1
|
Kostyuchenko RP, Amosov AV. Spatial Colinear but Broken Temporal Expression of Duplicated ParaHox Genes in Asexually Reproducing Annelids, Nais communis and Pristina longiseta. Genes (Basel) 2023; 14:1501. [PMID: 37510405 PMCID: PMC10379933 DOI: 10.3390/genes14071501] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
ParaHox genes are key developmental regulators involved in the patterning of the digestive tract along the anteroposterior axis and the development of the nervous system. Most studies have focused on the function of these genes in embryogenesis, while their expression patterns in postembryonic development often remain unknown. In this study, we identified for the first time all ParaHox orthologs in two naidid oligochaetes, N. communis and P. longiseta, and described their expression patterns during normal growth and fission in these animals. We showed that Gsx and Cdx are presented by two paralogs, while Xlox is a single copy gene in both species. Using whole-mount in situ hybridization, we also found that orthologs, except for the Xlox gene, have similar activity patterns with minor differences in details, while the expression patterns of paralogs can differ significantly. However, all these genes are involved in axial patterning and/or in tissue remodeling during growth and asexual reproduction in naidids. Moreover, during paratomic fission, these genes are expressed with spatial colinearity but temporal colinearity is broken. The results of this study may be evidence of the functional diversification of duplicated genes and suggest involvement of the ParaHox genes in whole-body patterning during growth and asexual reproduction in annelids.
Collapse
Affiliation(s)
- Roman P Kostyuchenko
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia
| | - Artem V Amosov
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia
| |
Collapse
|
2
|
Nong W, Yu Y, Aase-Remedios ME, Xie Y, So WL, Li Y, Wong CF, Baril T, Law STS, Lai SY, Haimovitz J, Swale T, Chen SS, Kai ZP, Sun X, Wu Z, Hayward A, Ferrier DEK, Hui JHL. Genome of the ramshorn snail Biomphalaria straminea-an obligate intermediate host of schistosomiasis. Gigascience 2022; 11:6528774. [PMID: 35166339 PMCID: PMC8848322 DOI: 10.1093/gigascience/giac012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/02/2022] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Schistosomiasis, or bilharzia, is a parasitic disease caused by trematode flatworms of the genus Schistosoma. Infection by Schistosoma mansoni in humans results when cercariae emerge into water from freshwater snails in the genus Biomphalaria and seek out and penetrate human skin. The snail Biomphalaria straminea is native to South America and is now also present in Central America and China, and represents a potential vector host for spreading schistosomiasis. To date, genomic information for the genus is restricted to the neotropical species Biomphalaria glabrata. This limits understanding of the biology and management of other schistosomiasis vectors, such as B. straminea. FINDINGS Using a combination of Illumina short-read, 10X Genomics linked-read, and Hi-C sequencing data, our 1.005 Gb B. straminea genome assembly is of high contiguity, with a scaffold N50 of 25.3 Mb. Transcriptomes from adults were also obtained. Developmental homeobox genes, hormonal genes, and stress-response genes were identified, and repeat content was annotated (40.68% of genomic content). Comparisons with other mollusc genomes (including Gastropoda, Bivalvia, and Cephalopoda) revealed syntenic conservation, patterns of homeobox gene linkage indicative of evolutionary changes to gene clusters, expansion of heat shock protein genes, and the presence of sesquiterpenoid and cholesterol metabolic pathway genes in Gastropoda. In addition, hormone treatment together with RT-qPCR assay reveal a sesquiterpenoid hormone responsive system in B. straminea, illustrating that this renowned insect hormonal system is also present in the lophotrochozoan lineage. CONCLUSION This study provides the first genome assembly for the snail B. straminea and offers an unprecedented opportunity to address a variety of phenomena related to snail vectors of schistosomiasis, as well as evolutionary and genomics questions related to molluscs more widely.
Collapse
Affiliation(s)
- Wenyan Nong
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yifei Yu
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Madeleine E Aase-Remedios
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Yichun Xie
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yiqian Li
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Cheuk Fung Wong
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Sean T S Law
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Sheung Yee Lai
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | - Shan-Shan Chen
- Institute of Agro-food Standard and Testing Technology, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Zhen-Peng Kai
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, China
| | - Xi Sun
- Sun Yat-sen University, Guangdong, China
| | | | | | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St. Andrews, St. Andrews, UK
| | - Jerome H L Hui
- School of Life Science, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| |
Collapse
|
3
|
Evidence from oyster suggests an ancient role for Pdx in regulating insulin gene expression in animals. Nat Commun 2021; 12:3117. [PMID: 34035261 PMCID: PMC8149454 DOI: 10.1038/s41467-021-23216-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Hox and ParaHox genes encode transcription factors with similar expression patterns in divergent animals. The Pdx (Xlox) homeobox gene, for example, is expressed in a sharp spatial domain in the endodermal cell layer of the gut in chordates, echinoderms, annelids and molluscs. The significance of comparable gene expression patterns is unclear because it is not known if downstream transcriptional targets are also conserved. Here, we report evidence indicating that a classic transcriptional target of Pdx1 in vertebrates, the insulin gene, is a likely direct target of Pdx in Pacific oyster adults. We show that one insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue. Transcriptomic comparison suggests that this tissue plays a similar role to the vertebrate pancreas. Using ATAC-seq and ChIP, we identify an upstream regulatory element of the cgILP gene which shows binding interaction with cgPdx protein in oyster hepatopancreas and demonstrate, using a cell culture assay, that the oyster Pdx can act as a transcriptional activator through this site, possibly in synergy with NeuroD. These data argue that a classic homeodomain-target gene interaction dates back to the origin of Bilateria. In vertebrates insulin is a direct transcriptional target of Pdx: the same is true in Pacific oysters and the authors show insulin-related gene, cgILP, is co-expressed with cgPdx in oyster digestive tissue, showing this gene interaction dates back to the origin of Bilateria.
Collapse
|
4
|
Lin CY, Yu JK, Su YH. Evidence for BMP-mediated specification of primordial germ cells in an indirect-developing hemichordate. Evol Dev 2020; 23:28-45. [PMID: 33283431 DOI: 10.1111/ede.12361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/08/2020] [Accepted: 11/09/2020] [Indexed: 01/14/2023]
Abstract
Primordial germ cells (PGCs) are specified during development by either one of two major mechanisms, the preformation mode or the inductive mode. Because the inductive mode is widely employed by many bilaterians and early branching metazoan lineages, it has been postulated as an ancestral mechanism. However, among the deuterostome species that have been studied, invertebrate chordates use the preformation mode, while many vertebrate and echinoderm species are known to utilize an inductive mechanism, thus leaving the evolutionary history of PGC specification in the deuterostome lineage unclear. Hemichordates are the sister phylum of echinoderms, and together they form a clade called Ambulacraria that represents the closest group to the chordates. Thus, research in hemichordates is highly informative for resolving this issue. In this study, we investigate the developmental process of PGCs in an indirect-developing hemichordate, Ptychodera flava. We show that maternal transcripts of the conserved germline markers vasa, nanos, and piwi1 are ubiquitously distributed in early P. flava embryos, and these genes are coexpressed specifically in the dorsal hindgut starting from the gastrula stage. Immunostaining revealed that Vasa protein is concentrated toward the vegetal pole in early P. flava embryos, and it is restricted to cells in the dorsal hindgut of gastrulae and newly hatched larvae. The Vasa-positive cells later contribute to the developing trunk coeloms of the larvae and eventually reside in the adult gonads. We further show that bone morphogenetic protein (BMP) signaling is required to activate expression of the germline determinants in the gastrula hindgut, suggesting that PGC specification is induced by BMP signaling in P. flava. Our data support the hypothesis that the inductive mode is a conserved mechanism in Ambulacraria, which might even trace back to the common ancestor of Deuterostomes.
