Discussion - Aspergillus屬中的水平基因轉移及基因體中的GC變化

Stigmatella aurantiaca belongs to Myxobacterium. Myxobacterium existing biphasic cell cycle, the cells migrate to aggregate center and form fruiting body when nutrients depletion [20]. On the other hand, the transferred gene is most similar to glucuronan lyase A, which is responsible for catalyzation of eliminative cleavage of (1->4)-beta-D-glucuronans, which is from extracellular matrix. When cell migration, the extracellular matrix have to degrade and reconstruct [21]. It is possible the gene transferred between Stigmatella aurantiaca and fungi because Stigmatella aurantiaca and fungi both contain fruiting body phase and become active when cell migration.

Horizontal gene transfer events can be explored by different methods, but HGT can’t be sure by one method. Amounts of genome BLAST data through automatic filtration, there are still many genes to be examined. Combining sequences similarity and phylogenetic incongruence, I get seven candidate genes of HGT. Although the phylogenies of the candidates gene seems like HGT events, there are some problems would affect the accuracy of HGT. Not like bacterial genome, fewer fungal genomes are sequenced. Besides, the phylogenetic trees of HGT are hard to verify. For example, a phylogenetic tree that shows a bacteria gene or a clade out of a fungal clade looks like a HGT event. From the phylogenetic tree, the closest gene to the bacterial gene is unknown and if there are more sequences not sequenced yet is unsure. The sequenced

genome data is not complete, so there are many leakages in the true phylogeny.

Sometimes, losing part of the true phylogeny lead to a HGT-like phylogenetic tree;

even though, I exam the protein and nucleotide sequences’ similarities and distance to all database. There should be different data to support the HGT hypothesis.

Table 1 The candidate genes through automatic filtration.

The bold labeled genes are the candidate genes after first step of phylogenetic analysis.

No. Candidate Gene Gene Product

1 Afu1g00250 serine-rich protein

2 Afu1g01170 conserved hypothetical protein 3 Afu1g01300 GPI anchored protein

4 Afu1g01320 endo-polygalacturonase 5 Afu1g01370 glutathione S-transferase 6 Afu1g07190 ankyrin repeat protein

7 Afu2g00600 conserved hypothetical protein 8 Afu2g01190 Cu-dependent DNA-binding protein 9 Afu2g01380 GNAT family N-acetyltransferase 10 Afu2g01960 UbiA prenyltransferase family protein 11 Afu2g09580 UDP-N-acetylmuramate dehydrogenase

12 Afu2g09590 UDP-N-acetylglucosamine 1-carboxyvinyltransferase family protein 13 Afu2g11610 alpha-glucosidase/alpha-amylase

14 Afu2g11620 alpha-glucosidase

15 Afu2g12730 hypothetical protein AFUA_2G12730 16 Afu3g00790 methylaspartate ammonia-lyase 17 Afu3g00820 putative exported protein 18 Afu3g00950 ankyrin repeat protein

19 Afu3g01320 homocysteine S-methyltransferase 20 Afu3g02420 ThiJ/PfpI family transcriptional regulator 21 Afu3g02800 lipase/esterase

22 Afu3g07400 conserved hypothetical protein 23 Afu4g01400 ThiJ/PfpI family protein

24 Afu4g13950 GNAT family acetyltransferase 25 Afu4g14420 secreted glycosyl hydrolase 26 Afu5g07460 conserved hypothetical protein 27 Afu5g10930 conserved hypothetical protein 28 Afu5g14090 cell-associated beta-galactosidase 29 Afu6g00490 DUF521 domain protein

30 Afu6g00740 conserved hypothetical protein 31 Afu6g08280 ankyrin repeat protein

32 Afu6g08770 ankyrin repeat protein

33 Afu6g09340 hypothetical protein AFUA_6G09340 34 Afu6g09360 proline-glycine rich protein

35 Afu6g10170 spherulin 4 family protein 36 Afu6g10750 conserved hypothetical protein 37 Afu6g12030 rhamnosidase

38 Afu6g12170 FKBP-type peptidyl-prolyl isomerase 39 Afu7g00690 aminotransferase

40 Afu7g00830 alpha/beta hydrolase

41 Afu7g05060 MgtC/SapB family membrane protein 42 Afu7g06990 GDP-D-mannose dehydratase

43 Afu8g00630 conserved hypothetical protein 44 Afu8g01050 lipase/esterase

45 Afu8g01700 haloalkane dehalogenase family protein 46 Afu8g05880 chaperonin (GroES/Cpn10)

47 Afu8g06480 rhamnogalacturonan acetylesterase superfamily protein 48 Afu8g06820 dihydrofolate reductase family protein

49 Afu8g07170 conserved hypothetical protein 50 Afu1g13790 Histone H3

51 Afu2g17750 ankyrin 2,3/unc44

52 Afu5g01180 RAN small monomeric GTPase (Ran) 53 Afu5g01300 integral membrane protein

54 Afu5g09030 similar to ankyrin 2,3/unc44

55 Afu8g00260 f-box domain and ankyrin repeat protein 56 Afu8g02140 ankyrin repeat protein

57 Afu8g06990 ankyrin repeat protein

Figure 1 The phylogenetic tree of AFUA_5G10930.

