1
|
Galià-Camps C, Pegueroles C, Turon X, Carreras C, Pascual M. Genome composition and GC content influence loci distribution in reduced representation genomic studies. BMC Genomics 2024; 25:410. [PMID: 38664648 PMCID: PMC11046876 DOI: 10.1186/s12864-024-10312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Genomic architecture is a key evolutionary trait for living organisms. Due to multiple complex adaptive and neutral forces which impose evolutionary pressures on genomes, there is a huge variability of genomic features. However, their variability and the extent to which genomic content determines the distribution of recovered loci in reduced representation sequencing studies is largely unexplored. RESULTS Here, by using 80 genome assemblies, we observed that whereas plants primarily increase their genome size by expanding their intergenic regions, animals expand both intergenic and intronic regions, although the expansion patterns differ between deuterostomes and protostomes. Loci mapping in introns, exons, and intergenic categories obtained by in silico digestion using 2b-enzymes are positively correlated with the percentage of these regions in the corresponding genomes, suggesting that loci distribution mostly mirrors genomic architecture of the selected taxon. However, exonic regions showed a significant enrichment of loci in all groups regardless of the used enzyme. Moreover, when using selective adaptors to obtain a secondarily reduced loci dataset, the percentage and distribution of retained loci also varied. Adaptors with G/C terminals recovered a lower percentage of selected loci, with a further enrichment of exonic regions, while adaptors with A/T terminals retained a higher percentage of loci and slightly selected more intronic regions than expected. CONCLUSIONS Our results highlight how genome composition, genome GC content, RAD enzyme choice and use of base-selective adaptors influence reduced genome representation techniques. This is important to acknowledge in population and conservation genomic studies, as it determines the abundance and distribution of loci.
Collapse
Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain.
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, Blanes, 17300, Spain.
| | - Cinta Pegueroles
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Xavier Turon
- Department of Marine Ecology, Centre d'Estudis Avançats de Blanes (CEAB-CSIC), Accés Cala Sant Francesc 14, Blanes, 17300, Spain
| | - Carlos Carreras
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Pascual
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Avinguda Diagonal 643, Barcelona, 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| |
Collapse
|
2
|
Abstract
Many species from diverse and often distantly related animal groups (e.g. monkeys, crows, fish and bees) have a sense of number. This means that they can assess the number of items in a set - its 'numerosity'. The brains of these phylogenetically distant species are markedly diverse. This Review examines the fundamentally different types of brains and neural mechanisms that give rise to numerical competence across the animal tree of life. Neural correlates of the number sense so far exist only for specific vertebrate species: the richest data concerning explicit and abstract number representations have been collected from the cerebral cortex of mammals, most notably human and nonhuman primates, but also from the pallium of corvid songbirds, which evolved independently of the mammalian cortex. In contrast, the neural data relating to implicit and reflexive numerical representations in amphibians and fish is limited. The neural basis of a number sense has not been explored in any protostome so far. However, promising candidate regions in the brains of insects, spiders and cephalopods - all of which are known to have number skills - are identified in this Review. A comparative neuroscientific approach will be indispensable for identifying evolutionarily stable neuronal circuits and deciphering codes that give rise to a sense of number across phylogeny.
Collapse
Affiliation(s)
- Andreas Nieder
- Animal Physiology Unit, Institute of Neurobiology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| |
Collapse
|
3
|
Yang X, Kimmig J, Lieberman BS, Peng S. A new species of the deuterostome Herpetogaster from the early Cambrian Chengjiang biota of South China. Naturwissenschaften 2020; 107:37. [PMID: 32857275 PMCID: PMC7544619 DOI: 10.1007/s00114-020-01695-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 07/27/2020] [Accepted: 08/19/2020] [Indexed: 11/26/2022]
Abstract
The Cambrian radiation represents a key time period in the history of life. Here, we add to the mounting evidence accumulating on the nature of deuterostomes from this time period through description of a new species of stalked deuterostome, Herpetogaster haiyanensis nov. sp., from the lower Cambrian (series 2, stage 3) Chengjiang biota of China. This represents the first occurrence of the genus in Gondwana, the first juvenile specimen, and the oldest specimens to date. Herpetogaster haiyanensis nov. sp. differs from H. collinsi Caron et al. (2010) in having a stolon that is separated into an outer and inner layer, the segmentation of the body and in the shape and number of branches of the tentacles. The new species reiterates earlier suggestions of deuterostome affinities of the genus―it appears closely related to Phlogites and then successively more distantly related to Cotyledon and Eldonia―and may have fed on hyolithids.