Collapse
Affiliation(s)
- Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
5
|
Johnson AB, Lambert JD. The Caudal ParaHox gene is required for hindgut development in the mollusc Tritia (a.k.a. Ilyanassa). Dev Biol 2020; 470:1-9. [PMID: 33191200 DOI: 10.1016/j.ydbio.2020.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 11/26/2022]
Abstract
Caudal homeobox genes are found across animals, typically linked to two other homeobox genes in what has been called the ParaHox cluster. These genes have been proposed to pattern the anterior-posterior axis of the endoderm ancestrally, but the expression of Caudal in extant groups is varied and often occurs in other germ layers. Here we examine the role of Caudal in the embryo of the mollusc Tritia (Ilyanassa) obsoleta. ToCaudal expression is initially broad, then becomes progressively restricted and is finally only in the developing hindgut (a.k.a. intestine). Knockdown of ToCaudal using morpholino oligonucleotides specifically blocks hindgut development, indicating that despite its initially broad expression, the functional role of ToCaudal is in hindgut patterning. This is the first functional characterization of Caudal in an animal with spiralian development, which is an ancient mode of embryogenesis that arose early in bilaterian animal evolution. These results are consistent with the hypothesis that the ancestral role of the ParaHox genes was anterior-posterior patterning of the endoderm.
Collapse
Affiliation(s)
- Adam B Johnson
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - J David Lambert
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
| |
Collapse
|
6
|
On the origin of vertebrate body plan: Insights from the endoderm using the hourglass model. Gene Expr Patterns 2020; 37:119125. [PMID: 32599288 DOI: 10.1016/j.gep.2020.119125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 05/25/2020] [Accepted: 06/21/2020] [Indexed: 11/23/2022]
Abstract
The vertebrate body plan is thought to be derived during the early Cambrian from a worm-like chordate ancestor. While all three germ layers were clearly involved in this innovation, the role of the endoderm remains elusive. According to the hourglass model, the optimal window for investigating the evolution of vertebrate endoderm-derived structures during cephalochordate development is from the Spemann's organizer stage to the opening of the mouth (Stages 1-7, described herein). Regulatory gene expression, examined during these stages, illustrate that the cephalochordate endoderm is patterned into 12 organ primordia. Early vertebrates inherited at least a portion of 6 of these primordia, while the remainder were lost. Of those that were preserved, we demonstrate that the vertebrate symmetric mouth was built on a vestige of the anterior pre-oral pit, that the pre-existing pharyngeal pouch in this chordate ancestor laid the foundation for the new neural crest cell (NCC)-derived vertebrate-type pharyngeal arches, that the thyroid evolved from the posterior endostyle primordim, that the pancreas was derived from the Pdx1-expressing diverticulum primordium, and the small and large intestines originated with the Cdx1-expressing hindgut rudiments. This investigation uncovers the evolutionary foundations of vertebrate endoderm-derived structures, and demonstrates that the number of organ primordia were reduced during evolution.
Collapse
|
7
|
Zhong Y, Herrera-Úbeda C, Garcia-Fernàndez J, Li G, Holland PWH. Mutation of amphioxus Pdx and Cdx demonstrates conserved roles for ParaHox genes in gut, anus and tail patterning. BMC Biol 2020; 18:68. [PMID: 32546156 PMCID: PMC7296684 DOI: 10.1186/s12915-020-00796-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The homeobox genes Pdx and Cdx are widespread across the animal kingdom and part of the small ParaHox gene cluster. Gene expression patterns suggest ancient roles for Pdx and Cdx in patterning the through-gut of bilaterian animals although functional data are available for few lineages. To examine evolutionary conservation of Pdx and Cdx gene functions, we focus on amphioxus, small marine animals that occupy a pivotal position in chordate evolution and in which ParaHox gene clustering was first reported. RESULTS Using transcription activator-like effector nucleases (TALENs), we engineer frameshift mutations in the Pdx and Cdx genes of the amphioxus Branchiostoma floridae and establish mutant lines. Homozygous Pdx mutants have a defect in amphioxus endoderm, manifest as loss of a midgut region expressing endogenous GFP. The anus fails to open in homozygous Cdx mutants, which also have defects in posterior body extension and epidermal tail fin development. Treatment with an inverse agonist of retinoic acid (RA) signalling partially rescues the axial and tail fin phenotypes indicating they are caused by increased RA signalling. Gene expression analyses and luciferase assays suggest that posterior RA levels are kept low in wild type animals by a likely direct transcriptional regulation of a Cyp26 gene by Cdx. Transcriptome analysis reveals extensive gene expression changes in mutants, with a disproportionate effect of Pdx and Cdx on gut-enriched genes and a colinear-like effect of Cdx on Hox genes. CONCLUSIONS These data reveal that amphioxus Pdx and Cdx have roles in specifying middle and posterior cell fates in the endoderm of the gut, roles that likely date to the origin of Bilateria. This conclusion is consistent with these two ParaHox genes playing a role in the origin of the bilaterian through-gut with a distinct anus, morphological innovations that contributed to ecological change in the Cambrian. In addition, we find that amphioxus Cdx promotes body axis extension through a molecular mechanism conserved with vertebrates. The axial extension role for Cdx dates back at least to the origin of Chordata and may have facilitated the evolution of the post-anal tail and active locomotion in chordates.
Collapse
Affiliation(s)
- Yanhong Zhong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Carlos Herrera-Úbeda
- Department of Zoology, University of Oxford, Oxford, OX1 3SZ, UK.,Department of Genetics, Microbiology & Statistics, and Institute of Biomedicine (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology & Statistics, and Institute of Biomedicine (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Guang Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China.
| | | |
Collapse
|
8
|
BMP controls dorsoventral and neural patterning in indirect-developing hemichordates providing insight into a possible origin of chordates. Proc Natl Acad Sci U S A 2019; 116:12925-12932. [PMID: 31189599 DOI: 10.1073/pnas.1901919116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A defining feature of chordates is the unique presence of a dorsal hollow neural tube that forms by internalization of the ectodermal neural plate specified via inhibition of BMP signaling during gastrulation. While BMP controls dorsoventral (DV) patterning across diverse bilaterians, the BMP-active side is ventral in chordates and dorsal in many other bilaterians. How this phylum-specific DV inversion occurs and whether it is coupled to the emergence of the dorsal neural plate are unknown. Here we explore these questions by investigating an indirect-developing enteropneust from the hemichordate phylum, which together with echinoderms form a sister group of the chordates. We found that in the hemichordate larva, BMP signaling is required for DV patterning and is sufficient to repress neurogenesis. We also found that transient overactivation of BMP signaling during gastrulation concomitantly blocked mouth formation and centralized the nervous system to the ventral ectoderm in both hemichordate and sea urchin larvae. Moreover, this mouthless, neurogenic ventral ectoderm displayed a medial-to-lateral organization similar to that of the chordate neural plate. Thus, indirect-developing deuterostomes use BMP signaling in DV and neural patterning, and an elevated BMP level during gastrulation drives pronounced morphological changes reminiscent of a DV inversion. These findings provide a mechanistic basis to support the hypothesis that an inverse chordate body plan emerged from an indirect-developing ancestor by tinkering with BMP signaling.
