Huang Z, Xu L, Cai C, Zhou Y, Liu J, Xu Z, Zhu Z, Kang W, Cen W, Pei S, Chen D, Shi C, Wu X, Huang Y, Xu C, Yan Y, Yang Y, Xue T, He W, Hu X, Zhang Y, Chen Y, Bi C, He C, Xue L, Xiao S, Yue Z, Jiang Y, Yu JK, Jarvis ED, Li G, Lin G, Zhang Q, Zhou Q.
Proc Natl Acad Sci U S A. 2023 Mar 7;120(10):e2201504120. doi:10.1073/pnas.2201504120
Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.
Chromosomal assembly of Branchiostoma floridae (Bf),
Branchiostoma belcheri (Bb) and Branchiostoma japonicum (Bj). ”we devised
an interspecific trio sequencing strategy [...] for the F1 hybrids derived from
Bf-Bb or Bf-Bj crosses. [...] the hybrids contain two haploid parental genomes
that have become too diverged in sequences to form cross-species chimeric
assembly” “The three amphioxus genomes show a highly conserved chromosomal
synteny to each other, with most chromosomes showing a one-to-one homologous
relationship except for a few chromosome fusions.” ”genome-wide heterozygosity
[estimated to] range from 3.2 to 4.2%” ”Based on 3,653 single-copy orthologous
genes, we estimated that different chordate lineages diverged about 592.5 Mya,
and three amphioxus species diverged about 99.9 Mya”. “Using whole-genome
resequencing data of between 10 and 48 individuals per sex per species, we
identified the sexually differentiated regions (SDR) that harbor [...]
excessive female heterozygotes, and are not shared between the three amphioxus
species. In particular, the SDR of Bf is located on Chr16 and harbors 194
genes; and those of Bj and Bb are located at two different genomic loci of
Chr3, harboring 35 genes and one gene with unknown function respectively. Bf
Chr16 is not homologous with Chr3 of Bj or Bb.”
Mean and confidence interval for divergence times given in Table S2:
- B. belcheri and B. japonicum: 59.3 [12.2, 132.0].
- all Branchiostoma: 99.9 [22.1, 211.7].
- all chordates: 592.5 [530.8, 640.3]. Prior: [514, 636.1].
- Euarchontoglires: 116.1 [72.1, 163.1]. Prior: [65.6, 164.6].