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Yip, H. Y.

Publications and source records attributed to Yip, H. Y..

12 recordsLinked to original sources

Single-cell analyses reveal scyphozoan conserved and specific genes contribution during tissue regeneration in two jellyfish

The phylum Cnidaria is the outgroup of Bilateria and includes sea anemones, corals, hydroids, and jellyfish. Cnidarians play crucial ecological roles in marine ecosystems, including the formation of highly diverse and productive coral reefs, and acting as important predator and prey species. Cnidarians are also well known for their remarkable regeneration capacities. Here, we report single-cell RNA sequencing during bell regeneration in two species of scyphozoans or true jellyfish, Aurelia coerulea and Rhopilema esculentum. We delineated 12 cell populations in Aurelia and Rhopilema, and revealed their respective marker genes and enriched gene pathways. Conserved transcription factor Otx and Wnt/ {beta}-catenin signalling pathway genes were identified during regeneration processes. Additionally, we discovered two conserved, sequentially activated modules during regeneration, with stem cells, gastrodermal cells, neural cells, and secretory gland cells modulated in the first phase, followed by cnidocytes in the second phase. Further comparison among cnidarian genomes identified a suite of scyphozoan lineage-specific genes, a subset of which were frequently significantly expressed in cnidocytes in both jellyfish species during the first phase of regeneration. This study reveals key insights into the evolution and contribution of conserved and novel genes to the formation of lineage-specific genetic networks and biological processes.

evolutionary biology↗

Phylogenomics, Classification, and Lifestyle Evolution in Raft- and Nursery web- Spiders (Araneae: Dolomedidae and Pisauridae)

Pisauridae Simon, 1890 or "nursery web spiders" are a global and heterogenous assemblage of spider genera with diverse lifestyles, containing web builders and webless species, as well as terrestrial and semi-aquatic species, notably "fishing spiders", genus Dolomedes Latreille, 1804. Incomplete, unresolved, or conflicting phylogenies have so far hampered testing for Dolomedes and pisaurid monophyly and evolution. Here, we broadly address these questions within a phylogenomic and comparative framework. Our goals are i) reconstruction of a robust phylogeny to test the monophyly of Dolomedes and Pisauridae and to amend Dolomedes classification; ii) estimation of evolutionary shifts and trends in lifestyles and capture webs; and iii) evaluation of hypotheses of morphological trait association with a semi-aquatic lifestyle. To this end we generate subgenomic data (ultraconserved elements or UCE) for 53 Dolomedes species and 28 pisaurid genera. We analyze these data using maximum likelihood, Bayesian, and multi-species coalescence approaches, as well as using two different phylogenetic time calibration methods, RelTime and MCMCtree. Consistent across analytical approaches, our phylogenies reject the monophyly of both Pisauridae and Dolomedes. "Pisaurid" genera fall into three clades: 1) Focal Clade I groups the majority, including Pisaura Simon, 1886, hence representing true pisaurids; 2) Focal Clade II = Blandinia Tonini et al., 2016 is sister to Trechaleidae Simon, 1890 and Lycosidae Sundevall, 1833; 3) Focal Clade III with fishing and raft spiders groups Dolomedes, Megadolomedes Davies and Raven, 1980, and Ornodolomedes Raven and Hebron, 2018 and is sister to Focal Clade II, Trechaleidae, and Lycosidae. Our taxonomy, based on complementary taxa and morphological evidence, resurrects Dolomedidae Simon, 1876 to include Dolomedes and the Oceanic genera Bradystichus Simon, 1884, Megadolomedes, Caledomedes Raven and Hebron, 2018, Mangromedes Raven and Hebron, 2018, Ornodolomedes, and Tasmomedes Raven and Hebron, 2018. Both RelTime and MCMCtree analyses yield comparable divergence estimations: Pisauridae origin is estimated between 29 and 40 Ma; Blandinia between 21 and 34 Ma; Dolomedidae between 10 and 17 Ma; and Dolomedes between 9 and 16 Ma. In order to avoid misleading significant correlations and/or over-resolved ancestral states, we performed taxon sampling bias correction in all evolutionary analyses. Evolutionary analyses reconstruct semi-aquatic lifestyle as ancestral to a large clade containing pisaurids, lycosids, trechaleids, Blandinia, and dolomedids, with several reversals to terrestrial lifestyle. Capture webs evolved at least three times, with reversals. Counter to expectation, the evolution of lifestyles and capture webs are independent. Although leg and tarsus lengths do not indicate lifestyles, semi-aquatic taxa are significantly larger than terrestrial ones. We explain this pattern with a biomechanical threshold over which surface tension can be broken while spiders forage under water. Our time-calibrated analyses indicate that the evolution of terrestrial and web-building lifestyles from semi-aquatic ancestors in Pisauridae coincided with cooling and drying climates in the mid-Miocene. We therefore hypothesize that climatic changes have acted as strong selection pressures toward lifestyle diversification.