Collapse
|
9
|
He C, Han T, Liao X, Zhou Y, Wang X, Guan R, Tian T, Li Y, Bi C, Lu N, He Z, Hu B, Zhou Q, Hu Y, Lu Z, Chen JY. Phagocytic intracellular digestion in amphioxus ( Branchiostoma). Proc Biol Sci 2019; 285:rspb.2018.0438. [PMID: 29875301 PMCID: PMC6015868 DOI: 10.1098/rspb.2018.0438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/11/2018] [Indexed: 01/10/2023] Open
Abstract
The digestive methods employed by amphioxus (Branchiostoma)—both intracellular phagocytic digestion and extracellular digestion—have been discussed since 1937. Recent studies also show that epithelial cells lining the Branchiostoma digestive tract can express many immune genes. Here, in Branchiostoma belcheri, using a special tissue fixation method, we show that some epithelial cells, especially those lining the large diverticulum protruding from the gut tube, phagocytize food particles directly, and Branchiostoma can rely on this kind of phagocytic intracellular digestion to obtain energy throughout all stages of its life. Gene expression profiles suggest that diverticulum epithelial cells have functional features of both digestive cells and phagocytes. In starved Branchiostoma, these cells accumulate endogenous digestive and hydrolytic enzymes, whereas, when sated, they express many kinds of immune genes in response to stimulation by phagocytized food particles. We also found that the distal hindgut epithelium can phagocytize food particles, but not as many. These results illustrate phagocytic intercellular digestion in Branchiostoma, explain why Branchiostoma digestive tract epithelial cells express typical immune genes and suggest that the main physiological function of the Branchiostoma diverticulum is different from that of the vertebrate liver.
Collapse
Affiliation(s)
- Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Tingyu Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Xin Liao
- Nanjing Institute of Paleontology and Geology, Nanjing, People's Republic of China.,Guangxi Mangrove Research Center, Beihai, Guangxi, People's Republic of China
| | - Yuxin Zhou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Xiuqiang Wang
- Beihai Marine Science and Economy Park, Beihai, Guangxi, People's Republic of China
| | - Rui Guan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Tian Tian
- Department of Neurobiology, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yixin Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Changwei Bi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | - Ziyi He
- Electron Microscopy Research Center, School of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Bing Hu
- Electron Microscopy Research Center, School of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Qiang Zhou
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yue Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, People's Republic of China
| | | | | |
Collapse
|
10
|
Evolution of the bilaterian mouth and anus. Nat Ecol Evol 2018; 2:1358-1376. [PMID: 30135501 DOI: 10.1038/s41559-018-0641-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 06/26/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
It is widely held that the bilaterian tubular gut with mouth and anus evolved from a simple gut with one major gastric opening. However, there is no consensus on how this happened. Did the single gastric opening evolve into a mouth, with the anus forming elsewhere in the body (protostomy), or did it evolve into an anus, with the mouth forming elsewhere (deuterostomy), or did it evolve into both mouth and anus (amphistomy)? These questions are addressed by the comparison of developmental fates of the blastopore, the opening of the embryonic gut, in diverse animals that live today. Here we review comparative data on the identity and fate of blastoporal tissue, investigate how the formation of the through-gut relates to the major body axes, and discuss to what extent evolutionary scenarios are consistent with these data. Available evidence indicates that stem bilaterians had a slit-like gastric opening that was partially closed in subsequent evolution, leaving open the anus and most likely also the mouth, which would favour amphistomy. We discuss remaining difficulties, and outline directions for future research.
Collapse
|
11
|
Fan TP, Ting HC, Yu JK, Su YH. Reiterative use of FGF signaling in mesoderm development during embryogenesis and metamorphosis in the hemichordate Ptychodera flava. BMC Evol Biol 2018; 18:120. [PMID: 30075704 PMCID: PMC6091094 DOI: 10.1186/s12862-018-1235-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/26/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Mesoderm is generally considered to be a germ layer that is unique to Bilateria, and it develops into diverse tissues, including muscle, and in the case of vertebrates, the skeleton and notochord. Studies on various deuterostome animals have demonstrated that fibroblast growth factor (FGF) signaling is required for the formation of many mesodermal structures, such as vertebrate somites, from which muscles are differentiated, and muscles in sea urchin embryos, suggesting an ancient role of FGF signaling in muscle development. However, the formation of trunk muscles in invertebrate chordates is FGF-independent, leading to ambiguity about this ancient role in deuterostomes. To further understand the role of FGF signaling during deuterostome evolution, we investigated the development of mesodermal structures during embryogenesis and metamorphosis in Ptychodera flava, an indirect-developing hemichordate that has larval morphology similar to echinoderms and adult body features that are similar to chordates. RESULTS Here we show that genes encoding FGF ligands, FGF receptors and transcription factors that are known to be involved in mesoderm formation and myogenesis are expressed dynamically during embryogenesis and metamorphosis. FGF signaling at the early gastrula stage is required for the specification of the mesodermal cell fate in P. flava. The mesoderm cells are then differentiated stepwise into the hydroporic canal, the pharyngeal muscle and the muscle string; formation of the last two muscular structures are controlled by FGF signaling. Moreover, augmentation of FGF signaling during metamorphosis accelerated the process, facilitating the transformation from cilia-driven swimming larvae into muscle-driven worm-like juveniles. CONCLUSIONS Our data show that FGF signaling is required for mesoderm induction and myogenesis in the P. flava embryo, and it is reiteratively used for the morphological transition during metamorphosis. The dependence of muscle development on FGF signaling in both planktonic larvae and sand-burrowing worms supports its ancestral role in deuterostomes.
Collapse
Affiliation(s)
- Tzu-Pei Fan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529, Taiwan.,Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan.,Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Hsiu-Chi Ting
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan
| | - Yi-Hsien Su
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529, Taiwan. .,Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Rd., Sec. 2, Nankang, Taipei, 11529, Taiwan. .,Biotechnology Center, National Chung Hsing University, Taichung, 40227, Taiwan.
| |
Collapse
|
12
|
Gonzalez P, Uhlinger KR, Lowe CJ. The Adult Body Plan of Indirect Developing Hemichordates Develops by Adding a Hox-Patterned Trunk to an Anterior Larval Territory. Curr Biol 2016; 27:87-95. [PMID: 27939313 DOI: 10.1016/j.cub.2016.10.047] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/12/2016] [Accepted: 10/25/2016] [Indexed: 01/27/2023]
Abstract
Many animals are indirect developers with distinct larval and adult body plans [1]. The molecular basis of differences between larval and adult forms is often poorly understood, adding a level of uncertainty to comparative developmental studies that use data from both indirect and direct developers. Here we compare the larval and adult body plans of an indirect developing hemichordate, Schizocardium californicum [2]. We describe the expression of 27 transcription factors with conserved roles in deuterostome ectodermal anteroposterior (AP) patterning in developing embryos, tornaria larvae, and post-metamorphic juveniles and show that the tornaria larva of S. californicum is transcriptionally similar to a truncated version of the adult. The larval ectoderm has an anterior molecular signature, while most of the trunk, defined by the expression of hox1-7, is absent. Posterior ectodermal activation of Hox is initiated in the late larva prior to metamorphosis, in preparation for the transition to the adult form, in which the AP axis converges on a molecular architecture similar to that of the direct developing hemichordate Saccoglossus kowalevskii. These results identify a molecular correlate of a major difference in body plan between hemichordate larval and adult forms and confirm the hypothesis that deuterostome larvae are "swimming heads" [3]. This will allow future comparative studies with hemichordates to take into account molecular differences caused by early life history evolution within the phylum. Additionally, comparisons with other phyla suggest that a delay in trunk development is a feature of indirect development shared across distantly related phyla.