Collapse
Affiliation(s)
- Xianfeng Yang
- Yunnan Key Laboratory for Palaeobiology, MEC International Joint Laboratory for Palaeobiology and Palaeoenvironment, Yunnan University, Kunming, 650091, China.
- State Key Laboratory of Palaeobiology and Stratigraphy, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Julien Kimmig
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA.
- Earth and Mineral Sciences Museum & Art Gallery, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Bruce S Lieberman
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
- Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
| | - Shanchi Peng
- State Key Laboratory of Palaeobiology and Stratigraphy, Chinese Academy of Sciences, Nanjing, 210008, China
- Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, 210008, China
| |
Collapse
|
4
|
Abstract
One of the definitive characteristics of chordates (cephalochordates, vertebrates) is the somites, which are a series of paraxial mesodermal blocks exhibiting segmentation. The presence of somites in the basal chordate amphioxus and in vertebrates, but not in tunicates (the sister group of vertebrates), suggests that the tunicates lost the somites secondarily. Somites are patterned from anterior to posterior during embryogenesis. How such a segmental pattern evolved from deuterostome ancestors is mysterious. The classic enterocoel theory claims that chordate mesoderm evolved from the ancestral deuterostome mesoderm that organizes the trimeric body parts seen in extant hemichordates. Recent progress in molecular embryology has been tremendous, which has enabled us to test this classic theory. In this review, the history of the study on the evolution of the chordate mesoderm is summarized. This is followed by a review of the current understanding of genetic mapping on anterior/posterior (A/P) mesodermal patterning between chordates (cephalochordates, vertebrates) and a direct developing hemichordate (Saccoglossus kowalevskii). Finally, a possible scenario about the evolution of the chordate mesoderm from deuterostome ancestors is discussed.
Collapse
Affiliation(s)
- Takayuki Onai
- Department of Anatomy, School of Medical Sciences, University of Fukui, 23-3, Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan. .,Life Science Innovation Center, University of Fukui, 23-3, Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun, Fukui, 910-1193, Japan.
| |
Collapse
|
5
|
Nakano H, Miyazawa H, Maeno A, Shiroishi T, Kakui K, Koyanagi R, Kanda M, Satoh N, Omori A, Kohtsuka H. A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella. BMC Evol Biol 2017; 17:245. [PMID: 29249199 PMCID: PMC5733810 DOI: 10.1186/s12862-017-1080-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/16/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Xenoturbella is a group of marine benthic animals lacking an anus and a centralized nervous system. Molecular phylogenetic analyses group the animal together with the Acoelomorpha, forming the Xenacoelomorpha. This group has been suggested to be either a sister group to the Nephrozoa or a deuterostome, and therefore it may provide important insights into origins of bilaterian traits such as an anus, the nephron, feeding larvae and centralized nervous systems. However, only five Xenoturbella species have been reported and the evolutionary history of xenoturbellids and Xenacoelomorpha remains obscure. RESULTS Here we describe a new Xenoturbella species from the western Pacific Ocean, and report a new xenoturbellid structure - the frontal pore. Non-destructive microCT was used to investigate the internal morphology of this soft-bodied animal. This revealed the presence of a frontal pore that is continuous with the ventral glandular network and which exhibits similarities with the frontal organ in acoelomorphs. CONCLUSIONS Our results suggest that large size, oval mouth, frontal pore and ventral glandular network may be ancestral features for Xenoturbella. Further studies will clarify the evolutionary relationship of the frontal pore and ventral glandular network of xenoturbellids and the acoelomorph frontal organ. One of the habitats of the newly identified species is easily accessible from a marine station and so this species promises to be valuable for research on bilaterian and deuterostome evolution.
