Morphometrics and Mitochondrial DNA Genes Analysis Suggest a New Species of Penaeus (Crustacea: Penaeidae) from the Persian Gulf.

There are two morphotypes of Penaeus semisulcatus described hitherto in the Persian Gulf, namely the banded and non-banded antennae morphotypes. In this study, we used morphometric measurements and two mitochondrial genes (16S rRNA and cytochrome oxidase subunit I-COI) to assess relationships between the two morphotypes of P. semisulcatus. Out of 25 morphological characters examined, 10 characters were found significantly different between the two morphotypes when tested against separate sexes or both sexes combined. Results from the 16S rRNA and COI sequence analysis of two morphotypes of P. semisulcatus morphotype showed up to 6% and 17% sequence divergence, respectively. The 16S rDNA and COI sequences of the non-banding morphotype were not only very different to those of the banding morphotype but was also very different to all other Penaeus species (i.e., P. monodon, P. merguiensis, and P. indicus) included in the study. Both parsimony and Neighbor-Joining trees based on 16S rDNA and COI sequences provide similar tree topology that clearly separated the two morphotypes into two distinct groups. Based on these findings, we propose the two morphotypes of P. semisulcatus to be relegated as two sympatric species.

Construction of Pará rubber tree genome and multi-transcriptome database accelerates rubber researches.

BACKGROUND: Natural rubber is an economically important material. Currently the Pará rubber tree, Hevea brasiliensis is the main commercial source. Little is known about rubber biosynthesis at the molecular level. Next-generation sequencing (NGS) technologies brought draft genomes of three rubber cultivars and a variety of RNA sequencing (RNA-seq) data. However, no current genome or transcriptome databases (DB) are organized by gene. RESULTS: A gene-oriented database is a valuable support for rubber research. Based on our original draft genome sequence of H. brasiliensis RRIM600, we constructed a rubber tree genome and transcriptome DB. Our DB provides genome information including gene functional annotations and multi-transcriptome data of RNA-seq, full-length cDNAs including PacBio Isoform sequencing (Iso-Seq), ESTs and genome wide transcription start sites (TSSs) derived from CAGE technology. Using our original and publically available RNA-seq data, we calculated co-expressed genes for identifying functionally related gene sets and/or genes regulated by the same transcription factor (TF). Users can access multi-transcriptome data through both a gene-oriented web page and a genome browser. For the gene searching system, we provide keyword search, sequence homology search and gene expression search; users can also select their expression threshold easily. CONCLUSION: The rubber genome and transcriptome DB provides rubber tree genome sequence and multi-transcriptomics data. This DB is useful for comprehensive understanding of the rubber transcriptome. This will assist both industrial and academic researchers for rubber and economically important close relatives such as R. communis, M. esculenta and J. curcas. The Rubber Transcriptome DB release 2017.03 is accessible at http://matsui-lab.riken.jp/rubber/ .

Complete chloroplast genome of a montane plant Spathoglottis aurea Lindl.: Comparative analyses and phylogenetic relationships among members of tribe collabieae.

The yellow-flowered Spathoglottis aurea (tribe Collabieae; family Orchidaceae) is native to the mountainous areas of Peninsular Malaysia. The species is well known as an ornamental plant and for its role in artificial hybrid breeding. There is an interesting evolutionary relationship between S. aurea and the geographically isolated S. microchilina from Borneo that has encouraged further study of the S. aurea populations, but the genomic resource for S. aurea has not yet been reported. The present study reports the first work to characterize a chloroplast (cp) genome among the Spathoglottis genus. The complete cp genome of S. aurea was assembled from a sequence generated by the Illumina platform and analysed in comparison with other Collabieae species available in the GenBank database. The cp genome of S. aurea is 157,957 base pairs (bp) in length with guanine-cytosine (GC) content of 37.3%. The genome possessed a typical quadripartite cp genome structure with large single-copy (LSC) (86,888 bp), small single-copy (SSC) (18,125 bp) and inverted repeat (IR) (26,472 bp) sequences. A total of 134 genes were annotated, with 88 protein coding genes (PCGs), 38 transfer RNA (tRNA) genes and eight ribosomal RNA (rRNA) genes. Overall, 80 simple sequence repeats (SSR) or microsatellites were identified. Comparative analysis with other Collabieae species revealed high conservation in the cp genome arrangements with minimal difference in genome lengths. However, several mutational hotspots were also detected, with high potential to be developed as genetic markers for phylogenetic analysis. Characterization of the S. aurea cp genome revealed its conserved nature without gene loss or rearrangements when compared to other species of the Collabieae tribe. Phylogenetic analysis of Collabieae species also revealed that S. aurea has a distant evolutionary relationship to other members of the Collabieae species, despite the presence of problematic genera such as Phaius and Cephalantheropsis.