The gene STIAU_2222 and STAUR_2131 are genes of Bacteria but they distribute in a fungi phylogeny. This phylogeny shows that the genes of Stigmatella aurantiaca transferred from fungi. The two genes are the same gene but different annotation by different sequencing release data. The expression of the node is

“taxonomy|species|accession no.|protein product.” FA is fungi and ascomycete; B is Bacteria.

FA|A. oryzae|XP 001823345.1|glucuronan lyase A

FA|N. haematococca|XP 003041896.1|hypothetical protein NECHADRAFT 52969 FA|M. anisopliae|EFY98252.1|glucuronan lyase A

FA|H. jecorina|BAG80639.1|glucuronan lyase A

FA|C. globosum|XP 001226268.1|hypothetical protein CHGG 08341 FA|M. oryzae|XP 363838.1|hypothetical protein MGG 01764 100

Figure 2 The GC content of the neighbor genes of the HGT gene and Stigmatella aurantiaca genome.

Almost all of the GC content of neighbor genes are higher than Stigmatella aurantiaca genome or close to 67% except STAUR_2129 and STAUR_2131.

The STAUR_2131 is the HGT gene that has lower GC content.

Figure 3 The GC content of HGT gene compare with the foreign gene and genome.

Compare HGT genes STAUR_2131 and STIAU_2222 with the neighbor genes of Stigmatella aurantiaca genome and orthologs of Aspergillus clavatus, Neosartorya fischeri, and Aspergillus fumigatus. The GC level of HGT genes are more close to the orthologs of fungi.

Figure 4 The GC content of amino acid code 1,2 and code 3(wobble site)

There show the ribosomal proteins’ GC content of position 1, 2 and position 3 of amino acid code. The genes with star marks represent HGT orthologs. The left and right genes to the star marked gene are the genes before and behind the gene of HGT orthologs. Aor stands for Aspergillus oryzae, Afl stands for Aspergillus flavus, Tst stands for Talaromyces stipitatus, Pma stands for Penicillium marneffei, Sau stands for Stigmatella aurantiaca, Acl stands for Aspergillus clavatus, Nfi stands for Neosartorya fischeri, Afu stands for Aspergillus fumigatus, and Ncr stands for Neurospora crassa.

Node A Node B

Figure 5 The synonymous and nonsynonymous distance distribution.

The figure shows the distribution of the synonymous and non-synonymous distances between HGT orthologous gene. The distances between orthologs and STAUR_2131 are marked by red points and are labeled the species.

Figure 6 Scan the GC content of the transferred sequence region

The GC content scanning along Stigmatella aurantiaca genome near the HGT gene from gene STAUR_2129 to gene STAUR_2134. The blue line shows the GC content of whole nucleotides along sequences and the red line shows the GC content of wobble site in protein coding region. The GC contents of wobble site in protein coding regions are higher that the GC content of average sequence.

Figure 7 The GC content of intergenic region.

The GC content of the intergenic region between STAUR_2132 and STAUR_2133 are displayed by 3 site groups compared to the total GC content of the HGT region of Stigmatella aurantiaca.

Figure 8 The comparison of Pro codon usage bias.

The Pro codon bias usages are compared with ribosomal protein and genome codon usage in the second and third column. The first, second, and third rows are the HGT orthologous genes or ribosomal protein and genome codon bias in Stigmatella aurantiaca, Aspergillus clavatus, and Aspergillus fumigatus.

Figure 9 The comparison of Phe codon usage bias.

The Phe codon bias usages are compared with ribosomal protein and genome codon usage in the second and third column. The first, second, and third rows are the HGT orthologous genes or ribosomal protein and genome codon bias in Stigmatella aurantiaca, Aspergillus clavatus, and Aspergillus fumigatus.

Figure 10 The comparison of Leu codon usage bias.

The Leu codon bias usages are compared with ribosomal protein and genome codon usage in the second and third column. The first, second, and third rows are the HGT orthologous genes or ribosomal protein and genome codon bias in Stigmatella aurantiaca, Aspergillus clavatus, and Aspergillus fumigatus.

Figure 11 The comparison of Ile codon usage bias.

The Ile codon bias usages are compared with ribosomal protein and genome codon usage in the second and third column. The first, second, and third rows are the HGT orthologous genes or ribosomal protein and genome codon bias in Stigmatella aurantiaca, Aspergillus clavatus, and Aspergillus fumigatus.

Figure 12 The comparison of Ser codon usage bias.

The Ser codon bias usages are compared with ribosomal protein and genome codon usage in the second and third column. The first, second, and third rows are the HGT orthologous genes or ribosomal protein and genome codon bias in Stigmatella aurantiaca, Aspergillus clavatus, and Aspergillus fumigatus.

Figure 13 The comparison of Val codon usage bias.

The Val codon bias usages are compared with ribosomal protein and genome codon usage in the second and third column. The first, second, and third rows are the HGT orthologous genes or ribosomal protein and genome codon bias in Stigmatella aurantiaca, Aspergillus clavatus, and Aspergillus fumigatus.

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21. Reing, J.E., et al., Degradation products of extracellular matrix affect cell migration and proliferation. Tissue Eng Part A, 2009. 15(3): p. 605‐14.

在文檔中 Aspergillus屬中的水平基因轉移及基因體中的GC變化 (頁 22-40)