The first report of a Pelecaniformes defensin cluster: characterization of β-defensin genes in the crested ibis based on BAC libraries.
Defensins play a key role in the innate immunity of various organisms. Detailed genomic studies of the defensin cluster have only been reported in a limited number of birds. Herein, we present the first characterization of defensins in a Pelecaniformes species, the crested ibis (Nipponia nippon), which is one of the most endangered birds in the world. We constructed bacterial artificial chromosome libraries, including a 4D-PCR library and a reverse-4D library, which provide at least 40 equivalents of this rare bird's genome. A cluster including 14 β-defensin loci within 129 kb was assigned to chromosome 3 by FISH, and one gene duplication of AvBD1 was found. The ibis defensin genes are characterized by multiform gene organization ranging from two to four exons through extensive exon fusion. Splicing signal variations and alternative splice variants were also found. Comparative analysis of four bird species identified one common and multiple species-specific duplications, which might be associated with high GC content. Evolutionary analysis revealed birth-and-death mode and purifying selection for avian defensin evolution, resulting in different defensin gene numbers among bird species and functional conservation within orthologous genes, respectively. Additionally, we propose various directions for further research on genetic conservation in the crested ibis.
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
Hong
H
Lan
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
Hui
H
Chen
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
Li-Cheng
LC
Chen
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
Bei-Bing
BB
Wang
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
Li
L
Sun
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
Mei-Ying
MY
Ma
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
Sheng-Guo
SG
Fang
The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
Qiu-Hong
QH
Wan
D017398:Alternative Splicing; D000595:Amino Acid Sequence; D000818:Animals; D001717:Birds / Q000145:classification / Q000235:genetics* / Q000276:immunology; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D017124:Conserved Sequence; D056727:Endangered Species; D005091:Exons; D018628:Gene Dosage; D020440:Gene Duplication; D015723:Gene Library; D056426:Genetic Loci; D016678:Genome; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D016415:Sequence Alignment; D013045:Species Specificity; D023083:beta-Defensins / Q000235:genetics* / Q000276:immunology
D023083:beta-Defensins