evolutionary biology↗

Insect metamorphosis is regulated differently between sexes by members of a microRNA cluster

Insects comprise the majority of all described animal species and dominate the terrestrial habitats. The evolution of insect metamorphosis played a profound role in their successful adaptation and radiation. Insect metamorphosis is dependent on hormones ecdysteroids and sesquiterpenoids such as juvenile hormone. Despite the fact there are genuine differences between sexes during insect metamorphosis which facilitate their successful mating, how such sexual dimorphism in metamorphosis is being controlled is poorly known. We first generated transcriptomic profiles of male and female flies in late larvae and early pupae stages. Using a combination of genome-wide prediction and in vitro dual-luciferase validations, members of a microRNA cluster miR-277/34 were found to potentially regulate the neuropeptide receptor (AstC-R1) that when activated inhibits the sesquiterpenoid pathway and a juvenile hormone-dependent transcription factor (Kr-h1) in fly Drosophila melanogaster. Loss-of-function mutants were created deleting either miR-277 or miR-34, and expression levels of both AstC-R1 and Kr-h1 as well as ecdysteroid and sesquiterpenoid hormone titres were altered. Further comparison of transcriptomes of the late larvae and early pupae of both sexes revealed differential gene pathways being regulated by members of miR-277/34 between sexes during metamorphosis. This study highlights how members of a microRNA cluster control hormonal and developmental gene pathways in different sexes of insects during metamorphosis.

evolutionary biology↗

Genome of tropical bed bug Cimex hemipterus (Cimicidae, Hemiptera) reveals tetraspanin expanded in bed bug ancestor

Cimex species are ectoparasites that exclusively feed on warm-blooded animals such as birds and mammals. Three cimicid species are known to be persistent pests for humans, including the tropical bed bug C. hemipterus, common bed bug C. lectularius, and Eastern bat bug Leptocimex boueti. To date, genomic information is restricted to the common bed bug C. lectularius, which limits understand their biology and to provide controls of bed bug infestations. Here, a chromosomal-level genome assembly of C. hemipterus (495 Mb) containing on 16 pseudochromosomes (scaffold N50 = 34 Mb), together with 9 messenger RNA and small RNA transcriptomes were obtained. Comparison between hemipteran genomes, we found that the tetraspanin superfamily were expanded in the Cimex ancestor. This study provides the first genome assembly for the tropical bed bug C. hemipterus, and offers an unprecedented opportunity to address to questions relating to bed bug infestations, as well as genomic evolution to hemipterans more widely.

genomics↗

Response of protein coding genes and microRNAs to temperature changes in four insect species

