Sequence properties of certain GC rich avian genes, their origins and absence from genome assemblies: case studies

Abstract

Background More and more eukaryotic genomes are sequenced and assembled, most of them presented as a complete model in which missing chromosomal regions are filled by Ns and where a few chromosomes may be lacking. Avian genomes often contain sequences with high GC content, which has been hypothesized to be at the origin of many missing sequences in these genomes. We investigated features of these missing sequences to discover why some may not have been integrated into genomic libraries and/or sequenced. Results The sequences of five red jungle fowl cDNA models with high GC content were used as queries to search publicly available datasets of Illumina and Pacbio sequencing reads. These were used to reconstruct the leptin, TNFα, MRPL52, PCP2 and PET100 genes, all of which are absent from the red jungle fowl genome model. These gene sequences displayed elevated GC contents, had intron sizes that were sometimes larger than non-avian orthologues, and had non-coding regions that contained numerous tandem and inverted repeat sequences with motifs able to assemble into stable G-quadruplexes and intrastrand dyadic structures. Our results suggest that Illumina technology was unable to sequence the non-coding regions of these genes. On the other hand, PacBio technology was able to sequence these regions, but with dramatically lower efficiency than would typically be expected. Conclusions High GC content was not the principal reason why numerous GC-rich regions of avian genomes are missing from genome assembly models. Instead, it is the presence of tandem repeats containing motifs capable of assembling into very stable secondary structures that is likely responsible.

A Novel Hypothalamic Factor, Neurosecretory Protein GM, Causes Fat Deposition in Chicks

“…In mammals, leptin is a hormone secreted by adipocytes and acts on the hypothalamus to suppress eating and obesity ( Halaas et al, 1995 ). Recently, the leptin gene has been identified in some bird and these findings suggest that avian leptin may have a different physiological function from that of lipid metabolism in mammals ( Seroussi et al, 2017 , 2019 ; Beauclair et al, 2019 ; Friedman-Einat and Seroussi, 2019 ). The present study showed that NPGM is a new player in regulating fat deposition in avian species, chicken.…”

Metformin attenuates steroidogenesis in ovarian follicles of the broiler breeder hen

“…Previous reports have suggested that the ERK1 gene may have been lost in the chicken due to its absence in sequenced chicken genome (Lefloch et al 2008) and the absence of ERK1 protein in chicken brain protein extracts (Buscà et al 2015). Furthermore, the chicken genome assemblies are still incomplete due to technical difficulties imposed by the existence of highly stable secondary gene structures (Beauclair et al 2019). Further studies are required to determine the existence of the ERK1 gene in chickens.…”

A Novel Hypothalamic Factor, Neurosecretory Protein GM, Causes Fat Deposition in Chicks

“…In addition, the presence of leptin in the peripheral circulation has been questioned because it was not detected in the blood of birds (Seroussi et al, 2016). Recently, the leptin gene has been identified in some birds, and avian leptin is expressed in the digestive organs (Friedman-Einat and Seroussi, 2019; Seroussi et al, 2017; Beauclair et al, 2019; Seroussi et al, 2019). These findings suggest that avian leptin may have a different physiological function from that of lipid metabolism in mammals.…”