Collapse
Affiliation(s)
- Paul Gonzalez
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950, USA
| | - Kevin R Uhlinger
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950, USA
| | - Christopher J Lowe
- Hopkins Marine Station, Department of Biology, Stanford University, 120 Ocean View Boulevard, Pacific Grove, CA 93950, USA.
| |
Collapse
|
13
|
Hemichordate models. Curr Opin Genet Dev 2016; 39:71-78. [DOI: 10.1016/j.gde.2016.05.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/28/2016] [Accepted: 05/30/2016] [Indexed: 11/23/2022]
|
14
|
Arnone MI, Andrikou C, Annunziata R. Echinoderm systems for gene regulatory studies in evolution and development. Curr Opin Genet Dev 2016; 39:129-137. [DOI: 10.1016/j.gde.2016.05.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/07/2016] [Accepted: 05/30/2016] [Indexed: 12/13/2022]
|
15
|
Garstang MG, Osborne PW, Ferrier DEK. TCF/Lef regulates the Gsx ParaHox gene in central nervous system development in chordates. BMC Evol Biol 2016; 16:57. [PMID: 26940763 PMCID: PMC4776371 DOI: 10.1186/s12862-016-0614-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/11/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ParaHox genes play an integral role in the anterior-posterior (A-P) patterning of the nervous system and gut of most animals. The ParaHox cluster is an ideal system in which to study the evolution and regulation of developmental genes and gene clusters, as it displays similar regulatory phenomena to its sister cluster, the Hox cluster, but offers a much simpler system with only three genes. RESULTS Using Ciona intestinalis transgenics, we isolated a regulatory element upstream of Branchiostoma floridae Gsx that drives expression within the central nervous system of Ciona embryos. The minimal amphioxus enhancer region required to drive CNS expression has been identified, along with surrounding sequence that increases the efficiency of reporter expression throughout the Ciona CNS. TCF/Lef binding sites were identified and mutagenized and found to be required to drive the CNS expression. Also, individual contributions of TCF/Lef sites varied across the regulatory region, revealing a partial division of function across the Bf-Gsx-Up regulatory element. Finally, when all TCF/Lef binding sites are mutated CNS expression is not only abolished, but a latent repressive function is also unmasked. CONCLUSIONS We have identified a B. floridae Gsx upstream regulatory element that drives CNS expression within transgenic Ciona intestinalis, and have shown that this CNS expression is dependent upon TCF/Lef binding sites. We examine the evolutionary and developmental implications of these results, and discuss the possibility of TCF/Lef not only as a regulator of chordate Gsx, but as a deeply conserved regulatory factor controlling all three ParaHox genes across the Metazoa.
Collapse
Affiliation(s)
- Myles G Garstang
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
| | - Peter W Osborne
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
| | - David E K Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK.
| |
Collapse
|
16
|
Ordered expression pattern of Hox and ParaHox genes along the alimentary canal in the ascidian juvenile. Cell Tissue Res 2016; 365:65-75. [DOI: 10.1007/s00441-016-2360-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/07/2016] [Indexed: 01/03/2023]
|
17
|
Chang YC, Pai CY, Chen YC, Ting HC, Martinez P, Telford MJ, Yu JK, Su YH. Regulatory circuit rewiring and functional divergence of the duplicate admp genes in dorsoventral axial patterning. Dev Biol 2016; 410:108-18. [DOI: 10.1016/j.ydbio.2015.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 10/22/2022]
|
18
|
Takeuchi T, Koyanagi R, Gyoja F, Kanda M, Hisata K, Fujie M, Goto H, Yamasaki S, Nagai K, Morino Y, Miyamoto H, Endo K, Endo H, Nagasawa H, Kinoshita S, Asakawa S, Watabe S, Satoh N, Kawashima T. Bivalve-specific gene expansion in the pearl oyster genome: implications of adaptation to a sessile lifestyle. ZOOLOGICAL LETTERS 2016; 2:3. [PMID: 26900483 PMCID: PMC4759782 DOI: 10.1186/s40851-016-0039-2] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 02/11/2016] [Indexed: 05/12/2023]
Abstract
INTRODUCTION Bivalve molluscs have flourished in marine environments, and many species constitute important aquatic resources. Recently, whole genome sequences from two bivalves, the pearl oyster, Pinctada fucata, and the Pacific oyster, Crassostrea gigas, have been decoded, making it possible to compare genomic sequences among molluscs, and to explore general and lineage-specific genetic features and trends in bivalves. In order to improve the quality of sequence data for these purposes, we have updated the entire P. fucata genome assembly. RESULTS We present a new genome assembly of the pearl oyster, Pinctada fucata (version 2.0). To update the assembly, we conducted additional sequencing, obtaining accumulated sequence data amounting to 193× the P. fucata genome. Sequence redundancy in contigs that was caused by heterozygosity was removed in silico, which significantly improved subsequent scaffolding. Gene model version 2.0 was generated with the aid of manual gene annotations supplied by the P. fucata research community. Comparison of mollusc and other bilaterian genomes shows that gene arrangements of Hox, ParaHox, and Wnt clusters in the P. fucata genome are similar to those of other molluscs. Like the Pacific oyster, P. fucata possesses many genes involved in environmental responses and in immune defense. Phylogenetic analyses of heat shock protein70 and C1q domain-containing protein families indicate that extensive expansion of genes occurred independently in each lineage. Several gene duplication events prior to the split between the pearl oyster and the Pacific oyster are also evident. In addition, a number of tandem duplications of genes that encode shell matrix proteins are also well characterized in the P. fucata genome. CONCLUSIONS Both the Pinctada and Crassostrea lineages have expanded specific gene families in a lineage-specific manner. Frequent duplication of genes responsible for shell formation in the P. fucata genome explains the diversity of mollusc shell structures. These duplications reveal dynamic genome evolution to forge the complex physiology that enables bivalves to employ a sessile lifestyle in the intertidal zone.