The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq.

Background: The chloroplast genome has the potential to be genetically engineered to enhance the agronomic value of major crops. As a crop plant with major economic value, it is important to understand every aspect of the genetic inheritance pattern among Elaeis guineensis individuals to ensure the traceability of agronomic traits. Methods: Two parental E. guineensis individuals and 23 of their F1 progenies were collected and sequenced using the next-generation sequencing (NGS) technique on the Illumina platform. Chloroplast genomes were assembled de novo from the cleaned raw reads and aligned to check for variations. The sequences were compared and analyzed with programming language scripting and relevant bioinformatic softwares. Simple sequence repeat (SSR) loci were determined from the chloroplast genome. Results: The chloroplast genome assembly resulted in 156,983 bp, 156,988 bp, 156,982 bp, and 156,984 bp. The gene content and arrangements were consistent with the reference genome published in the GenBank database. Seventy-eight SSRs were detected in the chloroplast genome, with most located in the intergenic spacer region.The chloroplast genomes of 17 F1 progenies were exact copies of the maternal parent, while six individuals showed a single variation in the sequence. Despite the significant variation displayed by the male parent, all the nucleotide variations were synonymous. This study show highly conserve gene content and sequence in Elaeis guineensis chloroplast genomes. Maternal inheritance of chloroplast genome among F1 progenies are robust with a low possibility of mutations over generations. The findings in this study can enlighten inheritance pattern of Elaeis guineensis chloroplast genome especially among crops' scientists who consider using chloroplast genome for agronomic trait modifications.

Mutagenic and antimutagenic assessment of methanol leaf extract of Myristica fragrans (Houtt.) using in vitro and in vivo genetic assays.

The role of diets in causing cancers necessitates the ongoing search for natural antimutagens of promising anticancer therapeutics. This study determined the potential anticancer efficacy of the leaf extract of Myristica fragrans (Houtt.). Methanol leaf extract of M. fragrans (Houtt.) alone was screened for mutagenicity in the bacterial reverse mutation (Ames) test, using the Salmonella typhimurium TA100 strain, the Allium cepa, and the mouse in vivo bone marrow micronucleus tests. The antimutagenicity of this extract against benzo[a]pyrene- and cyclophosphamide-induced mutations was evaluated. An antioxidant test on the extract was performed with 2,2-diphenyl-1-picrylhydrazyl, using butylated hydroxyanisole (BHA) and butylated hydroxytoluene (BHT) as the standards, whereas its phytochemicals were elucidated by following the gas chromatography/mass spectrometry protocol. In S. typhimurium (TA100), the mutagenicity ratio at 200,500 and 1,000 µg/well was >2. Cell division in the A. cepa root tips and mouse bone marrow was significantly (P ≤ 0.05) inhibited at 2,000 and 4,000 mg/kg, whereas the observed chromosomal aberrations and micronucleated polychromatic erythrocytes were non-dose-related and were insignificantly (P ≥ 0.05) different from the negative control. Inhibition of benzo[a]pyrene- and cyclophosphamide-induced mutagenicity by this extract was above 40%. Half-maximal inhibitory concentration of the extract in the antioxidant test was lower than that of BHA and BHT. Phytochemical compounds, possessing antioxidant activity, may be responsible for the observed effects, suggesting a strong antimutagenic activity of the MeOH leaf extract of M. fragrans, a necessary characteristic of a promising anticancer agent.

