvβ3 cloned in BacPAK6 vectors and expressed in Sf9 and High Five insect cells were compared with those of native placental αvβ3 and the receptor in situ on the cell surface. r-αvβ3 integrins were purified by affinity chromatography from detergent extracts of cells (full-length), and from the culture medium of cells expressing double-truncated r-αvβ3. r-αvβ3 had the same epitopes, ligand-binding specificities, bivalent cation requirements and susceptibility to RGD-containing peptides as native αvβ3. On M21-L4 melanoma cells, αvβ3 mediated binding to vitronectin, but not to fibrinogen unless activated with Mn2+. Non-activated αIIbβ3 integrin as control in M21-L-IIb cells had the opposite profile, mediating binding to fibrinogen, but not to vitronectin unless activated with Mn2+. Thus these receptors had moderate to low ligand affinity. In marked contrast, purified αvβ3 receptors, with or without transmembrane and cytoplasmic domains, were constitutively of high affinity and able to bind strongly to vitronectin, fibronectin and fibrinogen under physiological conditions. Our data suggest that, in contrast with the positive regulation of αIIbβ3 in situ, intracellular controls lower the affinity of αvβ3, and the cytoplasmic domains may act as a target for negative regulators of αvβ3 activity.

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