Microchromosome

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Image of chicken chromosomes featuring the many microchromosomes (appearing as dots). The arrows indicate a stained gene locus on homologous macrochromosomes. ChickenChromosomesBMC Genomics5-56Fig4.jpg
Image of chicken chromosomes featuring the many microchromosomes (appearing as dots). The arrows indicate a stained gene locus on homologous macrochromosomes.

A microchromosome is a chromosome defined for its relatively small size. They are typical components of the karyotype of birds, some reptiles, fish, amphibians, and monotremes. [1] As many bird genomes have chromosomes of widely different lengths, the name was meant to distinguish them from the comparatively large macrochromosomes. [2] The distinction referred to the measured size of the chromosome while staining for karyotype, and while there is not a strict definition, chromosomes resembling the large chromosomes of mammals were called macrochromosomes (roughly 3 to 6 μm), while the much smaller ones of less than around 0.5 μm were called microchromosomes. [3] In terms of base pairs, by convention, those of less than 20Mb were called microchromosomes, those between 20 and 40 Mb are classified as intermediate chromosomes, and those larger than 40Mb are macrochromosomes. [4] By this definition, all normal chromosomes in organisms with relatively small genomes (less than 100-200Mb) would be considered microchromosomes.

Contents

Function

Microchromosomes are characteristically very small and often cytogenetically indistinguishable in a karyotype, which makes ordering and identifying chromosomes into a coherent karyotype particularly difficult. While originally thought to be insignificant fragments of chromosomes, in species where they have been studied they have been found to be rich in genes and high in GC content. In chickens, microchromosomes have been estimated to contain between 50 and 75% of all genes. [5] [6] During metaphase, they appear merely as 0.5-1.5 μm long specks. Their small size and poor condensation into heterochromatin means they generally lack the diagnostic banding patterns and distinct centromere locations used for chromosome identification. [7]

Occurrence

Microchromosomes are found in many vertebrates, but not in most mammals. [1] Important comparisons were made using the genomic organization of the Florida lancelet – part of a sister group to all vertebrates – suggests that the ancestral amniote (and vertebrates in general) genome consisted entirely of microchromosomes. Comparison between lancelet and modern vertebrate chromosomes shows that the macrochromosomes were the result of fusion between ancestral microchromosomes. In addition, retention of microchromosomes is shown to be the norm; the complete loss of them in mammals is the outlier instead. [3]

Relationship among mentioned organisms

Lancelet

Vertebrates

Garfish

Lungfish

Tetrapods

Amphibians

Amniotes

Mammals

Reptiles
Lepidosaurs

Squamata (snakes, lizards)

A[...]formes

Turtles

Archosaurs

In birds

Chickens have a diploid number of 78 (2n = 78) chromosomes, and as is usual in birds, the majority are microchromosomes. Classification of chicken chromosomes varies by author. Some classify them as 6 pairs of macrochromosomes, one pair of sex chromosomes, with the remaining 32 pairs being intermediate or microchromosomes. [5] Other arrangements such as that used by the International Chicken Genome Sequencing Consortium include five pairs of macrochromosomes, five pairs of intermediate chromosomes, and twenty-eight pairs of microchromosomes. [4] [8] Microchromosomes represent approximately one third of the total genome size, and have been found to have a much higher gene density than macrochromosomes. Because of this, it is estimated that the majority of genes are located on microchromosomes, [6] though due to the difficulty in physically identifying microchromosomes and the lack of microsatellite markers, it has been difficult to place genes on specific microchromosomes. [8]

Birds (except Falconidae) usually have karyotypes of approximately 80 chromosomes (2n = 80), with only a few being distinguishable macrochromosomes and an average of 60 being microchromosomes. [7] They are more abundant in birds than any other group of animals. Chickens (Gallus gallus) are an important model organism for studying microchromosomes. [7] Examination of microchromosomes in birds has led to the hypotheses that they may have originated as conserved fragments of ancestral macrochromosomes, and conversely that macrochromosomes could have arisen as aggregates of microchromosomes. [7] Comparative genomic analysis shows that microchromosomes contain genetic information which has been conserved across multiple classes of chromosomes. This indicates that at least ten chicken microchromosomes arose from fission of larger chromosomes and that the typical bird karyotype arose 100–250 mya. [6]

Replication timing and recombination rates have been found to differ between micro- and macrochromosomes in chickens. Microchromosomes replicate earlier in the S phase of interphase than macrochromosomes. [5] Recombination rates have also been found to be higher on microchromosomes. [9] Possibly due to the high recombination rates, chicken chromosome 16 (a microchromosome) has been found to contain the most genetic diversity of any chromosome in certain chicken breeds. [9] This is likely due to the presence on this chromosome of the major histocompatibility complex (MHC).

