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Hemichordate genomes and deuterostome origins.

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.

SUBMITTER: Simakov O

PROVIDER: S-EPMC4729200 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Hemichordate genomes and deuterostome origins.

Simakov Oleg O Kawashima Takeshi T Marlétaz Ferdinand F Jenkins Jerry J Koyanagi Ryo R Mitros Therese T Hisata Kanako K Bredeson Jessen J Shoguchi Eiichi E Gyoja Fuki F Yue Jia-Xing JX Chen Yi-Chih YC Freeman Robert M RM Sasaki Akane A Hikosaka-Katayama Tomoe T Sato Atsuko A Fujie Manabu M Baughman Kenneth W KW Levine Judith J Gonzalez Paul P Cameron Christopher C Fritzenwanker Jens H JH Pani Ariel M AM Goto Hiroki H Kanda Miyuki M Arakaki Nana N Yamasaki Shinichi S Qu Jiaxin J Cree Andrew A Ding Yan Y Dinh Huyen H HH Dugan Shannon S Holder Michael M Jhangiani Shalini N SN Kovar Christie L CL Lee Sandra L SL Lewis Lora R LR Morton Donna D Nazareth Lynne V LV Okwuonu Geoffrey G Santibanez Jireh J Chen Rui R Richards Stephen S Muzny Donna M DM Gillis Andrew A Peshkin Leonid L Wu Michael M Humphreys Tom T Su Yi-Hsien YH Putnam Nicholas H NH Schmutz Jeremy J Fujiyama Asao A Yu Jr-Kai JK Tagawa Kunifumi K Worley Kim C KC Gibbs Richard A RA Kirschner Marc W MW Lowe Christopher J CJ Satoh Noriyuki N Rokhsar Daniel S DS Gerhart John J

Nature 20151118 7579

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 evoluti ...[more]

PMID: 26580012

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Project description:DNA replication initiates from multiple replication origins (ORIs) in eukaryotes. Discovery and characterization of replication origins are essential for a better understanding of the molecular mechanism of DNA replication. In this study, the features of autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae have been comprehensively analyzed as follows. Firstly, we carried out the analysis of the ARSs available in S. cerevisiae S288C. By evaluating the sequence similarity of experimentally established ARSs, we found that 94.32% of ARSs are unique across the whole genome of S. cerevisiae S288C and those with high sequence similarity are prone to locate in subtelomeres. Subsequently, we built a non-redundant dataset with a total of 520 ARSs, which are based on ARSs annotation of S. cerevisiae S288C from SGD and then supplemented with those from OriDB and DeOri databases. We conducted a large-scale comparison of ORIs among the diverse budding yeast strains from a population genomics perspective. We found that 82.7% of ARSs are not only conserved in genomic sequence but also relatively conserved in chromosomal position. The non-conserved ARSs tend to distribute in the subtelomeric regions. We also conducted a pan-genome analysis of ARSs among the S. cerevisiae strains, and a total of 183 core ARSs existing in all yeast strains were determined. We extracted the genes adjacent to replication origins among the 104 yeast strains to examine whether there are differences in their gene functions. The result showed that the genes involved in the initiation of DNA replication, such as orc3, mcm2, mcm4, mcm6, and cdc45, are conservatively located adjacent to the replication origins. Furthermore, we found the genes adjacent to conserved ARSs are significantly enriched in DNA binding, enzyme activity, transportation, and energy, whereas for the genes adjacent to non-conserved ARSs are significantly enriched in response to environmental stress, metabolites biosynthetic process and biosynthesis of antibiotics. In general, we characterized the replication origins from the genome-wide and population genomics perspectives, which would provide new insights into the replication mechanism of S. cerevisiae and facilitate the design of algorithms to identify genome-wide replication origins in yeast.

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Hemichordate genomes and deuterostome origins.

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Hemichordate genomes and deuterostome origins.

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