Transcriptome data for Hevea brasiliensis associated with powdery Mildew infection.

The Hevea brasiliensis or rubber tree belongs to the Euphorbiaceae family and is the only economically viable natural rubber source worldwide. The development of enhanced rubber tree clones with agronomically important traits is critical due to the growing demand for natural rubber around the world. Throughout the years, numerous disease-causing pathogens of H. brasiliensis have been identified and studied. One of the more prominent diseases affecting H. brasiliensis is powdery mildew caused by Oidium heveae. Oidium heveae primarily infects the newly formed leaves and buds of H. brasiliensis. Severe Oidium heveae infections cause extensive defoliation and yield loss. We performed RNA sequencing (RNA-Seq) for healthy and O. heveae-infected leaf tissues from RRIM 2025 and RRIM 929 rubber tree clones using the Illumina HiSeq 2000 platform. RNA-Seq generated 92007684 (12.9 GB) and 96070286 (13.5 GB) paired raw reads for healthy H. brasiliensis clones RRIM 2025 and RRIM 929 respectively. Similarly, RNA-Seq generated 93747858 (13.2 GB) and 93324564 (13.1 GB) paired raw reads for disease-infected H. brasiliensis clones RRIM 2025 and RRIM 929 respectively. The raw data were deposited in the NCBI under bio-project accession number PRJNA723431. The raw reads were quality trimmed and the reference-based transcriptome assembly was generated using the H. brasiliensis genome (ASM165405v1). The data were used to identify between the significantly differentially expressed genes of the healthy and diseased samples.

Complete chloroplast genome data for Cryptocoryne elliptica (Araceae) from Peninsular Malaysia.

The aquatic plant genus Cryptocoryne, a popular plant genus in the aquarium industry, is made up of more than 50 described species and some 15 naturally occurring named and unnamed interspecific hybrids. Cryptocoryne elliptica has a restricted distribution in the north part of Peninsular Malaysia. Destruction of its natural habitats for various human activities has led to a decline in numbers. Here, we report the complete chloroplast genome of C. elliptica and establish a molecular dataset for a maternally inherited genome. Here, we utilized an Illumina NovaSeq 6000 protocol to sequence the partial genome of C. elliptica and used bioinformatic tools to reconstruct the chloroplast genome in de novo mode. The assembled chloroplast genome is a circular DNA molecule 159,968 bp in length. The chloroplast genome has a quadripartite structure composed of a large single-copy region of 96,273 bp and a small single-copy (SSC) region of 15,205 bp, separated by a pair of inverted repeats (IRa and IRb), each of which is 24,245 bp. The chloroplast genome of C. elliptica encodes a total of 108 genes, comprising 74 protein-coding genes, 30 tRNA genes and 4 rRNA genes. In total, 204 SSR loci were identified, most of which were located within intergenic regions.

Prevalence of a koinobiont endoparasitoid Misotermes mindeni (Diptera: Phoridae) in colonies of the fungus-growing termite Macrotermes gilvus (Blattodea: Termitidae) in Malaysia.

A survey of the infestation rate of colonies of Macrotermes gilvus (Hagen) (Termitidae: Macrotermitinae) with the koinobiont endoparasitoid Misotermes mindeni Disney & Neoh (Diptera: Phoridae) was conducted in Malaysia from September 2009 to January 2011 in the states of Kedah, Penang, Perak, Selangor, Kuala Lumpur, Johor, Terengganu, and Sarawak. Of the 1,125 M. gilvus mounds surveyed, 12.4% contained termites parasitized by M. mindeni and these mounds occurred only in the states of Penang and Perak. High frequencies of mounds containing parasitized termites were found at sites in Penang: Bayan Lepas (21.1%), Minden Campus of Universiti Sains Malaysia ([USM]; 24.5%), Teluk Bahang (28.0%), and Bukit Mertajam (35.0%); the lowest frequency (4.0%) was recorded from Gelugor. The parasitized colonies at all sites were classified as healthy, with exception of several from the Minden Campus of USM (96.4% healthy) and Ayer Itam (87.5% healthy). Most parasitized colonies (71.2%) had a low level of M. mindeni infestation. Only 16.7 and 12.1% of the infested colonies had moderate or high parasite infestation levels, respectively. The height of infected mounds was significantly higher than that of the healthy mounds, but there was no difference between the mound diameters of infested and uninfested mounds. Parasite infestation level was not significantly correlated with mound height or mound diameter. The ambient light intensity at sites with infested mounds was significantly lower than that of uninfested mounds. There was also a significant negative relationship between light intensity and degree of parasitism.