For the many small linkage groups in the chicken genome which have not been placed on chromosomes, the assumption has been made that they are located on the microchromosomes. Groups of these correspond almost exactly with large sections of certain human chromosomes. For example, linkage groups E29C09W09, E21E31C25W12, E48C28W13W27, E41W17, E54 and E49C20W21 correspond with chromosome 7. [8]

Turkey

The turkey has a diploid number of 80 (2n = 80) chromosomes. The karyotype contains an additional chromosomal pair relative to the chicken due to the presence of at least two fission/fusion differences (GGA2 = MGA3 and MGA6 and GGA4 = MGA4 and MGA9). Given these differences involving the macrochromosomes, an additional fission/fusion must also exist between the species involving the microchromosomes if the diploid numbers are valid. Other rearrangements have been identified through comparative genetic maps, [10] physical maps and whole genome sequencing. [11]

In turtles

Microchromosomes play a key role in sex determination in soft-shelled turtles. [12]

In humans and other animals

Microchromosomes are absent from the karyotypes of mammals [3] and some amphibians. [13] (The monotreme platypus has an intermediate karyotype with smaller chromosomes that are not quite "micro".) [3]

In rare cases, microchromosomes have been observed in the karotypes of individual humans. A link has been suggested between microchromosome presence and certain genetic disorders like Down syndrome [14] and fragile X syndrome. [15] The smallest chromosome in humans is normally chromosome 21, which is 47 Mb.

See also

Related Research Articles

<span class="mw-page-title-main">Chromosome</span> DNA molecule containing genetic material of a cell

A chromosome is a package of DNA with part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells the most important of these proteins are the histones. These proteins, aided by chaperone proteins, bind to and condense the DNA molecule to maintain its integrity. These chromosomes display a complex three-dimensional structure, which plays a significant role in transcriptional regulation.

<span class="mw-page-title-main">Genome</span> All genetic material of an organism

In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA. The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences, and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome. Algae and plants also contain chloroplasts with a chloroplast genome.

<span class="mw-page-title-main">Meiosis</span> Cell division producing haploid gametes

Meiosis (; from Ancient Greek μείωσις 'lessening', is a special type of cell division of germ cells in sexually-reproducing organisms that produces the gametes, the sperm or egg cells. It involves two rounds of division that ultimately result in four cells, each with only one copy of each chromosome. Additionally, prior to the division, genetic material from the paternal and maternal copies of each chromosome is crossed over, creating new combinations of code on each chromosome. Later on, during fertilisation, the haploid cells produced by meiosis from a male and a female will fuse to create a zygote, a cell with two copies of each chromosome again.

<span class="mw-page-title-main">Ploidy</span> Number of sets of chromosomes of a cell

Ploidy is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Here sets of chromosomes refers to the number of maternal and paternal chromosome copies, respectively, in each homologous chromosome pair—the form in which chromosomes naturally exist. Somatic cells, tissues, and individual organisms can be described according to the number of sets of chromosomes present : monoploid, diploid, triploid, tetraploid, pentaploid, hexaploid, heptaploid or septaploid, etc. The generic term polyploid is often used to describe cells with three or more sets of chromosomes.

<span class="mw-page-title-main">Human genome</span> Complete set of nucleic acid sequences for humans

The human genome is a complete set of nucleic acid sequences for humans, encoded as the DNA within each of the 24 distinct chromosomes in the cell nucleus. A small DNA molecule is found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs. It also includes promoters and their associated gene-regulatory elements, DNA playing structural and replicatory roles, such as scaffolding regions, telomeres, centromeres, and origins of replication, plus large numbers of transposable elements, inserted viral DNA, non-functional pseudogenes and simple, highly repetitive sequences. Introns make up a large percentage of non-coding DNA. Some of this non-coding DNA is non-functional junk DNA, such as pseudogenes, but there is no firm consensus on the total amount of junk DNA.

<span class="mw-page-title-main">Sex-determination system</span> Biological system that determines the development of an organisms sex

A sex-determination system is a biological system that determines the development of sexual characteristics in an organism. Most organisms that create their offspring using sexual reproduction have two common sexes and a few less common intersex variations.

<span class="mw-page-title-main">Polyploidy</span> Condition where cells of an organism have more than two paired sets of chromosomes

Polyploidy is a condition in which the cells of an organism have more than two paired sets of (homologous) chromosomes. Most species whose cells have nuclei (eukaryotes) are diploid, meaning they have two complete sets of chromosomes, one from each of two parents; each set contains the same number of chromosomes, and the chromosomes are joined in pairs of homologous chromosomes. However, some organisms are polyploid. Polyploidy is especially common in plants. Most eukaryotes have diploid somatic cells, but produce haploid gametes by meiosis. A monoploid has only one set of chromosomes, and the term is usually only applied to cells or organisms that are normally diploid. Males of bees and other Hymenoptera, for example, are monoploid. Unlike animals, plants and multicellular algae have life cycles with two alternating multicellular generations. The gametophyte generation is haploid, and produces gametes by mitosis; the sporophyte generation is diploid and produces spores by meiosis.

