The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization

Yi-Jyun Luo (), Takeshi Takeuchi, Ryo Koyanagi, Lixy Yamada, Miyuki Kanda, Mariia Khalturina, Manabu Fujie, Shin-ichi Yamasaki, Kazuyoshi Endo and Noriyuki Satoh ()
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Yi-Jyun Luo: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University
Takeshi Takeuchi: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University
Ryo Koyanagi: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University
Lixy Yamada: Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University
Miyuki Kanda: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University
Mariia Khalturina: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University
Manabu Fujie: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University
Shin-ichi Yamasaki: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University
Kazuyoshi Endo: Graduate School of Sciences, University of Tokyo
Noriyuki Satoh: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University

Nature Communications, 2015, vol. 6, issue 1, 1-10

Abstract: Abstract The evolutionary origins of lingulid brachiopods and their calcium phosphate shells have been obscure. Here we decode the 425-Mb genome of Lingula anatina to gain insights into brachiopod evolution. Comprehensive phylogenomic analyses place Lingula close to molluscs, but distant from annelids. The Lingula gene number has increased to ∼34,000 by extensive expansion of gene families. Although Lingula and vertebrates have superficially similar hard tissue components, our genomic, transcriptomic and proteomic analyses show that Lingula lacks genes involved in bone formation, indicating an independent origin of their phosphate biominerals. Several genes involved in Lingula shell formation are shared by molluscs. However, Lingula has independently undergone domain combinations to produce shell matrix collagens with EGF domains and carries lineage-specific shell matrix proteins. Gene family expansion, domain shuffling and co-option of genes appear to be the genomic background of Lingula’s unique biomineralization. This Lingula genome provides resources for further studies of lophotrochozoan evolution.

Date: 2015
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DOI: 10.1038/ncomms9301

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