Genome 3 T A Brown Pdf.zip

Genome 3 T A Brown Pdf.zip

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Genome 3 T A Brown Pdf.zip

secretory pathway genes. genes involved in protein transport from the endoplasmic reticulum to the golgi and plasma membrane in the insect endomembrane system, including all known component proteins, were identified in the h. halys draft genome using the domp () pipeline (see methods). here, we chose representatives of all proteins of the endoplasmic reticulum, endosome, golgi apparatus, and plasma membrane as targets for screening the h. halys genome. in detail, the domp pipeline (methods) annotates proteins by the uniprot and pfam databases. the proteins secreted by the endoplasmic reticulum to golgi apparatus secretory pathway (er-golgi) are processed and sorted by the golgi apparatus and transferred to the plasma membrane by vesicular carriers.

the sequencing and assembly of the h. halys genome has provided access to a set of gene models that enables a range of analyses, including protein family, pathway, gene ontology, and motif discovery. for example, the putative insect cuticle protein family is dominated by arthropod-specific members, while the h. halys‘ homologs are missing the chitinase catalytic domain (exemplified in fig. s4 of sparks et al. (2017) [ 145 ]). from a functional perspective, the long list of potentially venomous proteins (fig. 8) may be of particular interest to those who study heteroptera; however, care must be taken to differentiate between toxic and non-toxic members of this toxin gene family, as this subset of proteins does not constitute a universal toxin gene family in the insect order [ 146 ].

sequencing of the h. halys genome has also allowed us to characterize the gene family and pathway structure of the honey bee, a. mellifera, and compare it to that of h. halys. as would be expected from the highly plesiomorphic organization of the honey bee genome [ 147 ], this includes many of the same protein families we observed in the previous two pentatomid genome drafts, including some copies of candidate venom proteins and various cuticular proteins. the gene set of the honey bee genome is more than twice the size of h. halys, and roughly half the size of the n. viridula genome [ 148, 149 ]; however, there are fewer predicted proteins associated with immunity and signal transduction and more with metabolism. the a. mellifera genome is also more fragmented (compared to n. viridula), which results in more numerous pseudogenes and introns. it is also more heterozygous, with a higher degree of duplication across the genome [ 150 ].

comparative analysis of the a. mellifera and h. halys genomes with n. viridula, the latter two of which are also closely related (see fig. 5 ), has shown them to be more highly conserved than the genomes of the honey bee and migratory locust, p. migratultum [ 148, 149 ] (fig. 5 ). the honey bee is much more highly conserved than n. viridula, which is the result of the relatively more fragmented a. mellifera genome; only n. viridula is more highly conserved than a. mellifera. the honey bee genome is more heterozygous and more fragmented than n. viridula, and the latter two have more immune-related genes.
among the three genomes, we identified a core set of 315 proteins that are orthologous to other insect genomes, representing the core set of proteins for the insecta. of the remaining proteins, we identified another 16,725 proteins from the h. halys assembly that were unique to this species. these represent an additional set of genes or gene families that are specifically present in the h. halys genome and are therefore expected to play some role in the biology and ecology of this species.
using the h. halys genome, we predicted and analyzed the complete complement of coding sequences, splice sites and non-coding rnas. a combined set of 1,054 structural and non-coding rnas were identified, including 90 long non-coding rnas (lncrna), 1,120 micrornas, and 809 small nucleolar rnas. of the non-coding rnas, 26 were annotated as putative microrna precursors and one putative snorna precursor. in addition, we identified five trnas, seven 5s rrnas, two 5.8s rrnas, one 7s rrna and one 18s rrna. using the lncrnas as a benchmark, we showed that prediction of lncrnas in h. halys was among the most sensitive and accurate. our results suggest that this genome represents a rich resource of developmental and regulatory rnas for further analysis.
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