Molecular evidence of the hybrid origin of Cryptocoryne ×purpurea Ridl. nothovar. purpurea (Araceae).

Natural hybridization has been considered a source of taxonomic complexity in Cryptocoryne. A combined study of DNA sequencing data from the internal transcribed spacer (ITS) of nuclear ribosomal DNA and the trnK-matK region of chloroplast DNA was used to identify the parents of Cryptocoryne putative hybrids from Peninsular Malaysia. Based on the intermediate morphology and sympatric distribution area, the plants were tentatively identified as the hybrid Cryptocoryne ×purpurea nothovar. purpurea. The plants were pollen sterile and had long been considered as hybrids, supposedly between two related and co-existing species, C. cordata var. cordata and C. griffithii. The status of C. ×purpurea nothovar. purpurea was independently confirmed by the presence of an additive ITS sequence pattern from these two parental species in hybrid individuals. An analysis of the chloroplast trnK-matK sequences showed that the hybridization is bidirectional with the putative hybrids sharing identical sequences from C. cordata var. cordata and C. griffithii, indicating that both putative parental species had been the maternal parent in different accessions.

Mitochondrial Markers Identify a Genetic Boundary of the Green Tiger Prawn (Penaeus semisulcatus) in the Indo-Pacific Ocean.

A population genetics study of the commercially important Green Tiger Prawn (Penaeus semisulcatus) was conducted in the Indo-Pacific Ocean with a focus on the Indo-Malay Archipelago waters of the South China Sea (SCS), Sulu Sea (SLS), Celebes Sea (CLS) and the Strait of Malacca (SOM), the latter being the main waterway that connects the Indian Ocean with the Pacific Ocean. A 548-base-pair region of mitochondrial COI and 571 base pairs of the control region (CR) were analysed in 284 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI ranged from 0.1% to 7.2% and CR 2.3% to 21.7%, with Bagan Pasir (BGP) in central SOM being the most genetically different from other populations (COI: 3.3-4.2%; CR: 7.1-16.5%). All populations were differentiated into two lineages with a genetic break in the vicinity of BGP; Lineage I comprised populations south of this site (SCS, SLS, CLS and part of SOM) and Lineage II comprised populations north of BGP (part of the SOM). Specifically, most individuals of Bagan Pasir (BGP) and another site just south of it, Batu Pahat (BPT), clustered in Lineage I, while all SOM populations to the north of these sites clustered in Lineage II. The BGP population is believed to be a mixed gene pool between the two lineages. The results could be attributed to the fluctuations of Pleistocene sea levels and a possible influence of the One Fathom Bank in SOM. High genetic diversity was recorded, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). Demographic statistics revealed that both lineages underwent a sudden expansion and consequent stabilisation in genetic variability. The findings of this study have wide implications for fisheries in the Indo-Pacific. The increased sampling effort within a narrower geographical scale by the current study permitted a precise locality of the genetic break for this species within the Indo-Pacific Ocean to be identified. The substantial genetic diversity within both lineages should be considered in fishery management and aquaculture development programs of this species in this region.

Cloning and characterization of poly(3-hydroxybutyrate) biosynthesis genes from Pseudomonas sp. USM 4-55.

Pseudomonas sp. USM 4-55 is a locally isolated bacterium that possesses the ability to produce polyhydroxyalkanoates (PHA) consisting of both poly(3-hydroxybutyrate) [P(3HB)] homopolymer and medium-chain length (mcl) monomers (6 to 14 carbon atoms) when sugars or fatty acids are utilized as the sole carbon source. In this study, the P(3HB) biosynthesis operon carrying the phbC(Ps) P(3HB) synthase was successfully cloned and sequenced using a homologous probe. Three open reading frames encoding NADPH-dependent acetoacetyl-coenzyme A reductase (PhbB(Ps)), beta-ketothiolase (PhbA(Ps)) and P(3HB) synthase (PhbC(Ps)) were found in the phb operon. The genetic organization of phb operon showed a putative promoter region, followed by phbB(Ps)-phbA(Ps)-phbC(Ps). phbR(Ps)which encoded a putative transcriptional activator was located in the opposite orientation, upstream of phbBAC(Ps). Heterologous expression of pGEM''ABex harboring phbC(Ps) in Escherichia coli JM109 resulted in P(3HB) accumulation of up to 40% of dry cell weight (DCW).

DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia.

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

Transcriptome dataset from bark and latex tissues of three Hevea brasiliensis clones.

Hevea brasiliensis is exploited for its latex production, and it is the only viable source of natural rubber worldwide. The demand for natural rubber remains high due its high-quality properties, which synthetic rubber cannot compete with. In this paper, we present transcriptomic data and analysis of three H. brasiliensis clones using tissue from latex and bark tissues collected from 10-year-old plant. The combined, assembled transcripts were mapped onto an H. brasiliensis draft genome. Gene ontology analysis showed that the most abundant transcripts related to molecular functions, followed by biological processes and cellular components. Simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) were also identified, and these can be useful for selection of parental and new clones in a breeding program. Data generated by RNA sequencing were deposited in the NCBI public repository under accession number PRJNA629890.

Identification and characterization of jasmonic acid- and linolenic acid-mediated transcriptional regulation of secondary laticifer differentiation in Hevea brasiliensis.

Hevea brasiliensis remains the primary crop commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. Here, we described the transcriptional events related to jasmonic acid (JA)- and linolenic acid (LA)-induced secondary laticifer differentiation (SLD) in H. brasiliensis clone RRIM 600 based on RNA-seq approach. Histochemical approach proved that JA- and LA-treated samples resulted in SLD in H. brasiliensis when compared to ethephon and untreated control. RNA-seq data resulted in 86,614 unigenes, of which 2,664 genes were differentially expressed in JA and LA-induced secondary laticifer harvested from H. brasiliensis bark samples. Among these, 450 genes were unique to JA and LA as they were not differentially expressed in ethephon-treated samples compared with the untreated samples. Most transcription factors from the JA- and LA-specific dataset were classified under MYB, APETALA2/ethylene response factor (AP2/ERF), and basic-helix-loop-helix (bHLH) gene families that were involved in tissue developmental pathways, and we proposed that Bel5-GA2 oxidase 1-KNOTTED-like homeobox complex are likely involved in JA- and LA-induced SLD in H. brasiliensis. We also discovered alternative spliced transcripts, putative novel transcripts, and cis-natural antisense transcript pairs related to SLD event. This study has advanced understanding on the transcriptional regulatory network of SLD in H. brasiliensis.

Single-nucleotide polymorphism markers within MVA and MEP pathways among Hevea brasiliensis clones through transcriptomic analysis.

In this study, RNA sequencing of several Hevea brasiliensis clones grown in Malaysia with different annual rubber production yields and disease resistance was performed on the Illumina platform. A total of 29,862,548 reads were generated, resulting in 101,269 assembled transcripts that were used as the reference transcripts. A similarity search against the non-redundant (nr) protein databases presented 83,771 (83%) positive BLASTx hits. The transcriptome was annotated using gene ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Pfam database. A search for putative molecular markers was performed to identify single-nucleotide polymorphisms (SNPs). Overall, 3,210,629 SNPs were detected and a total of 1314 SNPs associated with the genes involved in MVA and MEP pathways were identified. A total of 176 SNP primer pairs were designed from sequences that were related to the MVA and MEP pathways. The transcriptome of RRIM 3001 and RRIM 712 were subjected to pairwise comparison and the results revealed that there were 1262 significantly differentially expressed genes unique to RRIM 3001, 1499 significantly differentially expressed genes unique to RRIM 712 and several genes related to the MVA and MEP pathways such as AACT, HMGS, PMK, MVD, DXS and HDS were included. The results will facilitate the characterization of H. brasiliensis transcriptomes and the development of a new set of molecular markers in the form of SNPs from transcriptome assembly for the genotype identification of various rubber varieties with superior traits in Malaysia.

Assessment of three plastid DNA barcode markers for identification of Clinacanthus nutans (Acanthaceae).

This study was conducted to determine the feasibility of using three plastid DNA regions (matK, trnH-psbA, and rbcL) as DNA barcodes to identify the medicinal plant Clinacanthus nutans. In this study, C. nutans was collected at several different locations. Total genomic DNA was extracted, amplified by polymerase chain reaction (PCR), and sequenced using matK, trnH-psbA, and rbcL, primers. DNA sequences generated from PCR were submitted to the National Center for Biotechnology Information's (NCBI) GenBank. Identification of C. nutans was carried out using NCBI's Basic Local Alignment Search Tool (BLAST). The rbcL and trnH-psbA regions successfully identified C. nutans with sequencing rates of 100% through BLAST identification. Molecular Evolutionary Genetics Analysis (MEGA) 6.0 was used to analyze interspecific and intraspecific divergence of plastid DNA sequences. rbcL and matK exhibited the lowest average interspecific distance (0.0487 and 0.0963, respectively), whereas trnH-psbA exhibited the highest average interspecific distance (0.2029). The R package Spider revealed that trnH-psbA correctly identified Barcode of Life Data System (BOLD) 96%, best close match 79%, and near neighbor 100% of the species, compared to matK (BOLD 72%; best close match 64%; near neighbor 78%) and rbcL (BOLD 77%; best close match 62%; near neighbor 88%). These results indicate that trnH-psbA is very effective at identifying C. nutans, as it performed well in discriminating species in Acanthaceae.

Genetic relationship between Coptotermes gestroi and Coptotermes vastator (Isoptera: Rhinotermitidae).

The phylogenetic relationship of Coptotermes gestroi (Wasmann) and Coptotermes vastator Light (Isoptera: Rhinotermitidae) was determined using DNA sequence comparisons of mitochondrial genes. Partial sequences of the ribosomal RNA small subunit 12S, ribosomal RNA large subunit 16S, and mitochondrial COII were obtained from nine populations of C. gestroi from South East Asia (Malaysia, Singapore, Thailand, and Indonesia) and four populations of C. vastator from the Philippines and Hawaii. In addition, four populations of Coptotermes formosanus Shiraki and Globitermes sulphureus (Haviland) were used as the outgroups. Consensus sequences were obtained and aligned. C. vastator and C. gestroi are synonymous, based on high sequence homology across the 12S, 16S, and COII genes. The interspecific pairwise sequence divergence, based on Kimura 2-parameter model between C. gestroi and C. vastator, varied only up to 0.80%. Morphometric measurements of 16 characteristics revealed numerous overlaps between the examined individuals of both species. Based on the molecular phylogenetics and morphometric data, it is proposed that C. vastator is a junior synonym of C. gestroi.

Phylogeography of the termite Macrotermes gilvus and insight into ancient dispersal corridors in Pleistocene Southeast Asia.

Dispersal of soil-dwelling organisms via the repeatedly exposed Sunda shelf through much of the Pleistocene in Southeast Asia has not been studied extensively, especially for invertebrates. Here we investigated the phylogeography of an endemic termite species, Macrotermes gilvus (Hagen), to elucidate the spatiotemporal dynamics of dispersal routes of terrestrial fauna in Pleistocene Southeast Asia. We sampled 213 termite colonies from 66 localities throughout the region. Independently inherited microsatellites and mtDNA markers were used to infer the phylogeographic framework of M. gilvus. Discrete phylogeographic analysis and molecular dating based on fossil calibration were used to infer the dynamics of M. gilvus dispersal in time and space across Southeast Asia. We found that the termite dispersal events were consistently dated within the Pleistocene time frame. The dispersal pattern was multidirectional, radiating eastwards and southwards out of Indochina, which was identified as the origin for dispersal events. We found no direct dispersal events between Sumatra and Borneo despite the presence of a terrestrial connection between them during the Pleistocene. Instead, central Java served as an important link allowing termite colonies to be established in Borneo and Sumatra. Our findings support the hypothesis of a north-south dispersal corridor in Southeast Asia and suggest the presence of alternative dispersal routes across Sundaland during the Pleistocene. For the first time, we also propose that a west-east dispersal through over-water rafting likely occurred across the Pleistocene South China Sea. We found at least two independent entry routes for terrestrial species to infiltrate Sumatra and Borneo at different times.

Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis.

Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer. With these data, we updated around 5,500 gene structures and newly annotated around 9,500 transcription start sites. Second, to elucidate the rubber biosynthetic pathways and their transcriptional regulation, we carried out tissue- and cultivar-specific RNA-Seq analysis. By using our recently published genome sequence, we confirmed the expression patterns of the rubber biosynthetic genes. Our data suggest that the cytoplasmic mevalonate (MVA) pathway is the main route for isoprenoid biosynthesis in latex production. In addition to the well-studied polymerization factors, we suggest that rubber elongation factor 8 (REF8) is a candidate factor in cis-polyisoprene biosynthesis. We have also identified 39 transcription factors that may be key regulators in latex production. Expression profile analysis using two additional cultivars, RRIM 901 and PB 350, via an RNA-Seq approach revealed possible expression differences between a high latex-yielding cultivar and a disease-resistant cultivar.

Identification of differentially expressed genes and signalling pathways in bark of Hevea brasiliensis seedlings associated with secondary laticifer differentiation using gene expression microarray.

The natural rubber of Para rubber tree, Hevea brasiliensis, is the main crop involved in industrial rubber production due to its superior quality. The Hevea bark is commercially exploited to obtain latex, which is produced from the articulated secondary laticifer. The laticifer is well defined in the aspect of morphology; however, only some genes associated with its development have been reported. We successfully induced secondary laticifer in the jasmonic acid (JA)-treated and linolenic acid (LA)-treated Hevea bark but secondary laticifer is not observed in the ethephon (ET)-treated and untreated Hevea bark. In this study, we analysed 27,195 gene models using NimbleGen microarrays based on the Hevea draft genome. 491 filtered differentially expressed (FDE) transcripts that are common to both JA- and LA-treated bark samples but not ET-treated bark samples were identified. In the Eukaryotic Orthologous Group (KOG) analysis, 491 FDE transcripts belong to different functional categories that reflect the diverse processes and pathways involved in laticifer differentiation. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) and KOG analysis, the profile of the FDE transcripts suggest that JA- and LA-treated bark samples have a sufficient molecular basis for secondary laticifer differentiation, especially regarding secondary metabolites metabolism. FDE genes in this category are from the cytochrome (CYP) P450 family, ATP-binding cassette (ABC) transporter family, short-chain dehydrogenase/reductase (SDR) family, or cinnamyl alcohol dehydrogenase (CAD) family. The data includes many genes involved in cell division, cell wall synthesis, and cell differentiation. The most abundant transcript in FDE list was SDR65C, reflecting its importance in laticifer differentiation. Using the Basic Local Alignment Search Tool (BLAST) as part of annotation and functional prediction, several characterised as well as uncharacterized transcription factors and genes were found in the dataset. Hence, the further characterization of these genes is necessary to unveil their role in laticifer differentiation. This study provides a platform for the further characterization and identification of the key genes involved in secondary laticifer differentiation.