A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis.

Pitaya (Hylocereus) is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide, and it has attracted significant attention because of its betalain-abundant fruits. Nonetheless, the lack of a pitaya reference genome significantly hinders studies focused on its evolution, as well as the potential for genetic improvement of this crop. Herein, we employed various sequencing approaches, namely, PacBio-SMRT, Illumina HiSeq paired-end, 10× Genomics, and Hi-C (high-throughput chromosome conformation capture) to provide a chromosome-level genomic assembly of 'GHB' pitaya (H. undatus, 2n = 2x = 22 chromosomes). The size of the assembled pitaya genome was 1.41 Gb, with a scaffold N50 of ~127.15 Mb. In total, 27,753 protein-coding genes and 896.31 Mb of repetitive sequences in the H. undatus genome were annotated. Pitaya has undergone a WGT (whole-genome triplication), and a recent WGD (whole-genome duplication) occurred after the gamma event, which is common to the other species in Cactaceae. A total of 29,328 intact LTR-RTs (~696.45 Mb) were obtained in H. undatus, of which two significantly expanded lineages, Ty1/copia and Ty3/gypsy, were the main drivers of the expanded genome. A high-density genetic map of F1 hybrid populations of 'GHB' × 'Dahong' pitayas (H. monacanthus) and their parents were constructed, and a total of 20,872 bin markers were identified (56,380 SNPs) for 11 linkage groups. More importantly, through transcriptomic and WGCNA (weighted gene coexpression network analysis), a global view of the gene regulatory network, including structural genes and the transcription factors involved in pitaya fruit betalain biosynthesis, was presented. Our data present a valuable resource for facilitating molecular breeding programs of pitaya and shed novel light on its genomic evolution, as well as the modulation of betalain biosynthesis in edible fruits.

The chromosome-level reference genome of Coptis chinensis provides insights into genomic evolution and berberine biosynthesis.

Coptis chinensis Franch, a perennial herb, is mainly distributed in southeastern China. The rhizome of C. chinensis has been used as a traditional medicine for more than 2000 years in China and many other Asian countries. The pharmacological activities of C. chinensis have been validated by research. Here, we present a de novo high-quality genome of C. chinensis with a chromosome-level genome of ~958.20 Mb, a contig N50 of 1.58 Mb, and a scaffold N50 of 4.53 Mb. We found that the relatively large genome size of C. chinensis was caused by the amplification of long terminal repeat (LTR) retrotransposons. In addition, a whole-genome duplication event in ancestral Ranunculales was discovered. Comparative genomic analysis revealed that the tyrosine decarboxylase (TYDC) and (S)-norcoclaurine synthase (NCS) genes were expanded and that the aspartate aminotransferase gene (ASP5) was positively selected in the berberine metabolic pathway. Expression level and HPLC analyses showed that the berberine content was highest in the roots of C. chinensis in the third and fourth years. The chromosome-level reference genome of C. chinensis provides important genomic data for molecular-assisted breeding and active ingredient biosynthesis.

Genome Sequence of Chrysotila roscoffensis, a Coccolithphore Contributed to Global Biogeochemical Cycles.

Chrysotila is a genus of coccolithophores. Together with Emiliania, it is one of the representative genera in the Haptophyta which have been extensively studied. They are photosynthetic unicellular marine algae sharing the common characteristic of the production of CaCO3 platelets (coccoliths) on the surface of their cells and are crucial contributors to global biogeochemical cycles. Here, we report the genome assembly of Chrysotila roscoffensis. The assembled genome size was ~636 Mb distributed across 769 scaffolds with N50 of 1.63 Mb, and maximum contig length of ~2.6 Mb. Repetitive elements accounted for approximately 59% of the genome. A total of 23,341 genes were predicted from C. roscoffensis genome. The divergence time between C. roscoffensis and Emiliania huxleyi was estimated to be around 537.6 Mya. Gene families related to cytoskeleton, cellular motility and morphology, and ion transport were expanded. The genome of C. roscoffensis will provide a foundation for understanding the genetic and phenotypic diversification and calcification mechanisms of coccolithophores.

Taeniothrips changbaiensis sp. n. (Thysanoptera, Thripidae) living on the leaves of a Poaceae species in China.

Taeniothrips changbaiensis sp. n. is described from specimens causing damage to the leaves of a species of Poaceae, Deyeuxia angustifolia, in Northeast China. This is one of three species of Taeniothrips with a banded fore wing, and one of only two species with an irregularly interrupted comb of microtrichia on abdominal tergite VIII. The number of setae is variable on the distal half of the fore wing first vein.

The genus Anaphothrips (Thysanoptera, Thripidae) in China, with three new species.

A key to, and distributional information about, is given concerning the 11 Anaphothrips species known from China, including the descriptions of three new species: A. nonporous sp. n., A. oroqeni sp. n. and A. qinghaiensis sp. n. The male and micropterous female of A. beijing Mirab-balou, Chen & Tong and the male of A. populi Zhang Tong are described for the first time. The European species A. atroapterus Priesner is newly recorded from China.

Female polymorphism in Chilothrips strobilus (Thysanoptera: Thripidae), with the first description of the male.

Polymorphism and sexual dimorphism are common in insects. Thrips have been reported to exhibit intraspecific variation in body size, color and wing length (Mound 2005), also sexual dimorphism in abdominal pore plates, antennal sensoria and fore leg armature (Tyagi et al. 2008). Chilothrips Hood is a small genus that currently comprises seven species (ThripsWiki 2017), three from USA, one from Japan, and three from China. No male has been reported in the three species from China, C. strobilus, C. jiuxiensis and C. hangzhouensis (Hu & Feng 2015), and C. strobilus was described on three female specimens from cones of Pinus in Liaoning Province, northeastern China (Tong & Zhang, 1994). Recently, we have surveyed different parts of northeastern China and collected many male individuals of C. strobilus. We have observed that this species shows sexual dimorphism in mouth cone length, and remarkable variation in form of abdominal segment X among females.

The genus Anaphothrips with one new species from China (Thysanoptera, Thripidae).

A key to six species of Anaphothrips known from China is provided, together with distribution information. Anaphothrips dentatussp. n. is described and illustrated from Sanjiang Plain in northeastern China, based on one male and five apterous females. This species is unusual in having the posterior margin of tergite VIII with a craspedum of small teeth rather than long microtrichia.