Insects are the most abundant described living creatures in the world, and they play important roles in our global ecosystem. Climate change affects global biodiversity, and researchers in many fields are striving to better understand the impact of the climate crisis. One such endeavour is the study of temperature-dependent effects on insects. At present, we know little of how climate affects gene expression in insects of different sexes. Here, we took four species of fruit flies of the genus Drosophila (D. melanogaster, D. virilis, D. pseudoobscura, and D. erecta), and subjected the male and female flies of each species to three different temperatures to test their sex-specific gene expression responses. A total of 144 transcriptomic profiles of protein-coding genes and microRNAs were generated. We found that, at the same temperature, there were more male-biased than female-biased protein-coding genes and microRNAs in all four investigated drosophilid species. Interestingly, upon temperature changes, there were more differentially expressed protein-coding genes in females than in males in all four investigated species, while the microRNAs were highly species- and sex-specific. This study provides the first evidence that sex-biased protein-coding gene and microRNA expression responses to temperature change differ between insect species within the same genus, and demonstrates the complexity of sex-specific responses of insects to climate change. HighlightsO_LIAt the same temperature, protein coding gene and microRNA expression showed a greater bias towards males than towards females in all four tested insect species. C_LIO_LIIn response to increasing temperature, females of all 4 tested species exhibited more differentially expressed genes than did males, and enrichment analyses showed that they are species-specific. C_LIO_LIDifferentially expressed microRNAs did not show a conserved trend between insects upon temperature changes. C_LIO_LISex-specific gene and microRNA expression of insects in response to climate change evidently involves a complex adaptation mechanism. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/591511v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1037b18org.highwire.dtl.DTLVardef@18683f3org.highwire.dtl.DTLVardef@40dee5org.highwire.dtl.DTLVardef@e9a108_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)

The edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae) is wood-decaying and can be commonly found worldwide. It has also been used in food additives given its ability to synthesize long-chain glycolipids. In this study, we present the genome assembly of D. spathularia using a combination of PacBio HiFi reads and Omni-C data. The genome size of D. spathularia is 29.2 Mb and in high sequence contiguity and completeness, including scaffold N50 of 1.925 Mb and 92.0% BUSCO score, respectively. A total of 11,510 protein-coding genes, and 474.7 kb repeats accounting for 1.62% of the genome, were also predicted. The D. spathularia genome assembly generated in this study provides a valuable resource for understanding their ecology such as wood decaying capability, evolutionary relationships with other fungus, as well as their unique biology and applications in the food industry.

genomics↗

Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

The long-spined sea urchin Diadema setosum is an algal and coral feeder widely distributed in the Indo-Pacific and can cause severe bioerosion on the reef community. Nevertheless, the lack of genomic information has hindered the study its ecology and evolution. Here, we report the chromosomal-level genome (885.8 Mb) of the long-spined sea urchin D. setosum using a combination of PacBio long-read sequencing and Omni-C scaffolding technology. The assembled genome contained scaffold N50 length of 38.3 Mb, 98.1 % of BUSCO (Geno, metazoa_odb10) genes, and with 98.6% of the sequences anchored to 22 pseudo-molecules/chromosomes. A total of 27,478 genes including 23,030 protein-coding genes were annotated. The high-quality genome of D. setosum presented here provides a significant resource for further understanding on the ecological and evolutionary studies of this coral reef associated sea urchin.

genomics↗

Genome assembly of the rare and endangered Grantham's camellia, Camellia granthamiana

The Granthams camellia (Camellia granthamiana Sealy) is a rare and endangered tea species that is endemic to southern China, and was first discovered in Hong Kong in 1955. Despite its high conservation value, genomic resources of C. granthamiana remain limited. Here, we present a chromosome-scale draft genome of the tetraploid C. granthamiana (2n = 4x = 60) using a combination of PacBio long read sequencing and Omni-C data. The assembled genome size is [~]2.4 Gb with most sequences anchored to 15 pseudochromosomes that resemble a monoploid genome. The genome is of high contiguity, with a scaffold N50 of 139.7 Mb, and high completeness with a 97.8% BUSCO score. Gene model prediction resulted in a total 76,992 protein-coding genes with a BUSCO score of 85.9%. 1.65 Gb of repeat content was annotated, which accounts for 68.48% of the genome. The Granthams camellia genome assembly provides a valuable resource for future investigations on its biology, ecology, phylogenomic relationships with other Camellia species, as well as set up a foundation for further conservation measures.

