Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications

Abstract

The Indian black clam Villorita cyprinoides (Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data of Villorita. The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome of V. cyprinoides using next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin to Corbicula fluminea. The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs, rrnS and rrnL) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clustered V. cyprinoides and Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship of V. cyprinoides and C. fluminea, analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genus Villorita. Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.

Towards a systematic revision of the superfamily Cyrenoidea (Bivalvia: Imparidentia): species delimitation, multi-locus phylogeny and mitochondrial phylogenomics

“…The monophyly of the superfamily Cyrenoidea including the freshwater-brackish water families Cyrenoididae, Cyrenidae and Glauconomidae in Imparidentia has been confirmed(Taylor et al 2009;Sharma et al 2012;Bieler et al 2014;Combosch et al 2017). Subsequent studies(Rahuman et al 2020;Crouch et al 2021) further confirmed the close relationship of three families in Cyrenoidea as (Cyrenidae + (Cyrenoididae + Glauconomidae)). More recently, the transcriptomic study conducted byLemer et al (2019) included representatives from Cyrenidae (Corbicula f luminea (O. F. Müller, 1774) and Polymesoda caroliniana (Bosc, 1801)), Glauconomidae (Glauconome rugosa Hanley, 1843) and Cyrenoididae (Cyrenoida floridana).…”

Tidings from the Tides–De novo transcriptome assembly of the endemic estuarine bivalve Villorita cyprinoides

“…The healthy adult black clam specimens with a shell length (SL) of 30 ± 3.5 mm and a total body weight (BW) of 35–40 grams were collected using kolli (an indigenous hand rake net) from Vembanad Lake, a Ramsar site in Kerala, India in March 2021. The study locations in Vembanad Lake included the southern dominant freshwater region, Muhamma: 9°36′18.6″N 76°22′01.2″E and the northern saltwater region, Vaikom: 9°44′35.8″N 76°23′03.4″E, divided seasonally by the Thaneermukkom barrage 10 . Individuals were primarily identified using malacological literature 26 .…”

“…Popularly known as the Indian black clam, Villorita cyprinoides is an endemic cyrenid clam inhabiting the estuaries of Peninsular India. Being a readily available and affordable protein source, this artisanal fishery accounts for more than 70 percent of the Indian clam fishery, making it economically valuable and overutilized 10 . However, the wild population of the clam faces significant challenges including multiple climatic stressors and anthropogenic pressures such as overfishing and habitat destruction.…”