Collapse
Affiliation(s)
- Takeshi Takeuchi
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Ryo Koyanagi
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Fuki Gyoja
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Miyuki Kanda
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Kanako Hisata
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Manabu Fujie
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Hiroki Goto
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Shinichi Yamasaki
- />DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Kiyohito Nagai
- />Pearl Research Institute, Mikimoto CO. LTD, Shima, Mie 517-0403 Japan
| | - Yoshiaki Morino
- />Graduate School of Life and Environmental Science, University of Tsukuba, Ibaraki, 305-8572 Japan
| | - Hiroshi Miyamoto
- />Department of Genetic Engineering, Faculty of Biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama 649-6493 Japan
| | - Kazuyoshi Endo
- />Department of Earth and Planetary Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hirotoshi Endo
- />Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564 Japan
| | - Hiromichi Nagasawa
- />Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
- />College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 People’s Republic of China
| | - Shigeharu Kinoshita
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Shuichi Asakawa
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
| | - Shugo Watabe
- />Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 Japan
- />Kitasato University School of Marine Bioscience, Sagamihara, Kanagawa 252-0373 Japan
| | - Noriyuki Satoh
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
| | - Takeshi Kawashima
- />Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495 Japan
- />Present Address: Graduate School of Life and Environmental Science, University of Tsukuba, Ibaraki, 305-8572 Japan
| |
Collapse
|
19
|
Wollesen T, Rodríguez Monje SV, McDougall C, Degnan BM, Wanninger A. The ParaHox gene Gsx patterns the apical organ and central nervous system but not the foregut in scaphopod and cephalopod mollusks. EvoDevo 2015; 6:41. [PMID: 26715985 PMCID: PMC4693441 DOI: 10.1186/s13227-015-0037-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 12/17/2015] [Indexed: 11/21/2022] Open
Abstract
Background It has been hypothesized that the ParaHox gene Gsx patterned the foregut of the last common bilaterian ancestor. This notion was corroborated by Gsx expression in three out of four lophotrochozoan species, several ecdysozoans, and some deuterostomes. Remarkably, Gsx is also expressed in the bilaterian anterior-most central nervous system (CNS) and the gastropod and annelid apical organ. To infer whether these findings are consistent with other mollusks or even lophotrochozoans, we investigated Gsx expression in developmental stages of representatives of two other molluscan classes, the scaphopod Antalis entalis and the cephalopod Idiosepius notoides. Results Gsx is not expressed in the developing digestive tract of Antalis entalis and Idiosepius notoides. Instead, it is expressed in cells of the apical organ in the scaphopod trochophore and in two cells adjacent to this organ. Late-stage trochophores express Aen-Gsx in cells of the developing cerebral and pedal ganglia and in cells close to the pavilion, mantle, and foot. In postmetamorphic specimens, Aen-Gsx is expressed in the cerebral and pedal ganglia, the foot, and the nascent captacula. In early squid embryos, Ino-Gsx is expressed in the cerebral, palliovisceral, and optic ganglia. In late-stage embryos, Ino-Gsx is additionally expressed close to the eyes and in the supraesophageal and posterior subesophageal masses and optic lobes. Developmental stages close to hatching express Ino-Gsx only close to the eyes. Conclusions Our results suggest that Gsx expression in the foregut might not be a plesiomorphic trait of the Lophotrochozoa as insinuated previously. Since neither ecdysozoans nor deuterostomes express Gsx in their gut, a role in gut formation in the last common bilaterian ancestor appears unlikely. Gsx is consistently expressed in the bilaterian anterior-most CNS and the apical organ of lophotrochozoan larvae, suggesting a recruitment of Gsx into the formation of this organ in the Lophotrochozoa. The cephalopod posterior subesophageal mass and optic ganglia and the scaphopod pedal ganglia also express Gsx. In summary, Gsx expression only appears to be conserved in the anterior-most brain region during evolution. Accordingly, Gsx appears to have been recruited into the formation of other expression domains, e.g., the apical organ or the foregut, in some lophotrochozoans.
Collapse
Affiliation(s)
- Tim Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| | | | - Carmel McDougall
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Bernard M Degnan
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Andreas Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
| |
Collapse
|
20
|
Lin CY, Tung CH, Yu JK, Su YH. Reproductive periodicity, spawning induction, and larval metamorphosis of the hemichordate acorn worm Ptychodera flava. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 326:47-60. [PMID: 26663879 DOI: 10.1002/jez.b.22665] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 11/24/2015] [Indexed: 02/05/2023]
Abstract
The indirect-developing enteropneust acorn worm Ptychodera flava has been used as a hemichordate model system for studying the developmental evolution of deuterostome body plans and the origins of chordate characteristics. However, research progress has been hindered by the limited accessibility of its embryonic materials and metamorphosing larvae. In this study, we identified an abundant population of P. flava in Penghu, Taiwan, and examined the feasibility of using this animal for developmental studies. Through histological examination, we established that the reproductive season of this population is between September and December, with a peak breeding period in October and November. In addition, we have developed new procedures that can induce P. flava spawning at any time of the day during the breeding season, with a higher successful rate than that achieved using a previously published method. Moreover, the culturing system we developed enables rearing of P. flava larvae through various planktonic stages and eventual metamorphosis into benthic juveniles, all under laboratory conditions. We anticipate that the animal resources and new technical procedures reported here will further facilitate the use of P. flava as a model organism for evolutionary and developmental biology research.
Collapse
Affiliation(s)
- Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan.,Department of Aquatic Biosciences, National Chiayi University, Chiayi, Taiwan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan.,Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Nankang, Taipei, Taiwan
| |
Collapse
|
21
|
Simakov O, Kawashima T, Marlétaz F, Jenkins J, Koyanagi R, Mitros T, Hisata K, Bredeson J, Shoguchi E, Gyoja F, Yue JX, Chen YC, Freeman RM, Sasaki A, Hikosaka-Katayama T, Sato A, Fujie M, Baughman KW, Levine J, Gonzalez P, Cameron C, Fritzenwanker JH, Pani AM, Goto H, Kanda M, Arakaki N, Yamasaki S, Qu J, Cree A, Ding Y, Dinh HH, Dugan S, Holder M, Jhangiani SN, Kovar CL, Lee SL, Lewis LR, Morton D, Nazareth LV, Okwuonu G, Santibanez J, Chen R, Richards S, Muzny DM, Gillis A, Peshkin L, Wu M, Humphreys T, Su YH, Putnam NH, Schmutz J, Fujiyama A, Yu JK, Tagawa K, Worley KC, Gibbs RA, Kirschner MW, Lowe CJ, Satoh N, Rokhsar DS, Gerhart J. Hemichordate genomes and deuterostome origins. Nature 2015; 527:459-65. [PMID: 26580012 PMCID: PMC4729200 DOI: 10.1038/nature16150] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/13/2015] [Indexed: 12/12/2022]
Abstract
Acorn worms, also known as enteropneust (literally, 'gut-breathing') hemichordates, are marine invertebrates that share features with echinoderms and chordates. Together, these three phyla comprise the deuterostomes. Here we report the draft genome sequences of two acorn worms, Saccoglossus kowalevskii and Ptychodera flava. By comparing them with diverse bilaterian genomes, we identify shared traits that were probably inherited from the last common deuterostome ancestor, and then explore evolutionary trajectories leading from this ancestor to hemichordates, echinoderms and chordates. The hemichordate genomes exhibit extensive conserved synteny with amphioxus and other bilaterians, and deeply conserved non-coding sequences that are candidates for conserved gene-regulatory elements. Notably, hemichordates possess a deuterostome-specific genomic cluster of four ordered transcription factor genes, the expression of which is associated with the development of pharyngeal 'gill' slits, the foremost morphological innovation of early deuterostomes, and is probably central to their filter-feeding lifestyle. Comparative analysis reveals numerous deuterostome-specific gene novelties, including genes found in deuterostomes and marine microbes, but not other animals. The putative functions of these genes can be linked to physiological, metabolic and developmental specializations of the filter-feeding ancestor.
