Hemichordate genomes and deuterostome origins

Simakov, Oleg; Kawashima, Takeshi; Marlétaz, Ferdinand; Jenkins, Jerry; Koyanagi, Ryo; Mitros, Therese; Hisata, Kanako; Bredeson, Jessen V.; Shoguchi, Eiichi; Gyoja, Fuki; Yue, Jia-Xing; Chen, Yi Chih; Freeman, Robert M.; Sasaki, Akane; Hikosaka-Katayama, Tomoe; Sato, Atsuko; Fujie, Manabu; Baughman, Kenneth W.; Levine, Judith; Gonzalez, Paul; Cameron, Christopher B.; Fritzenwanker, Jens H.; Pani, Ariel M.; Goto, Hironobu; Kanda, Miyuki; Arakaki, Nana; Yamasaki, Shin‐ichi; Qu, Jiaxin; Cree, Andrew; Ding, Yan; Dinh, Huyen; Dugan, Shannon; Holder, Michael; Jhangiani, Shalini N.; Kovar, Christie; Lee, Sandra L.; Lewis, Lora; Morton, Donna; Nazareth, Lynne V.; Okwuonu, Geoffrey; Santibanez, Jireh; Chen, Rui; Richards, Stephen; Muzny, Donna M.; Gillis, J. Andrew; Peshkin, Leonid; Wu, Michael; Humphreys, Tom; Su, Yea-Huey; Putnam, Nicholas H.; Schmutz, Jeremy; Fujiyama, Asao; Yu, Jr-Kai; Tagawa, Kunifumi; Worley, Kim C.; Gibbs, Richard A.; Kirschner, Marc W.; Lowe, Christopher J.; Satoh, Noriyuki; Rokhsar, Daniel S.; Gerhart, John C.

doi:10.1038/nature16150

Cited by 226 publications

(245 citation statements)

References 62 publications

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“…Later, Janies et al (2011) used combined Sanger sequencing data and morphology to show that Asterozoa and Echinozoa are methods-dependent when alignment and optimality criteria are varied. Recent transcriptomic studies with limited taxonomic and locus sampling have supported Asterozoa-Echinozoa (Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015) and were reviewed by Peterson and Eernisse (2016). These studies also strongly supported a monophyletic Asteroidea, consistent with prior morphological analyses including fossils (Blake et al, 2000;Shackleton, 2005) and molecular studies (Janies, 2001;Janies et al, 2011).…”

Section: Introductionsupporting

confidence: 52%

“…1 underscores the need for a wellsupported molecular phylogeny for asteroids, to permit the resolution of early divergence of asteroid orders as well as allow the placement of problematic and morphologically unusual taxa. Here, we used the recent demonstration, via molecular analyses of echinoderms (Janies, 2001;Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015) and our own broader analyses, that ophiuroids (brittlestars) are the sister group to asteroids and the outgroup of choice. However, recent transcriptomic analyses sampled asteroids poorly (Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…Here, we used the recent demonstration, via molecular analyses of echinoderms (Janies, 2001;Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015) and our own broader analyses, that ophiuroids (brittlestars) are the sister group to asteroids and the outgroup of choice. However, recent transcriptomic analyses sampled asteroids poorly (Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015). Specifically, O'Hara et al (2014) and Telford et al (2014) each sampled two asteroids, Simakov et al (2015) sampled one asteroid and Cannon et al (2014) sampled four asteroids.…”

Section: Introductionmentioning

confidence: 99%

“…However, recent transcriptomic analyses sampled asteroids poorly (Cannon et al, 2014;O'Hara et al, 2014;Telford et al, 2014;Reich et al, 2015;Simakov et al, 2015). Specifically, O'Hara et al (2014) and Telford et al (2014) each sampled two asteroids, Simakov et al (2015) sampled one asteroid and Cannon et al (2014) sampled four asteroids. Reich et al (2015) sampled 11 asteroids, but only four families that represented four orders were studied.…”

Section: Introductionmentioning

confidence: 99%

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The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics

