Dataset Information

Revisiting avian 'missing' genes from de novo assembled transcripts.

ABSTRACT: BACKGROUND:Argument remains as to whether birds have lost genes compared with mammals and non-avian vertebrates during speciation. High quality-reference gene sets are necessary for precisely evaluating gene gain and loss. It is essential to explore new reference transcripts from large-scale de novo assembled transcriptomes to recover the potential hidden genes in avian genomes. RESULTS:We explored 196 high quality transcriptomic datasets from five bird species to reconstruct transcripts for the purpose of discovering potential hidden genes in the avian genomes. We constructed a relatively complete and high-quality bird transcript database (1,623,045 transcripts after quality control in five birds) from a large amount of avian transcriptomic data, and found most of the presumed missing genes (83.2%) could be recovered in at least one bird species. Most of these genes have been identified for the first time in birds. Our results demonstrate that 67.94% genes have GC content over 50%, while 2.91% genes are AT-rich (AT%?>?60%). In our results, 239 (53.59%) genes had a tissue-specific expression index of more than 0.9 in chicken. The missing genes also have lower Ka/Ks values than average (genome-wide: Ka/Ks?=?0.99; missing gene: Ka/Ks?=?0.90; t-test?=?1.25E-14). Among all presumed missing genes, there were 135 for which we did not find any meaningful orthologues in any of the 5 species studied. CONCLUSION:Insufficient reference genome quality is the major reason for wrongly inferring missing genes in birds. Those presumably missing genes often have a very strong tissue-specific expression pattern. We show multi-tissue transcriptomic data from various species are necessary for inferring gene family evolution for species with only draft reference genomes.

SUBMITTER: Yin ZT

PROVIDER: S-EPMC6321700 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Revisiting avian 'missing' genes from de novo assembled transcripts.

Yin Zhong-Tao ZT Zhu Feng F Lin Fang-Bin FB Jia Ting T Wang Zhen Z Sun Dong-Ting DT Li Guang-Shen GS Zhang Cheng-Lin CL Smith Jacqueline J Yang Ning N Hou Zhuo-Cheng ZC

BMC genomics 20190105 1

<h4>Background</h4>Argument remains as to whether birds have lost genes compared with mammals and non-avian vertebrates during speciation. High quality-reference gene sets are necessary for precisely evaluating gene gain and loss. It is essential to explore new reference transcripts from large-scale de novo assembled transcriptomes to recover the potential hidden genes in avian genomes.<h4>Results</h4>We explored 196 high quality transcriptomic datasets from five bird species to reconstruct tran ...[more]

PMID: 30611188

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Project description:Insecticide resistance has recently become a critical concern for control of many insect pest species. Genome sequencing and global quantization of gene expression through analysis of the transcriptome can provide useful information relevant to this challenging problem. The oriental fruit fly, Bactrocera dorsalis, is one of the world's most destructive agricultural pests, and recently it has been used as a target for studies of genetic mechanisms related to insecticide resistance. However, prior to this study, the molecular data available for this species was largely limited to genes identified through homology. To provide a broader pool of gene sequences of potential interest with regard to insecticide resistance, this study uses whole transcriptome analysis developed through de novo assembly of short reads generated by next-generation sequencing (NGS). The transcriptome of B. dorsalis was initially constructed using Illumina's Solexa sequencing technology. Qualified reads were assembled into contigs and potential splicing variants (isotigs). A total of 29,067 isotigs have putative homologues in the non-redundant (nr) protein database from NCBI, and 11,073 of these correspond to distinct D. melanogaster proteins in the RefSeq database. Approximately 5,546 isotigs contain coding sequences that are at least 80% complete and appear to represent B. dorsalis genes. We observed a strong correlation between the completeness of the assembled sequences and the expression intensity of the transcripts. The assembled sequences were also used to identify large numbers of genes potentially belonging to families related to insecticide resistance. A total of 90 P450-, 42 GST-and 37 COE-related genes, representing three major enzyme families involved in insecticide metabolism and resistance, were identified. In addition, 36 isotigs were discovered to contain target site sequences related to four classes of resistance genes. Identified sequence motifs were also analyzed to characterize putative polypeptide translational products and associate them with specific genes and protein functions.

Dataset Information

Revisiting avian 'missing' genes from de novo assembled transcripts.

Publications

Revisiting avian 'missing' genes from de novo assembled transcripts.

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