TY - JOUR

T1 - Unravelling unusual subgenomic organization in the neopolyploid free-living flatworm Macrostomum lignano

AU - Zadesenets, Kira S

AU - Ershov, Nikita I

AU - Bondar, Natalya P

AU - Rubtsov, Nikolai B

N1 - The authors gratefully acknowledge the resources provided by the “Molecular and Cellular Biology” core facility of the IMCB SB RAS (Novosibirsk, Russia). Microscopy was performed at the Interinstitutional Shared Center for Microscopic Analysis of Biological Objects (ICG SB RAS, Novosibirsk). Resource-intensive calculations were performed at the CCU “Bioinformatics” SB RAS. Generation and sequencing of the gDNA libraries was funded by the Russian Science Foundation (RSF) under grant 19-14-00211. Maintenance of the laboratory lines of M. lignano, including the establishment of sublines and worm pools for the current study, was supported by project FWNR-2022-0015. © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.

PY - 2023/12/1

Y1 - 2023/12/1

N2 - Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of WGD, allo- or autopolyploidization, lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are important for understanding the early stages of genome evolution. However, assembling neopolyploid is a challenging task due to the presence of two homologous (or homeologous) chromosome sets and therefore the existence of the extended paralogous regions in its genome. Post-WGD evolution of polyploids includes cytogenetic diploidization leading to the formation of species, whose polyploid origin might be hidden by disomic inheritance. Earlier we uncovered the hidden polyploid origin of the free-living flatworms of the genus Macrostomum (Macrostomum lignano, M. janickei, and M. mirumnovem). Cytogenetic diploidization in these species accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we unravel the M. lignano genome organization through generation and sequencing of two sublines of the commonly used inbred line of M. lignano (called DV1) differring only in a copy number of the largest chromosome (MLI1). Using non-trivial assembly-free comparative analysis of their genomes, we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano, which consists in (1) presence of three subgenomes, emerged via formation of large fused chromosome and its variants, and (2) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.

AB - Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of WGD, allo- or autopolyploidization, lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are important for understanding the early stages of genome evolution. However, assembling neopolyploid is a challenging task due to the presence of two homologous (or homeologous) chromosome sets and therefore the existence of the extended paralogous regions in its genome. Post-WGD evolution of polyploids includes cytogenetic diploidization leading to the formation of species, whose polyploid origin might be hidden by disomic inheritance. Earlier we uncovered the hidden polyploid origin of the free-living flatworms of the genus Macrostomum (Macrostomum lignano, M. janickei, and M. mirumnovem). Cytogenetic diploidization in these species accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we unravel the M. lignano genome organization through generation and sequencing of two sublines of the commonly used inbred line of M. lignano (called DV1) differring only in a copy number of the largest chromosome (MLI1). Using non-trivial assembly-free comparative analysis of their genomes, we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano, which consists in (1) presence of three subgenomes, emerged via formation of large fused chromosome and its variants, and (2) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85180542829&origin=inward&txGid=fc48defef013f2cf47ba68bb15c02d9b

UR - https://www.mendeley.com/catalogue/28a4fd26-de77-36a6-aec3-72975f45484c/

U2 - 10.1093/molbev/msad250

DO - 10.1093/molbev/msad250

M3 - Article

C2 - 37979163

VL - 40

JO - Molecular Biology and Evolution

JF - Molecular Biology and Evolution

SN - 0737-4038

IS - 12

M1 - msad250

ER -