Genome Structure of the American Cockroach

By Kevin E. Noonan --

Perhaps somewhat ironically, a group of Chinese researchers* recently published a report on the genome of the American cockroach (Periplaneta americana), entitled "The genomic and functional landscapes of developmental plasticity in the American cockroach" in Nature Communications.  These researchers,** applying a variety of modern genomic analysis techniques, elucidated aspects of the animal's genomic DNA having implications for its range, behavior, and ecology.

The report details genetic assessment of the P. americana genome, comprising 3.38Gb; this is the second largest genome to locusts (Locusta migratoria) among insect species.  P. americana was introduced into Americas from Africa in 16th century and is related to other cockroach species as well as two termite species.  Using a consensus gene set, the researcher found expansion of genes associated with environmental adaptation, including chemoreception and detoxification.  "Multiple pathways" that regulate metamorphic development well-conserved, and 20-hydroxyecdysone, juvenile hormone, insulin, and decapentaplegic signals are involved in regulating developmental and behavioral plasticity.

The report details the results produced from more than 1 terrabasepairs from 3 individuals, assembled de novo to 295-fold coverage; for comparison, samples from the Australian cockroach (P. australasiae) and the smoky brown cockroach (P. fuliginosa) were sequenced to forty-fold coverage.  About 60% of genomic sequences comprise repetitive elements, but otherwise the genomic DNA composition found for this species is typical for species in Order Blattodea (which comprises more than 4,000 species of cockroaches and more than 3,000 species of termites).  The American cockroach genome comprises 21,336 protein-coding genes, 95% of which were detected to be expressed; 90% of these genes are inherited in common with other species in this Order, with 84% found in related cockroach species and 82% in the dampwood termite.  13,555 of these are genes are termed "multicopy universal" genes.  Median intron length (3 kp) found in the cockroach genes is half the average size in locust genes but larger than in other insect species.  A total of 17.5 Gb transcriptome sequencing data were generated from three independent libraries, with inserts of 1–2 Kb, 2–3 Kb, and 3–6 Kb, for the messenger RNA pool of all stages of cockroach development.

Using this data the researchers compared 12 insect species for "gene repertories" and found 479 orthologs specific for species in Order Blattodea in ~1,000 cockroach genes; the American and German cockroaches (B. germanica) encode largest gene sets, but showed fewer species-specific genes than other insect species.  In more detail analyses, 2,000 single copy universal genes were identified, 538 chosen to establish phylogenetic relationships between the 12 insect species.  Comparisons with other cockroach species showed that P. americana, P. fuliginosa and P. australasiae, shared about 88% amino acid identity between orthologous proteins.  P. americana shares only 75% sequence identity with B. germanica, which was a lesser degree of relatedness than was found between P. americana and two termite species:  Z. nevadensis (which shares 79% sequence identity) and M. natalensis (which shares 80% sequence).  Among 7,640 common orthologs between these species, approximately two-thirds of the American cockroach genes are more closely related to the termite genes in sequence identity, while only one-third being more closely related to the German cockroach.

The genes shared between the American cockroach and termite species were "significantly over-represented in 29 pathways, including a number of classic functional components in insects, such as development, nutrition, and immunity."  In contrast, genes shared between the American cockroach and the German cockroach were "significantly enriched" in only 6 such pathways, two of which are related to signal transduction.

With regard to the genes analyzed to identify those genes important to evolution of the cockroach, the researchers started from the presumption that "[a]daptation to host and environment is mainly mediated by chemical communication and subsequent abilities to tolerate chemical and biological factors, such as toxins or pathogens."  These were genes from families involved in chemoreception, detoxification, and immunity.  For chemoreception genes, a total of 154 olfactory receptor genes (ORs) were found in the P. americana genome, while other Blattodean species were found with only half as many ORs.  The P. Americana genome comprises 522 gustatory receptor genes (GRs), which represents the greatest expansion of GRs in the insect species reported to date.  Interestingly, 329 of these GRs formed a specific clade in the phylogeny and were annotated as potential bitter receptors.  The ionotropic glutamate receptor (IR) gene family also has experienced a substantial expansion in the P. americana genome, in which were found a total of 640 candidate IRs (Fig. 2c), much more than that in the termite genome (148 in Z. nevadensis; Fig. 2a) (see Figure 2).

Other genes arising from this analysis include odorant binding protein (OBP) genes, the number of OBPs in Blattodean species (with the most in P. americana) being dramatically reduced compared to Drosophila and other insects (Fig. 2a), suggesting to these researchers that the transport of odorant molecules may be functionally conserved in cockroaches.

