title: The Lingula genome provides insights into brachiopod evolution and the origin of phosphate biomineralization.
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.
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Yi-Jyun
authors.identifier: http://orcid.org/0000-0002-3418-3146
authors.initials: YJ
authors.lastname: Luo
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Takeuchi
authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Ryo
authors.initials: R
authors.lastname: Koyanagi
authors.affiliation: Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Toba, Aichi 517-0004, Japan.
authors.forename: Lixy
authors.initials: L
authors.lastname: Yamada
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Miyuki
authors.initials: M
authors.lastname: Kanda
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Mariia
authors.initials: M
authors.lastname: Khalturina
authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Manabu
authors.initials: M
authors.lastname: Fujie
authors.affiliation: DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Shin-Ichi
authors.initials: SI
authors.lastname: Yamasaki
authors.affiliation: Department of Earth and Planetary Science, Graduate School of Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Endo
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Satoh
mesh_terms: D000818:Animals; D000845:Annelida / Q000235:genetics; D001483:Base Sequence; D005075:Biological Evolution; D002113:Calcification, Physiologic / Q000235:genetics*; D002130:Calcium Phosphates / Q000378:metabolism*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D023281:Genomics; D007448:Invertebrates / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D008974:Mollusca / Q000235:genetics; D010802:Phylogeny; D040901:Proteomics
chemical_list: D002130:Calcium Phosphates