Dataset Information

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis).

ABSTRACT: Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3' truncated and containing only 5' UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.

SUBMITTER: Liang D

PROVIDER: S-EPMC7947781 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis).

Liang Dong D Zhao Pengju P Si Jingfang J Fang Lingzhao L Pairo-Castineira Erola E Hu Xiaoxiang X Xu Qing Q Hou Yali Y Gong Yu Y Liang Zhengwen Z Tian Bing B Mao Huaming H Yindee Marnoch M Faruque Md Omar MO Kongvongxay Siton S Khamphoumee Souksamlane S Liu George E GE Wu Dong-Dong DD Barker James Stuart F JSF Han Jianlin J Zhang Yi Y

Molecular biology and evolution 20210301 3

Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion ...[more]

PMID: 33212507

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Project description:Traumatic pericarditis (TP) remains a serious problem facing bovine producers; particularly in the developing countries; causing severe economic losses. This study was carried out on 47 buffaloes including; control buffaloes (n = 20) and buffaloes with TP (n = 27) at Assiut governorate, Egypt. All animals were subjected to thorough clinical examination, whole blood profiling, blood serum biochemical assays, and radiographic and ultrasonographic examinations. The recorded ultrasonographic findings included; the contractility, contour and shape of the reticulum, shape and size of the heart and spleen involvement. All data were statistically analysed. Buffaloes with TP showed lymphocytic leucocytosis, increase in serum activities of AST, hyperproteinaemia, hypoalbuminaemia and hyperglobulinaemia. Radio-opaque metal foreign bodies, cardiomegaly and loss of the normal cardiac shape and contour were the most common radiographic findings in the diseased buffaloes. Ultrasonographically, the diseased buffaloes showed either acute pericarditis (n = 10) or chronic suppurative pericarditis (n = 17). Complete cessation of reticular contractions (0/3 min) and displacement of the reticulum from the diaphragm by a distance about 2.6-4.5 cm were the most common ultrasonographic findings of both types of pericarditis. In addition, the reticulum had uneven contour and the heart showed characteristic changes in its size, shape and contractility that was either accelerated or reduced. Reticular abscesses and peritoneal effusions were also imaged in all diseased buffaloes. In acute TP; the affected heart was enlarged with strong and clear cardiac contractions. Accumulation of hypoechoic fluids interspersed with echogenic deposits of fibrin within heart tissue and pericardium was observed. In chronic suppurative pericarditis, cardiomegaly, thickening of the cardiac wall and loss of the characteristic recognisable heart shape were the common ultrasonographic findings. Accumulation of hypoechoic fluids (usually pus) interspersing with echogenic deposits of fibrin within the pericardium, ventricles, atria and valves was also observed. In conclusion, ultrasonography with the aids of other diagnostic tools such as clinical findings, laboratory analysis and radiography has a high efficacy in evaluation of diseased buffaloes with TP.

Project description:Bovine tuberculosis (bTB) remains endemic in domestic water buffaloes (Bubalus bubalis) in India and elsewhere, with limited options for control other than testing and slaughter. The prescribed tuberculin skin tests with purified protein derivative (PPD) for diagnosis of bTB preclude the use of Bacille Calmette-Guérin (BCG)-based vaccination because of the antigenic cross-reactivity of vaccine strains with Mycobacterium bovis and related pathogenic members of the M. tuberculosis complex (MTBC). For the diagnosis of bTB in domestic water buffaloes, we here assessed a recently described defined-antigen skin test (DST) that comprises overlapping peptides representing the ESAT-6, CFP-10 and Rv3615c antigens, present in disease-causing members of the MTBC but missing in BCG strains. The performance characteristics of three doses (5, 10 or 20 μg/peptide) of the DST were assessed in natural tuberculin skin test reactor (n = 11) and non-reactor (n = 35) water buffaloes at an organized dairy farm in Hisar, India, and results were compared with the single intradermal skin test (SIT) using standard bovine tuberculin (PPD-B). The results showed a dose-dependent response of DST in natural reactor water buffaloes, although the SIT induced a significantly greater (P < 0.001) skin test response than the highest dose of DST used. However, using a cut-off of 2 mm or greater, the 5, 10, and 20 μg DST cocktail correctly classified eight, 10 and all 11 of the SIT-positive reactors, respectively, suggesting that the 20 μg DST cocktail has a diagnostic sensitivity (Se) of 1.0 (95% CI: 0.72-1.0) identical to that of the SIT. Importantly, none of the tested DST doses induced any measurable skin induration responses in the 35 SIT-negative animals, suggesting a specificity point estimate of 1.0 (95% CI: 0.9-1.0), also identical to that of the SIT and compares favorably with that of the comparative cervical test (Se = 0.85; 95% CI: 0.55-0.98). Overall, the results suggest that similar to tuberculin, the DST enables sensitive and specific diagnosis of bTB in water buffaloes. Future field trials to explore the utility of DST as a defined antigen replacement for tuberculin in routine surveillance programs and to enable BCG vaccination of water buffaloes are warranted.

Dataset Information

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis).

Publications

Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis).

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