Collapse
Affiliation(s)
- Oleg Simakov
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.,Department of Molecular Evolution, Centre for Organismal Studies, University of Heidelberg, 69115 Heidelberg, Germany
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | | | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Ryo Koyanagi
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jessen Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Fuki Gyoja
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jia-Xing Yue
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA
| | - Yi-Chih Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Robert M Freeman
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Akane Sasaki
- Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan
| | - Tomoe Hikosaka-Katayama
- Natural Science Center for Basic Research and Development, Gene Science Division, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Atsuko Sato
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Manabu Fujie
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kenneth W Baughman
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Judith Levine
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Paul Gonzalez
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Christopher Cameron
- Départment de sciences biologiques, University of Montreal, Quebec H3C 3J7, Canada
| | - Jens H Fritzenwanker
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Ariel M Pani
- University of North Caroline at Chapel Hill, North Carolina 27599, USA
| | - Hiroki Goto
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Nana Arakaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Shinichi Yamasaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Andrew Cree
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Yan Ding
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Huyen H Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Michael Holder
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Lora R Lewis
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Donna Morton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Lynne V Nazareth
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Geoffrey Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Andrew Gillis
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Wu
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| | - Tom Humphreys
- Institute for Biogenesis Research, University of Hawaii, Hawaii 96822, USA
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Nicholas H Putnam
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas 77005, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama 35806, USA
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Kunifumi Tagawa
- Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS BCM226, Houston, Texas 77030, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher J Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California 93950, USA
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Daniel S Rokhsar
- Molecular Genetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.,Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA.,US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - John Gerhart
- Department of Molecular and Cell Biology, University of California, Berkeley California 94720-3200, USA
| |
Collapse
|
22
|
Merabet S, Galliot B. The TALE face of Hox proteins in animal evolution. Front Genet 2015; 6:267. [PMID: 26347770 PMCID: PMC4539518 DOI: 10.3389/fgene.2015.00267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 07/31/2015] [Indexed: 01/22/2023] Open
Abstract
Hox genes are major regulators of embryonic development. One of their most conserved functions is to coordinate the formation of specific body structures along the anterior-posterior (AP) axis in Bilateria. This architectural role was at the basis of several morphological innovations across bilaterian evolution. In this review, we traced the origin of the Hox patterning system by considering the partnership with PBC and Meis proteins. PBC and Meis belong to the TALE-class of homeodomain-containing transcription factors and act as generic cofactors of Hox proteins for AP axis patterning in Bilateria. Recent data indicate that Hox proteins acquired the ability to interact with their TALE partners in the last common ancestor of Bilateria and Cnidaria. These interactions relied initially on a short peptide motif called hexapeptide (HX), which is present in Hox and non-Hox protein families. Remarkably, Hox proteins can also recruit the TALE cofactors by using specific PBC Interaction Motifs (SPIMs). We describe how a functional Hox/TALE patterning system emerged in eumetazoans through the acquisition of SPIMs. We anticipate that interaction flexibility could be found in other patterning systems, being at the heart of the astonishing morphological diversity observed in the animal kingdom.
Collapse
Affiliation(s)
- Samir Merabet
- Centre National de Recherche Scientifique, Institut de Génomique Fonctionnelle de Lyon Lyon, France ; Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon Lyon, France
| | - Brigitte Galliot
- Department of Genetics and Evolution, Faculty of Science, Institute of Genetics and Genomics in Geneva, University of Geneva Geneva, Switzerland
| |
Collapse
|
23
|
Urata M. Molecular Identification of Ptychodera flava (Hemichordata: Enteropneusta): Reconsideration in Light of Nucleotide Polymorphism in the 18S Ribosomal RNA Gene. Zoolog Sci 2015; 32:307-13. [PMID: 26003987 DOI: 10.2108/zs140144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Seven nuclear and mitochondrial DNA markers were examined in 12 specimens of Ptychodera flava, a model acorn worm used in molecular biology, collected in Japan from three local populations with different modes of living. A comparison of intraspecific results did not show genetically isolated populations despite the species' enclave habitats and asexual reproduction. Moreover, both the nuclear 18S ribosomal RNA gene and mitochondrial 16S ribosomal RNA gene sequences were identical to those from Moorea in French Polynesia, nearly 10,000 kilometers away from Japan. I also provide the first definitive information regarding polymorphisms in 18S ribosomal RNA gene, the external transcribed spacer (ETS), internal transcribed spacers (ITS), and mitochondrial cytochrome c oxidase subunit 1 (mtCO1) sequence in hemichordates using newly designed primer sets, and I show both high larval vagility and certain criteria for the molecular identification of this species.
Collapse
Affiliation(s)
- Makoto Urata
- Takehara Marine Science Station, Setouchi Field Science Center, Graduate School of Biosphere Science, Hiroshima University, 5-8-1 Minato-machi, Takehara, Hiroshima 725-0024, Japan
| |
Collapse
|
24
|
Röttinger E, DuBuc TQ, Amiel AR, Martindale MQ. Nodal signaling is required for mesodermal and ventral but not for dorsal fates in the indirect developing hemichordate, Ptychodera flava. Biol Open 2015; 4:830-42. [PMID: 25979707 PMCID: PMC4571091 DOI: 10.1242/bio.011809] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Nodal signaling plays crucial roles in vertebrate developmental processes such as endoderm and mesoderm formation, and axial patterning events along the anteroposterior, dorsoventral and left-right axes. In echinoderms, Nodal plays an essential role in the establishment of the dorsoventral axis and left-right asymmetry, but not in endoderm or mesoderm induction. In protostomes, Nodal signaling appears to be involved only in establishing left-right asymmetry. Hence, it is hypothesized that Nodal signaling has been co-opted to pattern the dorsoventral axis of deuterostomes and for endoderm, mesoderm formation as well as anteroposterior patterning in chordates. Hemichordata, together with echinoderms, represent the sister taxon to chordates. In this study, we analyze the role of Nodal signaling in the indirect developing hemichordate Ptychodera flava. In particular, we show that during gastrulation nodal transcripts are detected in a ring of cells at the vegetal pole that gives rise to endomesoderm and in the ventral ectoderm at later stages of development. Inhibition of Nodal function disrupts dorsoventral fates and also blocks formation of the larval mesoderm. Interestingly, molecular analysis reveals that only mesodermal, apical and ventral gene expression is affected while the dorsal side appears to be patterned correctly. Taken together, this study suggests that the co-option of Nodal signaling in mesoderm formation and potentially in anteroposterior patterning has occurred prior to the emergence of chordates and that Nodal signaling on the ventral side is uncoupled from BMP signaling on the dorsal side, representing a major difference from the molecular mechanisms of dorsoventral patterning events in echinoderms.
