Muntjac chromosome evolution and architecture

Abstract

Despite their recent divergence, muntjac deer show striking karyotype differences. Here we describe new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) and Muntiacus muntjak (2n=6/7), and analyze their evolution and architecture. We identified six fusion events shared by both species relative to the cervid ancestor and therefore present in the muntjac common ancestor, six fusion events unique to the M. reevesi lineage, and twenty-six fusion events unique to the M. muntjak lineage. One of these M. muntjak fusions reverses an earlier fission in the cervid lineage. Although comparative Hi-C analysis revealed differences in long-range genome contacts and A/B compartment structures, we discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. A small number of genes involved in chromosome maintenance show evidence for rapid evolution, possibly associated with the dramatic changes in karyotype. Analysis of muntjac genomes reveals new insights into this unique case of rapid karyotype evolution and the resulting biological variation.

Genome and Karyotype Reorganization after Whole Genome Duplication in Free-Living Flatworms of the Genus Macrostomum

“…One potential difficulty with Scenario II is that it suggests that the two different WGD events were followed by very similar independent karyotype reorganization processes. While this suggestion looks like an argument against the hypothesis of independent WGD events, numerous chromosome fusions have previously been described in the karyotype evolution of many taxa, for instance, the mole vole, Ellobius tancrei; the common shrew, Sorex araneus; and other mammalian species [50][51][52][53]. They led to the formation of chromosome races that differed with respect to the combination of fused chromosomes ("Robertsonian fans") [50,51] or to a strong reduction in chromosome number, as observed in the evolution of small deer of the genus Muntiacus [52,54,55].…”

Amphibian Hymenochirus boettgeri as an experimental model for infection studies with the chytrid fungus Batrachochytrium dendrobatidis

“…Originally inhabiting pools, rivers, and stagnant waters in forested regions of subequatorial Africa, H. boettgeri can be readily purchased from the aquarium trade, allowing laboratories worldwide to use it. In addition, H. boettgeri is a promising species for use as a model organism in the Bd-amphibian system as it: i) is susceptible to Bd [ 12–14 ]; ii) tolerates high temperatures that eliminate Bd infection ([ 12 , 15 ]; also supported by our data); iii) reproduces throughout the year and completes metamorphosis in approximately 5 weeks [ 16 , 17 ]; iv) is small and fully aquatic, which simplifies husbandry and environmental manipulation; v) has a complete genome sequence [ 18 ] and belongs to the same family as X. laevis [ 19 ], which means that tools that work on X. laevis may be applied here; and vi) has a characterized antimicrobial peptide repertoire [ 20 ], and general inferences about the functioning of its immune system can be made based on the extensively characterized immune system of the closely related species, X. laevis [ 21 ].…”

Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity

“…The quality and impact of read filtering were examined for all samples by running FastQC again, and the results were visualised using MultiQC, thereby ensuring high-quality filtered data for alignment (overall c. 96% of reads passed quality filtering resulting in a mean of 73,147,491 reads per sample). The filtered reads were mapped to an early release of the túngara reference genome assembly (Mudd, 2019; GenBank accession no: GCA_019512145.1). For each sample, paired-end read mapping was performed using Bowtie2 v2.3.5.1 (Langmead & Salzberg, 2012) with default parameters aside from specifying local read alignment (--local) and a maximum fragment length of 700 (-X 700).…”

“…Given the recent availability of a high-quality reference genome (Mudd, 2019), túngara frogs appear to be an ideal study system to examine the impact of urbanisation on population dynamics and urban adaptation more generally.…”

“…Whether or not this phenotypic divergence is related to and/or enhanced or constrained by genetic variation remains unknown. Given the recent availability of a high‐quality reference genome (Mudd, 2019), túngara frogs appear to be an ideal study system to examine the impact of urbanisation on population dynamics and urban adaptation more generally.…”