Collapse
Affiliation(s)
- Hiroaki Nakano
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan.
| | - Hideyuki Miyazawa
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, 415-0025, Japan
| | - Akiteru Maeno
- Mammalian Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Toshihiko Shiroishi
- Mammalian Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Keiichi Kakui
- Faculty of Science, Hokkaido University, N10 W8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Ryo Koyanagi
- 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
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Akihito Omori
- Misaki Marine Biological Station, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan.,Present address: Sado Marine Biological Station, Faculty of Science, Niigata University, Sado, Niigata, 952-2135, Japan
| | - Hisanori Kohtsuka
- Misaki Marine Biological Station, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa, 238-0225, Japan
| |
Collapse
|
6
|
Tisler M, Wetzel F, Mantino S, Kremnyov S, Thumberger T, Schweickert A, Blum M, Vick P. Cilia are required for asymmetric nodal induction in the sea urchin embryo. BMC Dev Biol 2016; 16:28. [PMID: 27553781 PMCID: PMC4994401 DOI: 10.1186/s12861-016-0128-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/29/2016] [Indexed: 01/22/2023]
Abstract
Background Left-right (LR) organ asymmetries are a common feature of metazoan animals. In many cases, laterality is established by a conserved asymmetric Nodal signaling cascade during embryogenesis. In most vertebrates, asymmetric nodal induction results from a cilia-driven leftward fluid flow at the left-right organizer (LRO), a ciliated epithelium present during gastrula/neurula stages. Conservation of LRO and flow beyond the vertebrates has not been reported yet. Results Here we study sea urchin embryos, which use nodal to establish larval LR asymmetry as well. Cilia were found in the archenteron of embryos undergoing gastrulation. Expression of foxj1 and dnah9 suggested that archenteron cilia were motile. Cilia were polarized to the posterior pole of cells, a prerequisite of directed flow. High-speed videography revealed rotating cilia in the archenteron slightly before asymmetric nodal induction. Removal of cilia through brief high salt treatments resulted in aberrant patterns of nodal expression. Our data demonstrate that cilia - like in vertebrates - are required for asymmetric nodal induction in sea urchin embryos. Conclusions Based on these results we argue that the anterior archenteron represents a bona fide LRO and propose that cilia-based symmetry breakage is a synapomorphy of the deuterostomes. Electronic supplementary material The online version of this article (doi:10.1186/s12861-016-0128-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Matthias Tisler
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Franziska Wetzel
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Sabrina Mantino
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Stanislav Kremnyov
- Department of Embryology, Lomonosov Moscow State University, Moscow, Russia
| | - Thomas Thumberger
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany.,Present Address: Centre for Organismal Studies, Im Neuenheimer Feld 230, Heidelberg University, 69120, Heidelberg, Germany
| | - Axel Schweickert
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Martin Blum
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany
| | - Philipp Vick
- University of Hohenheim, Institute of Zoology, 70593, Stuttgart, Germany.
| |
Collapse
|
7
|
Garner S, Zysk I, Byrne G, Kramer M, Moller D, Taylor V, Burke RD. Neurogenesis in sea urchin embryos and the diversity of deuterostome neurogenic mechanisms. Development 2015; 143:286-97. [PMID: 26511925 DOI: 10.1242/dev.124503] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 10/19/2015] [Indexed: 01/08/2023]
Abstract
A single origin to the diverse mechanisms of metazoan neurogenesis is suggested by the involvement of common signaling components and similar classes of transcription factors. However, in many forms we lack details of where neurons arise, patterns of cell division, and specific differentiation pathway components. The sea urchin larval nervous system is composed of an apical organ, which develops from neuroepithelium and functions as a central nervous system, and peripheral neurons, which differentiate in the ciliary band and project axons to the apical organ. To reveal developmental mechanisms of neurogenesis in this basal deuterostome, we developed antibodies to SoxC, SoxB2, ELAV and Brn1/2/4 and used neurons that develop at specific locations to establish a timeline for neurogenesis. Neural progenitors express, in turn, SoxB2, SoxC, and Brn1/2/4, before projecting neurites and expressing ELAV and SynB. Using pulse-chase labeling of cells with a thymidine analog to identify cells in S-phase, we establish that neurons identified by location are in their last mitotic cycle at the time of hatching, and S-phase is coincident with expression of SoxC. The number of cells expressing SoxC and differentiating as neurons is reduced in embryos injected with antisense morpholino oligonucleotides to SoxC, SoxB2 or Six3. Injection of RNA encoding SoxC into eggs does not enhance neurogenesis. In addition, inhibition of FGF receptors (SU5402) or a morpholino to FGFR1 reduces expression of SoxC. These data indicate that there are common features of neurogenesis in deuterostomes, and that sea urchins employ developmental mechanisms that are distinct from other ambulacraria.
Collapse
Affiliation(s)
- Sarah Garner
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Ivona Zysk
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Glynis Byrne
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Marabeth Kramer
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Daniel Moller
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Valerie Taylor
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| | - Robert D Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6
| |
Collapse
|