Birth and death in terminal complement pathway

Sharma, Ashutosh; Gupta, Saumya; Patil, Ajinkya Bharatraj; Vijay, Nagarjun

doi:10.1016/j.molimm.2022.07.006

Cited by 4 publications

(2 citation statements)

References 129 publications

(122 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Five BPI -like genes occur near BPI ( Chiang et al, 2011 ), which help arrest bacterial growth, are prominent in neutrophil phagocytosis, and work as a bactericidal protein ( Elsbach and Weiss, 1998 ; Weiss, 2003 ). In chickens, defense against Gram-negative bacteria may be especially important as they lack the complement C9 gene required to effectively eliminate pathogens through the membrane attack complex (MAC) formation ( Sharma et al, 2022a ). Notably, another BBC breed from Korea, YOSK, has signatures of selection at the TLR4 gene involved in detecting Gram-negative bacteria ( Cho et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

2023

Self Cite

View full text Add to dashboard Cite

Black-bone chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis (Fm) locus on the 20th chromosome results in increased endothelin-3 (EDN3) gene expression and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the Silkie breed to resolve high-confidence haplotypes at the Fm locus spanning both Dup1 and Dup2 regions and establish that the Fm_2 scenario is correct of the three possible scenarios of the complex chromosomal rearrangement. The relationship between Chinese and Korean BBC breeds with Kadaknath native to India is underexplored. Our data from whole-genome re-sequencing establish that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify two Fm locus proximal regions (∼70 Kb and ∼300 Kb) with signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the bactericidal/permeability-increasing-protein-like gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in the bactericidal/permeability-increasing-protein-like gene hitchhiked with the Fm locus in Kadaknath due to close physical linkage. Identifying this Fm locus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.

show abstract

Section: Discussionmentioning

confidence: 99%

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

2023

Self Cite

View full text Add to dashboard Cite

show abstract

“…In the chicken genome, five BPI-like genes occur near BPI [82], which help arrest bacterial growth, are prominent in phagocytosis by neutrophils, and work as a bactericidal protein [83,84]. In chickens, defense against gramnegative bacteria may be especially important as they lack the complement C9 gene required to effectively eliminate pathogens through the Membrane Attack Complex (MAC) formation [85]. Notably, another BBC breed from Korea, YOSK, has signatures of selection at the TLR4 gene involved in detecting Gram-negative bacteria [21].…”

Section: Selective Sweep Near Fm Locus May Be a Consequence Of Linkagementioning

confidence: 99%

Hitchhiking of bactericidal/permeability-increasing protein-like gene with the fibromelanosis locus in Kadaknath black-bone-chicken

Shinde

Sharma

Vijay

2022

Preprint

Self Cite

View full text Add to dashboard Cite

Black-bone-chicken (BBC) breeds are famous for their distinctive meat texture and taste. However, the relationship between BBC breeds, especially the Kadaknath breed native to India, is poorly understood. Here, we establish that all BBC breeds, including Kadaknath, share a common complex chromosomal rearrangement at the FM locus on the 20th chromosome, which is responsible for the melanin hyperpigmentation throughout the body. While we find breed-specific gene flow between BBC and commercial breeds, the shared ancestry of all BBC breeds and pattern of isolation by distance suggest Kadaknath is closely related to Tibetan BBC. Interestingly, two FM locus proximal regions (~70Kb and ~300 Kb) have signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the Bactericidal/permeability-increasing-protein-like (BPIL) gene having two Kadaknath-specific changes within the protein domains. The absence of these changes in other BBC breeds suggests this variation arose after the separation of these breeds. Our results indicate that the rearrangement at the FM locus and protein-coding changes in the BPIL gene were selected simultaneously in Kadaknath due to close physical linkage. The identification of this FM locus proximal selective sweep sheds light on the distinctiveness of Kadaknath compared to other BBC.

show abstract

Evolutionary diversity of CXCL16-CXCR6: Convergent substitutions and recurrent gene loss in sauropsids

Salve,

Sharma,

Vijay

2024

Immunogenetics

View full text Add to dashboard Cite

Birth and death in terminal complement pathway

Cited by 4 publications

References 129 publications

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken

Hitchhiking of bactericidal/permeability-increasing protein-like gene with the fibromelanosis locus in Kadaknath black-bone-chicken

Evolutionary diversity of CXCL16-CXCR6: Convergent substitutions and recurrent gene loss in sauropsids

Contact Info

Product

Resources

About