<span class="mw-page-title-main">Chromosomal crossover</span> Cellular process

Chromosomal crossover, or crossing over, is the exchange of genetic material during sexual reproduction between two homologous chromosomes' non-sister chromatids that results in recombinant chromosomes. It is one of the final phases of genetic recombination, which occurs in the pachytene stage of prophase I of meiosis during a process called synapsis. Synapsis begins before the synaptonemal complex develops and is not completed until near the end of prophase I. Crossover usually occurs when matching regions on matching chromosomes break and then reconnect to the other chromosome.

<span class="mw-page-title-main">Karyotype</span> Photographic display of total chromosome complement in a cell

A karyotype is the general appearance of the complete set of chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is discerned by determining the chromosome complement of an individual, including the number of chromosomes and any abnormalities.

<span class="mw-page-title-main">Y chromosome</span> Sex chromosome in the XY sex-determination system

The Y chromosome is one of two sex chromosomes in therian mammals and other organisms. Along with the X chromosome, it is part of the XY sex-determination system, in which the Y is the sex-determining chromosome because the presence of the Y chromosome causes offspring produced in sexual reproduction to be of male sex. In mammals, the Y chromosome contains the SRY gene, which triggers development of male gonads. The Y chromosome is passed only from male parents to male offspring.

<span class="mw-page-title-main">Synteny</span> Co-localization of genetic loci on a chromosome, or the conservation of gene order

In genetics, the term synteny refers to two related concepts:

<span class="mw-page-title-main">Copy number variation</span> Repeated DNA variation between individuals

Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variation is a type of structural variation: specifically, it is a type of duplication or deletion event that affects a considerable number of base pairs. Approximately two-thirds of the entire human genome may be composed of repeats and 4.8–9.5% of the human genome can be classified as copy number variations. In mammals, copy number variations play an important role in generating necessary variation in the population as well as disease phenotype.

<span class="mw-page-title-main">Chromosome 22</span> Human chromosome

Chromosome 22 is one of the 23 pairs of chromosomes in human cells. Humans normally have two copies of chromosome 22 in each cell. Chromosome 22 is the second smallest human chromosome, spanning about 51 million DNA base pairs and representing between 1.5 and 2% of the total DNA in cells.

<span class="mw-page-title-main">ZW sex-determination system</span> Chromosomal system

The ZW sex-determination system is a chromosomal system that determines the sex of offspring in birds, some fish and crustaceans such as the giant river prawn, some insects, the schistosome family of flatworms, and some reptiles, e.g. majority of snakes, lacertid lizards and monitors, including Komodo dragons. It is also present in some plants, where it has probably evolved independently on several occasions. The letters Z and W are used to distinguish this system from the XY sex-determination system. In the ZW system, females have a pair of dissimilar ZW chromosomes, and males have two similar ZZ chromosomes.

<span class="mw-page-title-main">Sex chromosome</span> Chromosome that differs from an ordinary autosome in form, size, and behavior

Sex chromosomes are chromosomes that carry the genes that determine the sex of an individual. The human sex chromosomes are a typical pair of mammal allosomes. They differ from autosomes in form, size, and behavior. Whereas autosomes occur in homologous pairs whose members have the same form in a diploid cell, members of an allosome pair may differ from one another.

The following outline is provided as an overview of and topical guide to genetics:

<span class="mw-page-title-main">Mega-telomere</span>

A mega-telomere, is an extremely long telomere sequence that sits on the end of chromosomes and prevents the loss of genetic information during cell replication. Like regular telomeres, mega-telomeres are made of a repetitive sequence of DNA and associated proteins, and are located on the ends of chromosomes. However, mega-telomeres are substantially longer than regular telomeres, ranging in size from 50 kilobases to several megabases.

The 2000s witnessed an explosion of genome sequencing and mapping in evolutionarily diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosomal regions from more than a few species is not yet possible. The intense focus on the building of comparative maps for domestic, laboratory and agricultural (cattle) animals has traditionally been used to understand the underlying basis of disease-related and healthy phenotypes.

<span class="mw-page-title-main">Genomic evolution of birds</span>

The genomic evolution of birds has come under scrutiny since the advent of rapid DNA sequencing, as birds have the smallest genomes of the amniotes despite acquiring highly derived phenotypic traits. Whereas mammalian and reptilian genomes range between 1.0 and 8.2 giga base pairs (Gb), avian genomes have sizes between 0.91 Gb and 1.3 Gb. Avian genomes reflect the action of natural selection and are the basis of their phenotypes, reflected in their morphology and behaviour, which have evolved significantly since their divergence from other archosaurian, diapsid, and amniotic lineages.

References

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    10. ↑ Reed, K.M.; Chaves, L.D.; Mendoza, K.M. (2007). "An integrated and comparative genetic map of the turkey genome". Cytogenetic and Genome Research. 119 (1–2): 113–26. doi:10.1159/000109627. PMID   18160790. S2CID   42494634.
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