How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes

Ruban, Alevtina; Schmutzer, Thomas; Scholz, Uwe; Houben, Andreas

doi:10.3390/genes8110294

Cited by 38 publications

(43 citation statements)

References 80 publications

(79 reference statements)

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“…Finally, a parallel could be drawn between marker chromosomes generated by chromoanagenesis events and the supernumerary chromosomes, named B chromosomes, found in many eukaryotic karyotypes. It has been established that these supernumerary chromosomes represent multichromosomal mosaics arising in taxa that experienced rapid genome changes [103], like the domestic dog which has one of the most rearranged karyotypes in mammals [104,105].…”

Section: Macro-evolutionary Implications Of Chromoanagenesismentioning

confidence: 99%

Chromoanagenesis: a piece of the macroevolution scenario

Pellestor

Gatinois

2020

Mol Cytogenet

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Over the last decade, new types of massive and complex chromosomal rearrangements based on the chaotic shattering and restructuring of chromosomes have been identified in cancer cells as well as in patients with congenital diseases and healthy individuals. These unanticipated phenomena are named chromothripsis, chromoanasynthesis and chromoplexy, and are grouped under the term of chromoanagenesis. As mechanisms for rapid and profound genome modifications in germlines and early development, these processes can be regarded as credible pathways for genomic evolution and speciation process. Their discovery confirms the importance of genome-centric investigations to fully understand organismal evolution. Because they oppose the model of progressive acquisition of driver mutations or rearrangements, these phenomena conceptually give support to the concept of macroevolution, known through the models of "Hopeful Monsters" and the "Punctuated Equilibrium". In this review, we summarize mechanisms underlying chromoanagenesis processes and we show that numerous cases of chromosomal speciation and short-term adaptation could be correlated to chromoanagenesis-related mechanisms. In the frame of a modern and integrative analysis of eukaryote evolutionary processes, it seems important to consider the unexpected chromoanagenesis phenomena.

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Section: Macro-evolutionary Implications Of Chromoanagenesismentioning

confidence: 99%

Chromoanagenesis: a piece of the macroevolution scenario

Pellestor

Gatinois

2020

Mol Cytogenet

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“…Sequences already on the B collect mutations at a high rate, and most are eventually lost. It has been difficult to produce sequence assemblies of B chromosomes due to their repetitive nature and their high levels of homology with sequences in the A chromosomes [16,17,18,19].…”

Section: Introductionmentioning

confidence: 99%

“…Current approaches to identifying B sequence can be categorized into two types: direct and indirect [16]. Direct methods, such as the sequencing of B chromosomes isolated through flow sorting or microdissection, have a high rate of contamination [12,16] and are only possible in a few organisms with large B chromosomes. Indirect methods, such as the comparison of whole genome sequence data between samples with and without a B chromosome, can be performed on any species.…”

Section: Introductionmentioning

confidence: 99%

Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

Clark

Conte

Kocher

2018

Preprint

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B chromosomes (Bs) were discovered a century ago, and since then most studies have focused on describing their distribution and abundance using traditional cytogenetics. Only recently have attempts been made to understand their structure and evolution at the level of DNA sequence. Many questions regarding the origin, structure, function and evolution of B chromosomes remain unanswered. Here we identify B chromosome sequences from several species of cichlid fish from Lake Malawi by examining the ratios of DNA sequence coverage in individuals with and without B chromosomes. We examine the efficiency of this method, and compare results using both Illumina and PacBio sequence data. The B chromosome sequences detected in 13 individuals from 7 species were compared to assess the rates of sequence replacement. B-specific sequence common to at least 12 of the 13 datasets are identified as the “Core” B chromosome. The location of B sequence homologs throughout the genome provides further support for theories of B chromosome evolution. Finally, we identified candidate genes located on the B chromosome which may regulate the segregation and maintenance of the B chromosome.

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“…It was shown that the Bs of several plant and animal species harbour gene-derived sequences. This allowed to trace their origin from duplicated fragments of multiple A chromosomes of their host species (reviewed in (Ruban et al, 2017). Hence, Bs could be considered as a by-product of standard chromosome (As) evolution.…”

Section: Introductionmentioning

confidence: 99%

Nondisjunction and unequal spindle organization accompany the drive ofAegilops speltoidesB chromosomes

Houben

Ruban

et al. 2019

Preprint

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18Supernumerary B chromosomes (Bs), which are often preferentially inherited, 19 deviating from usual Mendelian segregation. This chromosome drive is one of the 20 most important features of Bs. Here we analyzed the drive mechanism of Aegilops 21 speltoides Bs and provide direct insight into its cellular mechanism. Comparative 22 genomics resulted in the identification of the tandem repeat AesTR-183 of Ae. 23 speltoides Bs, which also can be found on the Bs of Ae. mutica and rye, was used to 24 track Bs during microgametogenesis. Nondisjunction of CENH3-positive, tubulin 25 interacting B sister chromatids and an asymmetric spindle during first pollen grain 26 mitosis are likely components of the accumulation process. A quantitative flow 27 cytometric approach revealed, that independent on the number of Bs present in the 28 mother plant Bs accumulate in the generative nuclei with more than 93%. Nine of 29 eleven tested (peri)centromeric repeats were shared by A and B chromosomes. A 30 common origin of the drive process in Poaceae is likely. 31 32 33 Keywords 34 supernumerary B chromosome, chromosome drive, chromosome nondisjunction, 35 centromere, pollen grain mitosis, chromosome segregation, asymmetric spindle, flow 36 cytometry, Aegilops speltoides 37 38 39 Introduction 40 Supernumerary B chromosomes (Bs) are considered as dispensable chromosomes, 41 which under standard conditions do not confer advantages on the organisms that 42 harbour them. Bs are found in thousands of fungi, plant and animal species and are 43 thought to stand for a specific type of selfish DNA (Jones and Rees, 1982). Recent 44 advances in deciphering the sequence composition of B chromosomes provided a 45 unique opportunity for the analysis of the origin and evolution of this enigmatic 46 genome component. It was shown that the Bs of several plant and animal species 47 harbour gene-derived sequences. This allowed to trace their origin from duplicated 48 fragments of multiple A chromosomes of their host species (reviewed in (Ruban et 49 al., 2017). Hence, Bs could be considered as a by-product of standard chromosome 50 (As) evolution. 51 52 Often the transmission rate of B chromosomes is higher than 0.5, not obeying the 53 Mendelian law of equal segregation. The resulting transmission advantage is 54 collectively referred to as 'drive'. The maximum number of Bs tolerated by the host 55 varies between species and depends on a balance between the B chromosome 56 drive, and the negative effects, especially on fertility and vigour, caused by B 57 chromosomes if they occur in higher numbers (Bougourd and Jones, 1997). Among 58 the relatively small number of B chromosome-positive species that have been 59 investigated, relative to the total number of known species, there is a variety of 60 mechanisms of B chromosome drive that occurs before, during or after meiosis, while 61 in some cases drive has not been found (reviewed in (Austin et al., 2009; Burt and drive, the non-Mendelian inheritance of Bs could also be affected by mitotic and 64 m...

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How Next-Generation Sequencing Has Aided Our Understanding of the Sequence Composition and Origin of B Chromosomes

Cited by 38 publications

References 80 publications

Chromoanagenesis: a piece of the macroevolution scenario

Chromoanagenesis: a piece of the macroevolution scenario

Genomic Characterization of a B Chromosome in Lake Malawi Cichlid Fishes

Nondisjunction and unequal spindle organization accompany the drive ofAegilops speltoidesB chromosomes

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