With regard to genes involved with detoxification, 178 cytochrome P450s, 90 carboxyl/choline esterases, 39 glutathione transferases, and 115 ATP-binding cassette transporters were detect in the P. Americana genome.  The P450 genes showed the greatest expansion in the American cockroach, compared with other Blattodean species.  Phylogenetic analysis of P450s across Blattodean species could be collected into four major clans, the CYP2, the CYP3, the CYP4, and the mitochondrial clade (Fig. 2d).  Most P450 genes in P. americana clustered with CYP3 (79/178 genes) and CYP4 (62/178 genes) lineages (Fig. 2d).  The researchers speculated that specific expansion of these P450 genes improved insecticide resistance in the American cockroach, which clearly has implications for improved survival.

Genes involved in immunity comprise "innate" immunity genes in the Imd, Toll, and Janus kinase-signal transducer and activator of transcription (JAK-STAT) gene pathways.  Compared with other insects, many of these genes, particularly in the Toll pathway, were found to have been extensively expanded.  In addition, Gram-negative binding proteins (GNBPs), pattern recognition proteins responsible for the detection of pathogens and activation of the Toll pathway, were found to be expanded, there being 12 GNBP1-like and 2 GNBP3-like genes in the American cockroach genome, which is more than in any of those insect species examined (for example, there are a maximum of 6 GNBPs in Z. nevadensis).  Similarly, Toll protein genes were expanded in American cockroach DNA (14 Toll protein genes) compared, for example, with the Drosophila genome (which encodes 9 Toll protein genes).  Eleven antimicrobial protein (AMP) genes were detected in the P. americana genome, including defensins, termicins, attacin, drosomycin, Pro-rich peptide (Paprp-1), and anti-fungus peptide (AFP).  In functional testing, these researchers found strong antimicrobial activity after injection with Escherichia coli (Gram-negative bacterium), moderate antimicrobial activity with Staphylococcus aureus (Gram-positive bacterium), and weak antimicrobial activity with Candida albicans (fungi), consistent with the cockroach habitat including decaying animal matter and other offal.

What the researchers termed "crucial biosynthesis and signaling pathways for regulating insect development" were "substantially expanded" in the American cockroach genome, including insulin-like peptide and genes involved in juvenile hormone biosynthesis and metabolism, and the cuticle protein family also appeared to be one of the most expanded gene families in P. americana.  These results are consistent with the increased size of the American cockroach, which has the largest size (up to 53 mm in body length, the frequency of molting (6-14 times), and the longest life cycle (700 days).  The researchers also report that signaling pathways thought to be involved in wound healing and tissue repair in insects (Drosophila) and vertebrates, were expanded in certain pathways (including the Grainy head (GRH), Wingless (Wg), and Notch pathways), which may also contribute to the hardiness of these insects.

In addition to the intrinsic interest of these results for understanding insect relatedness, ecology, and behavior, the results reported in this paper elucidate for the first time specific genetic correlates to traits that have permitted the American cockroach to thrive in disadvantageous environments.  To the extent that the common perception of this insect, that it can (and will) outlive the human species and even a nuclear holocaust, has any validity, this capacity relies at least in part on the genetic characteristics set forth in this paper.  There is something to be learned, about evolution, survival, and life on this planet, from these beasts.

*Sheng Li, Shiming Zhu, Qiangqiang Jia, Dongwei Yuan, Chonghua Ren, Kang Li, Suning Liu, Yingying Cui, Haigang Zhao, Yanghui Cao, Gangqi Fang, Daqi Li, Xiaoming Zhao, Jianzhen Zhang, Qiaoyun Yue, Yongliang Fan, Xiaoqiang Yu, Qili Feng & Shuai Zhan

**From Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou; CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai; the University of Chinese Academy of Sciences, Beijing; the Research Institute of Applied Biology, Shanxi University, Taiyuan; Zhongshan Entry-Exit Inspection and Quarantine Bureau Technology Center, Zhongshan; and State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on the Loess Plateau of Ministry of Agriculture, Northwest A&F University, Yangling

Comments

[Paul Cole]

I think this is a wonderful topic.

Under 35 USC 103, we can dispense with Graham/KSR. The key question now is:

Would the claimed subject matter have been obvious to a thoughtful American cockroach?

Adjudication of inventive step in future years can be expected to be greatly simplified. And the thoughtful cockroach is a character that can be invoked in many aspects of patent law, and possibly more general law.

[Kevin E Noonan]

For the squeamish, we did consider posting this cartoon (http://thumb101.shutterstock.com/display_pic_with_logo/1058333/203755297/stock-vector-vector-illustration-of-cartoon-cockroach-203755297.jpg) rather than the actual picture (but with a link to the actual picture from the paper now shown with the post). But scientific accuracy won the day; apologies to anyone who would rather not see this image with their morning coffee.

[Kevin E Noonan]

Don't diss the roach, Paul!