plant biology↗

Genome assembly of the milky mangrove Excoecaria agallocha

The milky mangrove Excoecaria agallocha is a latex-secreting mangrove that are distributed in tropical and subtropical regions. While its poisonous latex is regarded as a potential source of phytochemicals for biomedical applications, the genomic resources of E. agallocha remains limited. Here, we present a chromosomal level genome of E. agallocha, assembled from the combination of PacBio long-read sequencing and Omni-C data. The resulting assembly size is 1,332.45 Mb and has high contiguity and completeness with a scaffold N50 of 58.9 Mb and a BUSCO score of 98.4 %. 73,740 protein-coding genes were also predicted. The milky mangrove genome provides a useful resource for further understanding the biosynthesis of phytochemical compounds in E. agallocha.

genomics↗

Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

Troides aeacus, the golden birdwing (Lepidoptera, Papilionidae) is a large swallowtail butterfly widely distributed in Asia. Despite its occurrence, T. aeacus has been assigned as a major protective species in many places given the loss of their native habitats under urbanisation and anthropogenic activities. Nevertheless, the lack of its genomic resources hinders our understanding of their biology, diversity, as well as carrying out conservation measures based on genetic information or markers. Here, we report the first chromosomal-level genome assembly of T. aeacus using a combination of PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (351 Mb) contains 98.94% of the sequences anchored to 30 pseudo-molecules. The genome assembly also has high sequence continuity with scaffold length N50 = 12.2 Mb. A total of 28,749 protein-coding genes were predicted, and high BUSCO score completeness (98.9% of BUSCO metazoa_odb10 genes) was also revealed. This high-quality genome offers a new and significant resource for understanding the swallowtail butterfly biology, as well as carrying out conservation measures of this ecologically important lepidopteran species.

genomics↗

Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication

Whole genome duplication (WGD) has occurred in relatively few sexually reproducing invertebrates. Consequently, the WGD that occurred in the common ancestor of horseshoe crabs ~135 million years ago provides a rare opportunity to decipher the evolutionary consequences of a duplicated invertebrate genome. Here, we present a high-quality genome assembly for the mangrove horseshoe crab Carcinoscorpius rotundicauda (1.7Gb, N50 = 90.2Mb, with 89.8% sequences anchored to 16 pseudomolecules, 2n = 32), and a resequenced genome of the tri-spine horseshoe crab Tachypleus tridentatus (1.7Gb, N50 = 109.7Mb). Analyses of gene families, microRNAs, and synteny show that horseshoe crabs have undergone three rounds (3R) of WGD, and that these WGD events are shared with spiders. Comparison of the genomes of C. rotundicauda and T. tridentatus populations from several geographic locations further elucidates the diverse fates of both coding and noncoding genes. Together, the present study represents a cornerstone for a better understanding of the consequences of invertebrate WGD events on evolutionary fates of genes and microRNAs at individual and population levels, and highlights the genetic diversity with practical values for breeding programs and conservation of horseshoe crabs.

evolutionary biology↗

Varying constraints impact the miR-6/5/4/286/3/309 microRNA cluster in Drosophila leg development

A striking feature of microRNAs is that they are often clustered in the genomes of animals. The functional and evolutionary consequences of this clustering remain obscure. Here, we investigated a microRNA cluster miR-6/5/4/286/3/309 that is conserved across drosophilid lineages. Small RNA sequencing revealed expression of this microRNA cluster in Drosophila melanogaster leg discs, and conditional overexpression of the whole cluster resulted in leg appendage shortening. Transgenic overexpression lines expressing different combinations of microRNA cluster members were also constructed. Expression of individual microRNAs from the cluster resulted in a normal wild-type phenotype, but either the expression of several ancient microRNAs together (miR-5/4/286/3/309) or more recently evolved clustered microRNAs (miR-6-1/2/3) can recapitulate the phenotypes generated by the whole-cluster overexpression. Screening of transgenic fly lines revealed down-regulation of leg patterning gene cassettes in generation of the leg-shortening phenotype. Furthermore, cell transfection with different combinations of microRNA cluster members revealed a suite of downstream genes targeted by all cluster members, as well as complements of targets that are unique for distinct microRNAs. Considering together the microRNA targets and the evolutionary ages of each microRNA in the cluster demonstrates the importance of microRNA clustering, where new members can reinforce and modify the selection forces on both the cluster regulation and the gene regulatory network of existing microRNAs.

evolutionary biology↗