A research on different articles on the genomes of the giant panda

Once distributed across southern China and Southeast Asia, and historically covering a vast territory, the surviving pandas today belong to several divergent genetic populations located only in Shaanxi province or Gansu and Sichuan provinces, respectively.

A research on different articles on the genomes of the giant panda

Convergent pseudogenization of umami receptor gene TAS1R1 between the giant and red pandas, as opposed to the polar bear, ferret, dog, and tiger. The giant panda has one 2-bp insertion on the third exon and two deletions 6-bp and 4-bp on the sixth exon, and the red panda has one 1-bp deletion on the sixth exon.

Convergent evolution has long interested evolutionary biologists. Although the functional nature of these convergent specializations is often obvious, the genetic basis underpinning particular examples of convergent evolution is far less clear. Charles Darwin suggested that convergent evolution stems from similarity in independent changes that underpin the same features in different organisms To survive in a novel environment, animals can drastically change their diet, such as from carnivory to omnivory, to herbivory, or even become dietary specialists 40all of which have profound impacts on species ecology, behavior, physiology, and even morphology and genetics.

The giant panda and red panda are obligate bamboo-feeders that evolved from meat-eating ancestors and are remarkable examples of dietary shift and specialization 41representing an ideal model to study convergent evolution in these traits.

In the present study, comparative genomics has revealed the signatures of adaptive protein convergence associated with digestive physiology and limb development, taking the first step toward confirming D. Furthermore, we have identified convergent pseudogenization related to dietary shift from the perspective of selective relaxation of functional constraints on protein-coding genes.

Our findings provide rich insights into genetic convergence mechanisms underlying phenotypic convergence and adaptation to a specialized bamboo diet in both pandas. These findings demonstrate that genetic convergence occurred at multiple levels spanning metabolic pathways, amino acid convergence, and pseudogenization, providing a fascinating example for genome-scale convergent evolution analysis of dietary shift and specialization.

Materials and Methods Additional detailed information is provided in SI Appendix, SI Materials and Methodsincluding the genome and transcriptome sequencing, de novo genome assembly, genome assembly assessment, and genome annotation. Animal care and experiments were conducted according to the guidelines established by the Regulations for the Administration of Affairs Concerning Experimental Animals Ministry of Science and Technology, China, and were approved by the Committee for Animal Experiments of the Institute of Zoology, Chinese Academy of Sciences, China.

Phylogenomic Tree and Divergence Time Estimation. Protein sequences for each single-copy gene family were concatenated and aligned by MUSCLE 42and poorly aligned sites were trimmed by trimAl Then protein sequence alignment was transformed back to coding DNA sequence alignment.

Considering the potential impacts of convergent amino acid substitutions and the large GC-content variance in the third codon position of exons 4445we removed the genes with convergent amino acid substitutions and excluded the third codon position of exons before constructing the phylogenomic tree.

Additionally, we considered the partition of the first and second codon positions and separately determined their best-fitting nucleotide substitution models. The nucleotide substitution model was determined by ModelGenerator 46 and selected by Bayesian information criterion.

This article contains content that is written like an advertisement. Please help improve it by removing promotional content and inappropriate external links, and by adding encyclopedic content written from a neutral point of view. (March ) (Learn how and when to remove this template message). A K-mer graph is a form of de Bruijn graph. Its nodes represent all the fixed-length subsequences drawn from a larger sequence. Its edges represent all the fixed-length overlaps between subsequences that were consecutive in the larger sequence. This article contains content that is written like an advertisement. Please help improve it by removing promotional content and inappropriate external links, and by adding encyclopedic content written from a neutral point of view. (March ) (Learn how and when to remove this template message).

The posterior probability for each branch of the phylogenetic tree was determined from the remaining samples. To estimate divergence times between species, we performed strict molecular clock test in baseml program of PAML 4.

After removing the genes that significantly deviated from molecular clock model and excluding the third codon positions of exons, the mcmctree program of PAML 4. The draft nature of the genome made detailed comparisons of protein-coding genes inefficient because gene annotation was frequently incomplete because of gaps or missing exons.

To gain a better resolution for gene-level analysis, we took advantage of the prealigned vertebrate genomes in the University of California, Santa Cruz genome browser [ hgdownload. Exons with Ns or internal stop codons were excluded, and intact exons of the same gene were concatenated for positive selection and genomic convergence analyses.

Identification of Positively Selected Genes. Based on the MAF alignment sequences from six Carnivora species red panda, giant panda, polar bear, ferret, dog, and tigerpositive selections in the red panda and giant panda were tested under the reconstructed phylogenomic tree Fig.

To find positively selected genes related to the pseudothumb development and bamboo nutrient utilization, positive selections were analyzed through six different datasets by using the giant panda, red panda, or both pandas as foreground branches SI Appendix, Table S Then the positively selected genes were combined together for further analysis.

Because gene tree discordance resulting from incomplete lineage sorting or hybridization may affect the identification of positive selection signatures 24we constructed a gene tree for each positively selected gene by using MrBayes 3. We removed those genes whose positive selection signature was lost under the gene tree.

Finally, the functional enrichment of these positively selected genes in GO terms and KEGG pathways was tested by using the GeneTrail2 method 55with the 14, orthologous genes as the reference gene set. In this study, ancestral protein sequences were reconstructed for 14, orthologs among eight Eutherian species Fig.

We identified convergent amino acid sites between giant and red pandas with the following rules: To filter out noise resulting from chance amino acid substitutions 620we then performed a Poisson test to verify whether the observed number of convergent sites of each gene was significantly more than the expected number caused by random substitution under the JTT-fgene and JTT-fsite amino acid substitution models, respectively, by following the method of ref.In this study, they sequence the complete mtDNA of a ~22,year-old giant panda specimen.

A research on different articles on the genomes of the giant panda

This giant panda was found by Professor ZHANG Yingqi at IVPP and the caving team (Beijing Caver) in August at the Cizhutuo Cave located in the Leye County of Guangxi Province in China (Figure ).

The giant panda (Ailuropoda melanoleuca, literally "black and white cat-foot"; Chinese: 大熊猫; pinyin: dà xióng māo, literally "big bear cat"), also known as panda bear or simply panda, is a bear native to south central China.

It is easily recognized by the large, distinctive black patches around its eyes, over the ears, and across its round body. This article contains content that is written like an advertisement. Please help improve it by removing promotional content and inappropriate external links, and by adding encyclopedic content written from a neutral point of view.

A research on different articles on the genomes of the giant panda

(March ) (Learn how and when to remove this template message). A K-mer graph is a form of de Bruijn graph. Its nodes represent all the fixed-length subsequences drawn from a larger sequence.

Its edges represent all the fixed-length overlaps between subsequences that were consecutive in the larger sequence.

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The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to different families in the order Carnivora, but both have evolved a specialized bamboo diet and adaptive pseudothumb, representing a classic model of convergent evolution.

Abstract. In the last two decades, the widespread application of genetic and genomic approaches has revealed a bacterial world astonishing in its ubiquity and diversity.

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