Collapse
Affiliation(s)
- Eric Röttinger
- Université Nice Sophia Antipolis, IRCAN, UMR 7284, 06107 Nice, France CNRS, IRCAN, UMR 7284, 06107 Nice, France INSERM, IRCAN, U1081, 06107 Nice, France
| | - Timothy Q DuBuc
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, FL 32080-8610, USA
| | - Aldine R Amiel
- Université Nice Sophia Antipolis, IRCAN, UMR 7284, 06107 Nice, France CNRS, IRCAN, UMR 7284, 06107 Nice, France INSERM, IRCAN, U1081, 06107 Nice, France
| | - Mark Q Martindale
- The Whitney Marine Laboratory for Marine Science, University of Florida, St. Augustine, FL 32080-8610, USA
| |
Collapse
|
25
|
|
26
|
Satoh N, Tagawa K, Lowe CJ, Yu JK, Kawashima T, Takahashi H, Ogasawara M, Kirschner M, Hisata K, Su YH, Gerhart J. On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis 2014; 52:925-34. [PMID: 25303744 PMCID: PMC5673098 DOI: 10.1002/dvg.22831] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/02/2014] [Accepted: 10/07/2014] [Indexed: 01/24/2023]
Abstract
As a group closely related to chordates, hemichordate acorn worms are in a key phylogenic position for addressing hypotheses of chordate origins. The stomochord of acorn worms is an anterior outgrowth of the pharynx endoderm into the proboscis. In 1886 Bateson proposed homology of this organ to the chordate notochord, crowning this animal group "hemichordates." Although this proposal has been debated for over a century, the question still remains unresolved. Here we review recent progress related to this question. First, the developmental mode of the stomochord completely differs from that of the notochord. Second, comparison of expression profiles of genes including Brachyury, a key regulator of notochord formation in chordates, does not support the stomochord/notochord homology. Third, FoxE that is expressed in the stomochord-forming region in acorn worm juveniles is expressed in the club-shaped gland and in the endostyle of amphioxus, in the endostyle of ascidians, and in the thyroid gland of vertebrates. Based on these findings, together with the anterior endodermal location of the stomochord, we propose that the stomochord has evolutionary relatedness to chordate organs deriving from the anterior pharynx rather than to the notochord.
Collapse
Affiliation(s)
- Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kunifumi Tagawa
- Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima, Japan
| | - Christopher J. Lowe
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, California
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Hiroki Takahashi
- Division of Developmental Biology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Michio Ogasawara
- Department of Nanobiology, Graduate School of Advanced Integration Science, Chiba University, Chiba, Japan
| | - Marc Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | - John Gerhart
- Department of Molecular and Cell Biology, University of California, Berkeley, California
| |
Collapse
|
27
|
Tagawa K, Arimoto A, Arimito A, Sasaki A, Izumi M, Fujita S, Humphreys T, Fujiyama A, Kagoshima H, Shin-I T, Kohara Y, Satoh N, Kawashima T. A cDNA resource for gene expression studies of a hemichordate, Ptychodera flava. Zoolog Sci 2014; 31:414-20. [PMID: 25001912 DOI: 10.2108/zs130262] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recent investigations into the evolution of deuterostomes and the origin of chordates have paid considerable attention to hemichordates (acorn worms), as hemichordates and echinoderms are the closest chordate relatives. The present study prepared cDNA libraries from Ptychodera flava, to study expression and function of genes involved in development of the hemichordate body plan. Expressed sequence tag (EST) analyses of nine cDNA libraries yielded 18,832 cloned genes expressed in eggs, 18,739 in blastulae, 18,539 in gastrulae, 18,811 in larvae, 18,978 in juveniles, 11,802 in adult proboscis, 17,259 in stomochord, 11,886 in gills, and 11,580 in liver, respectively. A set of 34,159 uni-gene clones of P. flava was obtained. This cDNA resource will be valuable for studying temporal and spatial expression of acorn worm genes during development.
Collapse
Affiliation(s)
- Kuni Tagawa
- 1 Marine Biological Laboratory, Graduate School of Science, Hiroshima University, Onomichi, Hiroshima 722-0073, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Annunziata R, Arnone MI. A dynamic regulatory network explains ParaHox gene control of gut patterning in the sea urchin. Development 2014; 141:2462-72. [PMID: 24850857 DOI: 10.1242/dev.105775] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The anteroposterior patterning of the embryonic gut represents one of the most intriguing biological processes in development. A dynamic control of gene transcription regulation and cell movement is perfectly orchestrated to shape a functional gut in distinct specialized parts. Two ParaHox genes, Xlox and Cdx, play key roles in vertebrate and sea urchin gut patterning through molecular mechanisms that are still mostly unclear. Here, we have combined functional analysis methodologies with high-resolution imaging and RNA-seq to investigate Xlox and Cdx regulation and function. We reveal part of the regulatory machinery responsible for the onset of Xlox and Cdx transcription, uncover a Wnt10 signal that mediates Xlox repression in the intestinal cells, and provide evidence of Xlox- and Cdx-mediated control of stomach and intestine differentiation, respectively. Our findings offer a novel mechanistic explanation of how the control of transcription is linked to cell differentiation and morphogenesis for the development of a perfectly organized biological system such as the sea urchin larval gut.
Collapse
Affiliation(s)
- Rossella Annunziata
- Stazione Zoologica Anton Dohrn, Cellular and Developmental Biology, Villa Comunale, Napoli 80121, Italy
| | - Maria Ina Arnone
- Stazione Zoologica Anton Dohrn, Cellular and Developmental Biology, Villa Comunale, Napoli 80121, Italy
| |
Collapse
|
29
|
Chen SH, Li KL, Lu IH, Wang YB, Tung CH, Ting HC, Lin CY, Lin CY, Su YH, Yu JK. Sequencing and analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordate. Mar Genomics 2014; 15:35-43. [PMID: 24823299 DOI: 10.1016/j.margen.2014.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/28/2014] [Accepted: 04/28/2014] [Indexed: 12/13/2022]
Abstract
Hemichordates are the sister group of echinoderms, and together they are closely related to chordates within the deuterostome lineage. Therefore, hemichordates represent an important animal group for the understanding of both the evolution of developmental mechanisms in deuterostome animals and the origin of chordates. Recently, the majority of studies investigating hemichordates have focused on the direct-developing enteropneust hemichordate Saccoglossus kowalevskii; few have focused on the indirect-developing hemichordates, partly because of the lack of extensive genomic resources in these animals. In this study, we report the sequencing and analysis of a transcriptome from an indirect-developing enteropneust hemichordate Ptychodera flava. We sequenced a mixed cDNA library from six developmental stages using the Roche GS FLX Titanium System to generate more than 879,000 reads. These reads were assembled into 17,990 contigs with an average length of 1316bp. We found that 60% of the assembled contigs, along with 28% of the unassembled singleton reads, had significant hits to sequences in the NCBI database by a BLASTx search, and we also annotated these sequences and obtained Gene Ontology (GO) terms for 6744 contigs and 5802 singletons. We further identified candidate P. flava transcripts corresponding to genes involved in major developmental signaling pathways, including the Wnt, Notch and TGF-β signaling pathways. Using available genome/transcriptome datasets from the direct-developing hemichordate S. kowalevskii, the echinoderm Strongylocentrotus purpuratus and the chordate Branchiostoma floridae, we found that 90%, 80% and 73% of the annotated protein sequences in these respective species matched our P. flava transcriptome in a homology search. We also constructed a database for the P. flava transcriptome, and researchers can easily access this dataset online. Our dataset significantly increases the amount of available P. flava sequence data and can serve as a reference transcriptome for future studies using this species.
