The genomes of all lungfish inform on genome expansion and tetrapod evolution

• 成果类型: Article
• 署名作者: Schartl, Manfred; Woltering, Joost M.; Irisarri, Iker; Du, Kang; Kneitz, Susanne; Pippel, Martin; Brown, Thomas; Franchini, Paolo; Li, Jing; Li, Ming; Adolfi, Mateus; Winkler, Sylke; Sousa, Josane de Freitas; Chen, Zhuoxin; Jacinto, Sandra; Kvon, Evgeny Z.; de Oliveira, Luis Rogerio Correa; Monteiro, Erika; Baia Amaral, Danielson; Burmester, Thorsten; Chalopin, Domitille; Suh, Alexander; Myers, Eugene; Simakov, Oleg; Schneider, Igor; Meyer, Axel
• 署名单位: University of Wurzburg; Texas State University System; Texas State University San Marcos; University of Innsbruck; University of Konstanz; University of Wurzburg; Max Planck Society; Technische Universitat Dresden; Louisiana State University System; Louisiana State University; University of California System; University of California Irvine; Universidade Federal do Para; University of Hamburg; Centre National de la Recherche Scientifique (CNRS); Universite de Bordeaux; Uppsala University; University of East Anglia; University of Vienna; Uppsala University; Leibniz Institut fur Zoo und Wildtierforschung; Tuscia University
• 刊物名称: Nature
• ISSN/ISSBN: 0028-6815
• DOI: 10.1038/s41586-024-07830-1
• 发表日期: 2024-10-03
• 关键词: de-novo identification; pirna pathway; dna-content; cell-size; sequence; gene; reconstruction; alignments; families; clusters

摘要

The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Kr & uuml;ppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers. We find that massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and KRAB-domain protein genes that suppress transposable element expansion, and lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype.