The Developmental Transcriptome of Bagworm, Metisa Plana (Lepidoptera: Psychidae) and Insights Into Chitin Biosynthesis Genes
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G C A T T A C G G C A T genes Article The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes Nur Lina Rahmat 1, Anis Nadyra Zifruddin 1, Cik Mohd Rizuan Zainal Abidin 2, Nor-Azlan Nor Muhammad 1 and Maizom Hassan 1,* 1 Institute of Systems Biology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600 UKM, Selangor, Malaysia; [email protected] (N.L.R.); [email protected] (A.N.Z.); [email protected] (N.-A.N.M.) 2 Pest Management, FGV R&D Sdn. Bhd., Tun Razak 26400 PPP, Jengka, Pahang, Malaysia; [email protected] * Correspondence: [email protected] Abstract: Bagworm, Metisa plana (Lepidoptera: Psychidae) is a ubiquitous insect pest in the oil palm plantations. M. plana infestation could reduce the oil palm productivity by 40% if it remains untreated over two consecutive years. Despite the urgency to tackle this issue, the genome and transcriptome of M. plana have not yet been fully elucidated. Here, we report a comprehensive transcriptome dataset from four different developmental stages of M. plana, comprising of egg, third instar larva, pupa and female adult. The de novo transcriptome assembly of the raw data had produced a total of 193,686 transcripts, which were then annotated against UniProt, NCBI non-redundant (NR) database, Gene Ontology, Cluster of Orthologous Group, and Kyoto Encyclopedia of Genes and Genomes databases. From this, 46,534 transcripts were annotated and mapped to 146 known metabolic or signalling KEGG pathways. The paper further identified 41 differentially expressed transcripts encoding seven genes in the chitin biosynthesis pathways, and their expressions across each developmental stage were further analysed. The genetic diversity of M. plana was profiled whereby there were Citation: Rahmat, N.L.; Zifruddin, A.N.; Zainal Abidin, C.M.R.; Nor Muham- 21,516 microsatellite sequences and 379,895 SNPs loci found in the transcriptome of M. plana. These mad, N.; Hassan, M. The Develop- datasets add valuable transcriptomic resources for further study of developmental gene expression, mental Transcriptome of Bagworm, transcriptional regulations and functional gene activities involved in the development of M. plana. Metisa plana (Lepidoptera: Psychidae) Identification of regulatory genes in the chitin biosynthesis pathway may also help in developing an and Insights into Chitin Biosynthesis RNAi-mediated pest control management by targeting certain pathways, and functional studies of Genes. Genes 2021, 12, 7. https:// the genes in M. plana. dx.doi.org/doi:10.3390/genes12010007 Keywords: Metisa plana; transcriptome analysis; high throughput sequencing; expression profiling; Received: 18 November 2020 metamorphosis; bagworm; chitin Accepted: 12 December 2020 Published: 23 December 2020 Publisher’s Note: MDPI stays neu- 1. Introduction tral with regard to jurisdictional claims in published maps and institutional Oil palm is currently Malaysia’s most dominant oil crop with 4,186,914 hectares of oil affiliations. palm plantations, occupying up to 71.6% of the agricultural land by 2018 [1]. In 2015, the world market value of oil palm reached USD 65.73 billion, and it is predicted to reach USD 92.84 billion in 2021 [2]. M. plana (Lepidoptera: Psychidae), bagworm is one of the most destructive insect pest defoliators in the oil palm industry, specifically in Southeast Asia. Copyright: © 2020 by the authors. Li- M. plana is a holometabolous insect that completes its development from 80 to 113 days, censee MDPI, Basel, Switzerland. This depending on the climate of the time it grows. M. plana development starts from the article is an open access article distributed laying of eggs (Figure1A) from a mated female, and hatching into neonates, a term used to under the terms and conditions of the describe the newly hatched larva. The neonates will feed on oil palm leaves within 1–2 h of Creative Commons Attribution (CC BY) emergence to construct a small bag at the posterior end of their body. The case will enlarge license (https://creativecommons.org/ progressively with the amount of the plant materials it feeds on and the body size of the licenses/by/4.0/). Genes 2021, 12, 7. https://dx.doi.org/10.3390/genes12010007 https://www.mdpi.com/journal/genes Genes 2020, 11, x FOR PEER REVIEW 2 of 22 Genes 2021, 12, 7 2 of 20 neonates, a term used to describe the newly hatched larva. The neonates will feed on oil palm leaves within 1–2 h of emergence to construct a small bag at the posterior end of their body. The case will enlarge progressively larva.with the Male amount and female of the larva plant will materials take up to it fivefeeds and on seven and instarthe body stages, size respectively, of the before larva. Male and femalemetamorphosing larva will take into uppupa, to five with and the seven third instar larvastages, being respectively, the most activebefore leaf feeder metamorphosing into (Figurepupa, with1B). Thethe third pupa instar in the larv casinga being is mostly the most found active hanging leaf atfeeder the back (Figure of oil 1B). palm leaves The pupa in the casing(Figure is mostly1C). It found has remarkable hanging at differences the back betweenof oil palm the leaves male and (Figure female’s 1C). morphology, It has and remarkable differencessexual between segregation the male of and the female’s pupation morphology, site. The male and will sexual emerge segregation out of the of casing the as a fully pupation site. The maledeveloped will emerge moth out while of the the casing female as stays a fully inside developed the casing moth and resembleswhile the afemale maggot with no stays inside the casinglegs and and resembles wings (Figurea maggo1D)t with [3]. no legs and wings (Figure 1D) [3]. Figure 1.FigureDevelopmental 1. Developmental stages of stagesM. plana of .(M.A plana) Cluster. (A) ofCluster creamy-coloured of creamy-coloured eggs on eggs the left on withthe left its with casing its on the right. (B) Thirdcasing instar on larva. the (right.C) Pupa. (B) (ThirdD) adult instar on thelarva. left (C and) Pupa. male ( adultD) adult on theon the right. left (E and) Leaves male ofadult oil palm on the tree right. upon bagworm outbreak(E on) Leaves an oil palm of oil plantation palm tree inupon FELDA bagworm Besout outbreak 02, Perak, on Malaysia an oil palm (03◦ 46plantation0 N 100◦17 in0 FELDAE). Besout 02, Perak, Malaysia (03°46′ N 100°17′ E). The success of M. plana development and metamorphosis depends on several impor- The success of M.tant plana processes, development including and the regulationmetamorphosis of insect depends growth hormoneson several (ecdysone important and juvenile processes, including thehormone) regulation and of chitin insect biosynthesis, growth hormones modification, (ecdysone degradation, and juvenile and hormone) recycling. and Chitin forms a chitin biosynthesis, modification,significant portion degradation, of the integumentand recycling. layer Chitin of the forms exoskeleton a significant and peritrophicportion of matrix of the integument layer theof the alimentary exoskeleton canals. and Chitinperitrophic is biosynthesised matrix of the from alimentary the precursor, canals. trehalose,Chitin is and with biosynthesised from continuousthe precursor, enzymatic trehalose, reaction and with of eight continuous important enzymatic enzymes toreaction produce of the eight final polymer chain of UDP-N-acetyl-glucosamine collectively called chitin (Supplementary Figure S1). important enzymes to produce the final polymer chain of UDP-N-acetyl-glucosamine collectively During moulting, the chitin contents in the cuticle fluctuate with the simultaneous process called chitin (Supplementary Figure S1). During moulting, the chitin contents in the cuticle fluctuate of chitin biosynthesis and degradation to replace the old cuticle with the new one, espe- with the simultaneous process of chitin biosynthesis and degradation to replace the old cuticle with cially during larval moult and pupation [4]. Chitin is also required for several important the new one, especiallyprocesses during duringlarval moultingmoult and such pupation as in the [4]. attachment Chitin is also of cuticle required to epidermal for several cells and the important processes duringwing disk moulting formation such during as in th larvae attachment to pupa metamorphosis of cuticle to epidermal [5,6]. Chitin cells metabolic and the processes wing disk formation wereduring used larv asa insectto pupa growth metamorphosis regulators (IGRs) [5,6]. Chitin in the developmentmetabolic processes of biorational were pesticides used as insect growthas regulators chitin structure (IGRs) is uniquein the todevelopment arthropods. Sinceof biorational 1981, targeting pesticides chitin foras thechitin development structure is unique to ofarthropods. IGRs has beenSince conducted 1981, targeting [7], and chitin still for largely the development studied by many of IGRs researchers has been in targeting conducted [7], and stilldifferent largely stages studied of insectby many development researchers [8 –in12 targeting]. different stages of insect development [8–12]. The outbreak of M. plana can cause 50% of leaves defoliation and yield loss of up to The outbreak of M.40–47% plana can over cause two 50% consecutive of leaves years defoliation of serious and yield infestation loss of (Figure up to 40-47%1E) [ 13 over]. The current two consecutive yearspest of serious management infestation control (Figure of the 1E) insect [13]. inThe oil current palm plantations