Collapse
Affiliation(s)
- Shu-Hwa Chen
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Kun-Lin Li
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan
| | - I-Hsuan Lu
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Yu-Bin Wang
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Hsiu-Chi Ting
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Ching-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan; Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County 35053, Taiwan.
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan.
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan; Institute of Oceanography, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
30
|
Tung CH, Cheng YR, Lin CY, Ho JS, Kuo CH, Yu JK, Su YH. A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flava. THE BIOLOGICAL BULLETIN 2014; 226:69-80. [PMID: 24648208 DOI: 10.1086/bblv226n1p69] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Symbiotic copepods compose one-third of the known copepod species and are associated with a wide range of animal groups. Two parasitic copepods endoparasitic in acorn worms (Hemichordata), Ive balanoglossi and Ubius hilli, collected in the Mediterranean Sea and Australian waters, respectively, were described a century ago. Here we report a new parasitic copepod species, Ive ptychoderae sp. nov., found in Ptychodera flava, a widespread acorn worm in the Indo-Pacific Ocean and an emerging organism for developmental and evolutionary studies. The female of I. ptychoderae is characterized by having a reduced maxilliped and five pairs of annular swellings along the body that are morphologically similar but distinguishable from those in the two previously described parasitic copepods in acorn worms. Phylogenetic analysis based on the 18S rDNA sequence shows that I. ptychoderae may belong to Poecilostomatoida but represent a new family, which we name Iveidae fam. nov. Ive ptychoderae is commonly found in the acorn worm population with an average prevalence of 42% during the collecting period. The infection of the parasite induces the formation of cysts and causes localized lesions of the host tissues, suggesting that it may have negative effects on its host. Interestingly, most cysts contain a single female with one or multiple male copepods, suggesting that their sex determination may be controlled by environmental conditions. The relationships between the parasitic copepods and acorn worms thus provide a platform for understanding physiological and ecological influences and coevolution between parasites and hosts.
Collapse
Affiliation(s)
- Che-Huang Tung
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan
| | | | | | | | | | | | | |
Collapse
|
31
|
Annunziata R, Perillo M, Andrikou C, Cole AG, Martinez P, Arnone MI. Pattern and process during sea urchin gut morphogenesis: the regulatory landscape. Genesis 2014; 52:251-68. [PMID: 24376127 DOI: 10.1002/dvg.22738] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/16/2013] [Indexed: 01/02/2023]
Abstract
The development of the endoderm is a multistage process. From the initial specification of the endodermal domain in the embryo to the final regionalization of the gut, there are multiple stages that require the involvement of complex gene regulatory networks. In one concrete case, the sea urchin embryo, some of these stages and their genetic control are (relatively) well understood. Several studies have underscored the relevance of individual transcription factor activities in the process, but very few have focused the attention on gene interactions within specific gene regulatory networks (GRNs). Sea urchins offer an ideal system to study the different factors involved in the morphogenesis of the gut. Here we review the knowledge gained over the last 10 years on the process and its regulation, from the early specification of endodermal lineages to the late events linked to the patterning of functional domains in the gut. A lesson of remarkable importance has been learnt from comparison of the mechanisms involved in gut formation in different bilaterian animals; some of these genetic mechanisms are particularly well conserved. Patterning the gut seems to involve common molecular players and shared interactions, whether we look at mammals or echinoderms. This astounding degree of conservation reveals some key aspects of deep homology that are most probably shared by all bilaterian guts.
Collapse
Affiliation(s)
- Rossella Annunziata
- Cellular and Developmental Biology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | | | | | | | | | | |
Collapse
|
32
|
Annunziata R, Martinez P, Arnone MI. Intact cluster and chordate-like expression of ParaHox genes in a sea star. BMC Biol 2013; 11:68. [PMID: 23803323 PMCID: PMC3710244 DOI: 10.1186/1741-7007-11-68] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022] Open
Abstract
Background The ParaHox genes are thought to be major players in patterning the gut of several bilaterian taxa. Though this is a fundamental role that these transcription factors play, their activities are not limited to the endoderm and extend to both ectodermal and mesodermal tissues. Three genes compose the ParaHox group: Gsx, Xlox and Cdx. In some taxa (mostly chordates but to some degree also in protostomes) the three genes are arranged into a genomic cluster, in a similar fashion to what has been shown for the better-known Hox genes. Sea urchins possess the full complement of ParaHox genes but they are all dispersed throughout the genome, an arrangement that, perhaps, represented the primitive condition for all echinoderms. In order to understand the evolutionary history of this group of genes we cloned and characterized all ParaHox genes, studied their expression patterns and identified their genomic loci in a member of an earlier branching group of echinoderms, the asteroid Patiria miniata. Results We identified the three ParaHox orthologs in the genome of P. miniata. While one of them, PmGsx is provided as maternal message, with no zygotic activation afterwards, the other two, PmLox and PmCdx are expressed during embryogenesis, within restricted domains of both endoderm and ectoderm. Screening of a Patiria bacterial artificial chromosome (BAC) library led to the identification of a clone containing the three genes. The transcriptional directions of PmGsx and PmLox are opposed to that of the PmCdx gene within the cluster. Conclusions The identification of P. miniata ParaHox genes has revealed the fact that these genes are clustered in the genome, in contrast to what has been reported for echinoids. Since the presence of an intact cluster, or at least a partial cluster, has been reported in chordates and polychaetes respectively, it becomes clear that within echinoderms, sea urchins have modified the original bilaterian arrangement. Moreover, the sea star ParaHox domains of expression show chordate-like features not found in the sea urchin, confirming that the dynamics of gene expression for the respective genes and their putative regulatory interactions have clearly changed over evolutionary time within the echinoid lineage.
Collapse
Affiliation(s)
- Rossella Annunziata
- Stazione Zoologica Anton Dohrn di Napoli, Cellular and Developmental Biology, Villa Comunale, 80121 Napoli, Italy
| | | | | |
Collapse
|
33
|
Garstang M, Ferrier DEK. Time is of the essence for ParaHox homeobox gene clustering. BMC Biol 2013; 11:72. [PMID: 23803337 PMCID: PMC3694477 DOI: 10.1186/1741-7007-11-72] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 06/20/2013] [Indexed: 11/18/2022] Open
Abstract
ParaHox genes, and their evolutionary sisters the Hox genes, are integral to patterning the anterior-posterior axis of most animals. Like the Hox genes, ParaHox genes can be clustered and exhibit the phenomenon of colinearity - gene order within the cluster matching gene activation. Two new instances of ParaHox clustering provide the first examples of intact clusters outside chordates, with gene expression lending weight to the argument that temporal colinearity is the key to understanding clustering. See research articles:
http://www.biomedcentral.com/1741-7007/11/68 and
http://www.biomedcentral.com/1471-2148/13/129
Collapse
Affiliation(s)
- Myles Garstang
- The Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife, KY16 8LB, UK
| | | |
Collapse
|