Linchangco

Foltz

Reid

et al. 2017

Molecular Phylogenetics and Evolution

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A B S T R A C TMulti-locus phylogenetic studies of echinoderms based on Sanger and RNA-seq technologies and the fossil record have provided evidence for the Asterozoa-Echinozoa hypothesis. This hypothesis posits a sister relationship between asterozoan classes (Asteroidea and Ophiuroidea) and a similar relationship between echinozoan classes (Echinoidea and Holothuroidea). Despite this consensus around Asterozoa-Echinozoa, phylogenetic relationships within the class Asteroidea (sea stars or starfish) have been controversial for over a century. Open questions include relationships within asteroids and the status of the enigmatic taxon Xyloplax. Xyloplax is thought by some to represent a newly discovered sixth class of echinoderms -and by others to be an asteroid. To address these questions, we applied a novel workflow to a large RNA-seq dataset that encompassed a broad taxonomic and genomic sample. This study included 15 species sampled from all extant orders and 13 families, plus four ophiuroid species as an outgroup. To expand the taxonomic coverage, the study also incorporated five previously published transcriptomes and one previously published expressed sequence tags (EST) dataset. We developed and applied methods that used a range of alignment parameters with increasing permissiveness in terms of gap characters present within an alignment. This procedure facilitated the selection of phylogenomic data subsets from large amounts of transcriptome data. The results included 19 nested data subsets that ranged from 37 to 4,281 loci. Tree searches on all data subsets reconstructed Xyloplax as a velatid asteroid rather than a new class. This result implies that asteroid morphology remains labile well beyond the establishment of the body plan of the group. In the phylogenetic tree with the highest average asteroid nodal support several monophyletic groups were recovered. In this tree, Forcipulatida and Velatida are monophyletic and form a clade that includes Brisingida as sister to Forcipulatida. Xyloplax is consistently recovered as sister to Pteraster. Paxillosida and Spinulosida are each monophyletic, with Notomyotida as sister to the Paxillosida. Valvatida is recovered as paraphyletic. The results from other data subsets are largely consistent with these results. Our results support the hypothesis that the earliest divergence event among extant asteroids separated Velatida and Forcipulatacea from Valvatacea and Spinulosida.

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Section: Introductionsupporting

confidence: 52%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics

Linchangco

Foltz

Reid

et al. 2017

Molecular Phylogenetics and Evolution

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“…Assemblies and annotations for Symbiodinium minutum (Shoguchi et al 2013), Pinctada fucata (Takeuchi et al 2012), Acropora digitifera (Shinzato et al 2011), Lingula anatina (Luo et al 2015), Ptychodera flava (Simakov et al 2015), and Octopus bimaculoides (Albertin et al 2015) were downloaded from the OIST Marine Genomics Browser (http:// marinegenomics.oist.jp/gallery/).…”

Section: Genomic Data Sourcesmentioning

confidence: 99%

Similar ratios of introns to intergenic sequence across animal genomes

Francis

Wörheide

2016

Preprint

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One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here, we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation. We show that, regardless of genome size, the ratio of introns to intergenic sequence is comparable across essentially all animals, with nearly all deviations dominated by increased intergenic sequence. Genomes of model organisms have ratios much closer to 1:1, suggesting that the majority of published genomes of nonmodel organisms are underannotated and consequently omit substantial numbers of genes, with likely negative impact on evolutionary interpretations. Finally, our results also indicate that most animals transcribe half or more of their genomes arguing against differences in genome usage between animal groups, and also suggesting that the transcribed portion is more dependent on genome size than previously thought.

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Evolution of Human Multigene Families

Fatima

Pervaiz

Khalid

et al. 2021

Encyclopedia of Life Sciences

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The hypothesis that all the vertebrates, including humans, share two ancestral rounds of whole‐genome duplications (WGDs/2R) is correct or not has recently become quite controversial. Furthermore, the contribution of hypothesised WGDs to the evolution of novel developmental features in modern vertebrates is still unclear. Attempts to settle these ardently debated issues have been hampered by small and noisy sequence data. Recently, based on advances in sequencing technology, hundreds of genomes spread across the whole metazoan tree have been decoded. This increasing amount of sequence data and recent advances in evo‐devo have set the stage for understanding metazoan evolution, including genomic innovations and accompanying developmental transitions. New sources of data provide insights into the vertebrate genome evolutionary history, notably the status of controversial 2R duplications. Key Concepts Duplication is considered to be an important source of new genes, hence providing a substrate on which evolution can work. Duplicated genes are often referred to as paralogous genes, which form multigene families. An understanding of the mechanisms of gene duplication is crucial for revealing how do newly duplicated acquire novel functions. All vertebrate animals including humans, despite their generally diploid state, carry large numbers of duplicated genes. Widespread existence of multigene families in vertebrates has been interpreted by some as evidence that two rounds of whole‐genome duplication (2R hypothesis) occurred at the origin of the vertebrates. Whether or not 2R occurred and what role it played in later evolution of vertebrates has been a contentious concept among evolutionary developmental biologists. This article provides more insight into the phenomenon by applying the recent knowledge developed largely through ever‐increasing number of sequenced genomes of bilaterian animals.

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Hemichordate genomes and deuterostome origins

Cited by 226 publications

References 62 publications

The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics

The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics

Similar ratios of introns to intergenic sequence across animal genomes

Evolution of Human Multigene Families

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