Chromosome Size in Diploid Eukaryotic Species Centers on the Average Length with a Conserved Boundary

Abstract

Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation of living organisms. Although the genome of a species as a whole is important, chromosomes are the basic units subjected to genetic events that coin evolution to a large extent. Now many complete genome sequences are available, we can address evolution and variation of individual chromosomes across species. For example, “How are the repeat and nonrepeat proportions of genetic codes distributed among different chromosomes in a multichromosome species?” “Is there a general rule behind the intuitive observation that chromosome lengths tend to be similar in a species, and if so, can we generalize any findings in chromosome content and size across different taxonomic groups?” Here, we show that chromosomes within a species do not show dramatic fluctuation in their content of mobile genetic elements as the proliferation of these elements increases from unicellular eukaryotes to vertebrates. Furthermore, we demonstrate that, notwithstanding the remarkable plasticity, there is an upper limit to chromosome-size variation in diploid eukaryotes with linear chromosomes. Strikingly, variation in chromosome size for 886 chromosomes in 68 eukaryotic genomes (including 22 human autosomes) can be viably captured by a single model, which predicts that the vast majority of the chromosomes in a species are expected to have a base pair length between 0.4035 and 1.8626 times the average chromosome length. This conserved boundary of chromosome-size variation, which prevails across a wide taxonomic range with few exceptions, indicates that cellular, molecular, and evolutionary mechanisms, possibly together, confine the chromosome lengths around a species-specific average chromosome length.

Size of the Whole versus Number of Parts in Genomes

“…Laboratory experiments indicate that "upper and lower tolerance limits for chromosome size are apparently determined by the genome size, chromosome number and karyotype structure of a given species" (see [13] and references therein). Along these lines, a recent statistical study shows that it is possible to predict, for a given species, chromosome sizes by chromosome number, and furthermore, given either genome size or average chromosome length it is possible to predict the size range of all chromosomes of that species [14].…”

DNA fragment assembly using optimization

“…Under reasonable conditions (i. e. an eight core processor and a few days calculation), it would be possible to assemble problems with hundreds of thousands of fragments or tens of millions of bases. This includes all prokaryotes and most unicellular eukaryotes [31]. Large genomes are usually cut at specific places yielding smaller assembly problems.…”

USER-friendly image-based segmentation and analysis of chromosomes

“…It is based on the analysis of the number and morphology of chromosomes that become compacted into rod-like structures during metaphase, the first short phase of the cell division process. More generally, the assessment of chromosomal size as well as the analysis of shape parameters (such as centromere position and sizes of chromosome arms) through the microscopic analysis of metaphase spreads is a widely applied technique for the study of genomic structure, organization, function and evolution in different fields of biological and environmental sciences [1,2,3].…”