Stem cell differentiation trajectories in<i>Hydra</i>resolved at single-cell resolution

Siebert, Stefan; Farrell, Jeffrey A.; Cazet, Jack; Abeykoon, Yashodara; Primack, Abby S; Schnitzler, Christine E.; Juliano, Celina E.

doi:10.1101/460154

“…To further detect in which cell types phototransduction genes are likely expressed, we determined to which gene clusters they belong in a stem cell differentiation trajectories clustering by Siebert et al [49]. We expected to see phototransduction genes and one or more opsins expressed in similar cell clusters.…”

Section: Differentiation Trajectories Clusteringmentioning

confidence: 99%

“…To determine in which single cell clusters opsins and phototransduction genes were expressed, we searched the interactive browser containing data from Siebert et al [49]. We first used BLAST in the Hydra 2.0 Genome Project Portal https://research.nhgri.nih.gov/hydra/sequenceserver/ to align our sequences to the Juliano aepLRv2 database.…”

Section: Differentiation Trajectories Clusteringmentioning

confidence: 99%

“…HvOpA1 is the most highly expressed opsin and is expressed in all samples that we looked at, while HvOpB1 is highly expressed in the hypostome and its expression increases during budding and regeneration. By exploring stem cell trajectories [49] we determined that HvOpA1 and HvOpB1 may have functions in nematoblasts and mucous gland cells respectively. Furthermore, by incorporating expression patterns of phototransduction genes, we identified opsins that are co-expressed with other phototransduction genes and imply these opsins may function in the H. vulgaris phototransduction cascade.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Molecular evolution and expression of opsin genes in Hydra vulgaris

Macias-Muñoz

¹

,

Murad

²

,

Mortazavi

³

2019

Preprint

0

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Background: The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris (H. vulgaris) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris. We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions. Results: We identified 45 opsin genes in H. vulgaris, many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes (HvOpA1 and HvOpB1) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris. We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades. Conclusions: This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgarisopsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.

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“…Interestingly, HvOpA1 is the most highly expressed opsin and is expressed in all samples that we looked at, while HvOpB1 is highly expressed in the hypostome and its expression increases during budding and regeneration. By exploring stem cell trajectories [40] we determined that HvOpA1 and HvOpB1 may have functions in nematoblasts and mucous gland cells respectively. Furthermore, by incorporating expression patterns of phototransduction genes, we identified opsins that group together with other phototransduction genes and imply these opsins may function in the H. vulgaris phototransduction cascade.…”

Section: Introductionmentioning

confidence: 99%

Molecular evolution and expression of opsin genes in Hydra vulgaris

Macias-Muñoz

¹

,

Murad

²

,

Mortazavi

³

2019

Preprint

0

View full text Add to dashboard Cite

Background The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris ( H. vulgaris ) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris . We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions. Results We identified 45 opsin genes in H. vulgaris , many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes ( HvOpA1 and HvOpB1 ) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris . We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades. Conclusions This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgaris opsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.

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“…Differentiation trajectories clustering † Clustering according to data from Siebert et al[49] derived using the interactive tool at…”

mentioning

confidence: 99%

Molecular evolution and expression of opsin genes in Hydra vulgaris

Macias-Muñoz

¹

,

Murad

²

,

Mortazavi

³

2019

Preprint

0

View full text Add to dashboard Cite

Background: The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris (H. vulgaris) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris. We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions. Results: We identified 45 opsin genes in H. vulgaris, many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes (HvOpA1 and HvOpB1) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris. We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades. Conclusions: This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgarisopsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.

show abstract

Stem cell differentiation trajectories inHydraresolved at single-cell resolution

Cited by 21 publications

References 136 publications

Molecular evolution and expression of opsin genes in Hydra vulgaris

Molecular evolution and expression of opsin genes in Hydra vulgaris

Molecular evolution and expression of opsin genes in Hydra vulgaris

Molecular evolution and expression of opsin genes in Hydra vulgaris

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