Structure and evolution of supernumerary chromosomes in the Pacific giant salamander, Dicamptodon tenebrosus

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

Accessory, supernumerary, or-most simply-B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS), their structure comprises fragments of standard (A) chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences.

Possible interspecific origin of the B chromosome of Hypsiboas albopunctatus (Spix, 1824) (Anura, Hylidae), revealed by microdissection, chromosome painting, and reverse hybridisation

The B chromosome in the hylid Hypsiboas albopunctatus (2n = 22 + B) is small, almost entirely composed of C-positive heterochromatin, and does not pair with any chromosome of the A complement. B probe, obtained by microdissection and DOP-PCR amplification, was used to search for homology between the B and regular chromosomes of H. albopunctatus and of the related species H. raniceps (Cope, 1862). Reverse hybridisation was also carried out in the investigation. The B probe exclusively painted the supernumerary, not hybridising any other chromosomes in H. albopunctatus, but all H. raniceps chromosomes showed small labelling signals. This result might be an indication that differences exist between the repetitive sequences of A and B chromosomes of H. albopunctatus, and that the chromosomes of H. raniceps and the heterochromatin of the B chromosome of H. albopunctatus are enriched with the same type of repetitive DNA. In meiotic preparations, the B labelled about 30% of scored spermatids, revealing a non-mendelian inheritance, and the painted B in micronucleus suggests that the supernumerary is eliminated from germ line cells. Although our results could suggest an interespecific origin of the B at first sight, further analysis on its repetitive sequences is still necessary. Nevertheless, the accumulation of repetitive sequences, detected in another species, even though closely related, remains an intriguing question.

Microdissection and chromosome painting of X and B chromosomes in Locusta migratoria

Acquisition of knowledge of the nature and DNA content of B chromosomes has been triggered by a collection of molecular techniques, one of which, microdissection, has provided interesting results in a number of B chromosome systems. Here we provide the first data on the molecular composition of B chromosomes in Locusta migratoria, after microdissection of the B and X chromosomes, DNA amplification by one (B) or two (X) different methods, and chromosome painting. The results showed that B chromosomes share at least two types of repetitive DNA sequences with the A chromosomes, suggesting that Bs in this species most likely arose intraspecifically. One of these repetitive DNAs is located on the heterochromatic distal half of the B chromosome and in the pericentromeric regions of about half of the A chromosomes, including the X. The other type of repetitive DNA is located interspersedly over the non-centromeric euchromatic regions of all A chromosomes and in an interstitial part of the proximal euchromatic half of the B chromosome. Chromosome painting, however, did not provide results sufficiently reliable to determine, in this species, which A chromosome gave rise to the B; this might be done by detailed analysis of the microdissected DNA sequences.

Structure and evolution of B chromosomes in amphibians

B chromosomes are known from 26 species of salamanders and frogs, equivalent to about 2% of amphibian species that have been karyotyped. In most cases, the structure of amphibian B chromosomes has not been extensively investigated. The exceptions are the B chromosomes of Hochstetter's frog, Leiopelma hochstetteri, from New Zealand, and the Coastal Giant salamander, Dicamptodon tenebrosus, from North America. Dicamptodon tenebrosus carries from 0 to 10 non-heterochromatic, telocentric B chromosomes per individual, averaging 0 to 3.4 B chromosomes per individual in populations throughout its extensive range. The B chromosomes of L. hochstetteri occur in frequencies averaging from 0 to 11.4 per individual in different populations, with a known maximum of 15 B chromosomes. Amphibian B chromosomes vary in size, heterochromatin, occurrence and frequency. They are commensurate in size and structure with the rest of the A set of chromosomes of the same species in which they occur. The B chromosomes are at least partly composed of repetitive DNA sequences which exist in numerous copies throughout the autosomes, in conformity to an hypothesis of intraspecific B chromosome origins.

Differential gene expression in yellow-necked mice Apodemus flavicollis (Rodentia, Mammalia) with and without B chromosomes

Most B chromosomes are heavily heterochromatic, promoting the general idea that they are genetically inert. The B chromosomes of Apodemus flavicollis are euchromatic and show a high degree of homology with the A chromosomes. The euchromatic nature of B chromosomes in A. flavicollis suggests that they may carry active genes and have transcriptional activity. We applied the differential display reverse transcription-polymerase chain reaction (DD RT-PCR) in order to analyze and compare gene expression in animals possessing B chromosomes and animals without B chromosomes. After a second and third round of amplification, three cDNA fragments were differentially expressed in +B mice compared with 0B animals. These cDNAs were Chaperonin containing TCP-1, subunit 6b (zeta) (CCT6B), Fragile histidine triad gene (FHIT) and hypothetical gene XP transcript. The differential expression pattern was confirmed by Real Time RT-PCR. We suggest that altered expression of these important genes is due to the presence of B chromosomes. In elevating the expression of these genes, B chromosomes of A. flavicollis affect some of the crucial processes in the cell. The significance of these effects and the nature of B chromosomes of A. flavicollis are discussed in the context of the data presented.

Occurrence of B chromosomes in lizards: a review

Although B chromosomes have been reported in many species of plants and animals, few studies have revealed the presence of these extra chromosomes in lizards. B chromosomes of lizards show different morphologies and sizes, from microchromosomes to macrochromosomes, or elements of intermediate size between smaller and larger A chromosomes, and number variability at intra- and inter-individual levels. In most cases, they are late-replicating and show either heterochromatic or no distinctive patterns after C-banding. The great majority of the publications about supernumerary chromosomes in this group have been based on conventional staining analyses, and there is no study designed to address questions related to their composition and structure or origin and evolution.

Comparative cytogenetics and supernumerary chromosomes in the Brazilian lizard genus Enyalius (Squamata, Polychrotidae)

Cytogenetical analyses based on conventional and differential staining were performed for the first time on five species of the Brazilian lizard genus Enyalius: E. bibronii, E. bilineatus, E. iheringii, E. leechii, and E. perditus. The species share a similar 2n = 36 (12M + 24m) karyotype, comprised of 12 metacentric or submetacentric macrochromosomes, except for an acrocentric pair 6 that characterizes E. bibronii. The 24 microchromosomes were acrocentrics, but in E. perditus two meta/submetacentric microchromosome pairs were unambiguously identified. Karyotypes with 2n = 37 and 2n = 37/38 chromosomes were also observed in some specimens of E. bilineatus as a result of the presence of supernumerary chromosomes (Bs). Ag-NORs were always located at the distal region of the long arm of the submetacentric pair 2. The constitutive heterochromatin was mostly restricted to the pericentromeric regions of some macrochromosomes and microchromosomes. A XX:XY mechanism of sex determination with a dot-like Y microchromosome occurs in E. bilineatus, E. leechii, and E. perditus.